R Language PDF

R Language
#r
Table of Contents
About 1
Chapter 1: Getting started with R Language 2
Remarks 2
Editing R Docs on Stack Overflow 2
A few features of R that immigrants from other language may find unusual 2
Examples 2
Installing R 2
Windows only: 2
For Windows 2
For OSX / macOS 3
Alternative 1 3
Alternative 2 3
For Debian, Ubuntu and derivatives 3
For Red Hat and Fedora 3
For Archlinux 4
Hello World! 4
Getting Help 4
Interactive mode and R scripts 4
The interactive mode 4
Using R as a calculator 4
The first plot 6
R scripts 8
Chapter 2: *apply family of functions (functionals) 9
Remarks 9
Members of the *apply Family 9
Examples 9
Use anonymous functions with apply 10
Bulk File Loading 11
Combining multiple `data.frames` (`lapply`, `mapply`) 11

Using built-in functionals 13
Built-in functionals: lapply(), sapply(), and mapply() 13
lapply() 13
sapply() 13
mapply() 13
Using user-defined functionals 14
User-defined functionals 14
Chapter 3: .Rprofile 16
Remarks 16
Examples 16
.Rprofile - the first chunk of code executed 16
Setting your R home directory 16
Setting page size options 16
set the default help type 16
set a site library 16
Set a CRAN mirror 17
Setting the location of your library 17
Custom shortcuts or functions 17
Pre-loading the most useful packages 17
See Also 17
.Rprofile example 17
Startup 18
Options 18
Custom Functions 18
Chapter 4: Aggregating data frames 19
Introduction 19
Examples 19
Aggregating with base R 19
Aggregating with dplyr 20
Aggregating with data.table 21
Chapter 5: Analyze tweets with R 23

Introduction 23
Examples 23
Download Tweets 23
R Libraries 23
Get text of tweets 24
Chapter 6: ANOVA 25
Examples 25
Basic usage of aov() 25
Basic usage of Anova() 25
Chapter 7: Arima Models 27
Remarks 27
Examples 27
Modeling an AR1 Process with Arima 27
Chapter 8: Arithmetic Operators 36
Remarks 36
Examples 36
Range and addition 36
Addition and subtraction 37
Chapter 9: Bar Chart 40
Introduction 40
Examples 40
barplot() function 40
Chapter 10: Base Plotting 48
Parameters 48
Remarks 48
Examples 48
Basic Plot 48
Matplot 51
Histograms 57
Combining Plots 59
par() 59
layout() 60
Density plot 61
Empirical Cumulative Distribution Function 63
Getting Started with R_Plots 64
Chapter 11: Bibliography in RMD 66
Parameters 66
Remarks 66
Examples 67
Specifying a bibliography and cite authors 67
Inline references 68
Citation styles 68
Chapter 12: boxplot 71
Syntax 71
Parameters 71
Examples 71
Create a box-and-whisker plot with boxplot() {graphics} 71
Simple boxplot (Sepal.Length) 72
Boxplot of sepal length grouped by species 72
Bring order 73
Change groups names 74
Small improvements 75
Color 75
Proximity of the box 76
See the summaries which the boxplots are based plot=FALSE 76
Additional boxplot style parameters. 77
Box 77
Median 77
Whisker 77
Staple 77
Outliers 78
Example 78
Chapter 13: caret 80
Introduction 80
Examples 80
Preprocessing 80
Chapter 14: Classes 82
Introduction 82
Remarks 82
Examples 82
Vectors 82
Inspect classes 82
Vectors and lists 83
Chapter 15: Cleaning data 85
Introduction 85
Examples 85
Removing missing data from a vector 85
Removing incomplete rows 85
Chapter 16: Code profiling 87
Examples 87
System.time 87
proc.time() 87
Line Profiling 88
Microbenchmark 89
Benchmarking using microbenchmark 90
Chapter 17: Coercion 92
Introduction 92
Examples 92
Implicit Coercion 92
Chapter 18: Color schemes for graphics 93
Examples 93
viridis - print and colorblind friendly palettes 93
RColorBrewer 96
A handy function to glimse a vector of colors 98

colorspace - click&drag interface for colors 99
basic R color functions 100
Colorblind-friendly palettes 101
Chapter 19: Column wise operation 104
Examples 104
sum of each column 104
Chapter 20: Combinatorics 106
Examples 106
Enumerating combinations of a specified length 106
Without replacement 106
With replacement 106
Counting combinations of a specified length 107
Without replacement 107
With replacement 107
Chapter 21: Control flow structures 108
Remarks 108
Optimizing Structure of For Loops 108
Vectorizing For Loops 109
Examples 110
Basic For Loop Construction 110
Optimal Construction of a For Loop 110
Poorly optimized for loop 111
Well optimized for loop 111
vapply Function 111
colMeans Function 111
Efficiency comparison 111
The Other Looping Constructs: while and repeat 112
The while loop 112
The repeat loop 113
More on break 113
Chapter 22: Creating packages with devtools 115

Introduction 115
Remarks 115
Examples 115
Creating and distributing packages 115
Creation of the documentation 115
Construction of the package skeleton 116
Edition of the package properties 116
1. Package description 116
2. Optional folders 116
Finalization and build 117
Distribution of your package 117
Through Github 117
Through CRAN 117
Creating vignettes 117
Requirements 118
Vignette creation 118
Chapter 23: Creating reports with RMarkdown 119
Examples 119
Printing tables 119
Including LaTeX Preample Commands 121
Including bibliographies 122
Basic R-markdown document structure 123
R-markdown code chunks 123
R-markdown document example 123
Converting R-markdown to other formats 124
Chapter 24: Creating vectors 126
Examples 126
Sequence of numbers 126
seq() 126
Vectors 127
Creating named vectors 129

Expanding a vector with the rep() function 130
Vectors from build in constants: Sequences of letters & month names 131
Chapter 25: Data acquisition 133
Introduction 133
Examples 133
Built-in datasets 133
Example 133
Datasets within packages 134
Gapminder 134
World Population Prospects 2015 - United Nations Population Department 134
Packages to access open databases 134
Eurostat 134
Packages to access restricted data 136
Human Mortality Database 136
Chapter 26: Data frames 139
Syntax 139
Examples 139
Create an empty data.frame 139
Subsetting rows and columns from a data frame 140
Syntax for accessing rows and columns: [, [[, and $ 140
Like a matrix: data[rows, columns] 141
With numeric indexes 141
With column (and row) names 141
Rows and columns together 142
A warning about dimensions: 142
Like a list 142
With single brackets data[columns] 142
With double brackets data[[one_column]] 143
Using $ to access columns 143
Drawbacks of $ for accessing columns 143
Advanced indexing: negative and logical indices 144

Negative indices omit elements 144
Logical vectors indicate specific elements to keep 144
Convenience functions to manipulate data.frames 145
subset 145
transform 145
with and within 145
Introduction 146
Convert data stored in a list to a single data frame using do.call 147
Convert all columns of a data.frame to character class 148
Subsetting Rows by Column Values 148
Chapter 27: data.table 150
Introduction 150
Syntax 150
Remarks 151
Installation and support 151
Loading the package 152
Examples 152
Creating a data.table 152
Build 152
Read in 152
Modify a data.frame 153
Coerce object to data.table 153
Adding and modifying columns 153
Editing entire columns 154
Editing subsets of columns 154
Editing column attributes 155
Special symbols in data.table 155
.SD 155
.SDcols 156
.N 156
Writing code compatible with both data.frame and data.table 157

Differences in subsetting syntax 157
Strategies for maintaining compatibility with data.frame and data.table 158
Setting keys in data.table 159
Chapter 28: Date and Time 162
Introduction 162
Remarks 162
Classes 162
Selecting a date-time format 162
Specialized packages 163
Examples 163
Current Date and Time 163
Go to the End of the Month 164
Go to First Day of the Month 164
Move a date a number of months consistently by months 164
Chapter 29: Date-time classes (POSIXct and POSIXlt) 166
Introduction 166
Remarks 166
Pitfalls 166
Related topics 166
Examples 166
Formatting and printing date-time objects 166
Parsing strings into date-time objects 167
Notes 167
Missing elements 167
Time zones 167
Date-time arithmetic 168
Chapter 30: Debugging 169
Examples 169
Using browser 169
Using debug 170

Chapter 31: Distribution Functions 171
Introduction 171
Remarks 171
Examples 171
Normal distribution 171
Binomial Distribution 172
Chapter 32: dplyr 176
Remarks 176
Examples 176
dplyr's single table verbs 176
Syntax commonalities 176
filter 177
arrange 178
select 179
mutate 180
summarise 181
group_by 181
Putting it all togther 182
summarise multiple columns 182
Subset Observation (Rows) 185
dplyr::filter() - Select a subset of rows in a data frame that meet a logical criteria: 185
dplyr::distinct() - Remove duplicate rows: 185
Aggregating with %>% (pipe) operator 186
Examples of NSE and string variables in dpylr 187
Chapter 33: Expression: parse + eval 188
Remarks 188
Examples 188
Execute code in string format 188
Chapter 34: Extracting and Listing Files in Compressed Archives 189
Examples 189
Extracting files from a .zip archive 189

Listing files in a .zip archive 189
Listing files in a .tar archive 189
Extracting files from a .tar archive 189
Extract all .zip archives in a directory 190
Chapter 35: Factors 191
Syntax 191
Remarks 191
Mapping the integer to the level 192
Modern use of factors 192
Examples 193
Basic creation of factors 193
Consolidating Factor Levels with a List 194
Consolidating levels using factor (factor_approach) 195
Consolidating levels using ifelse (ifelse_approach) 195
Consolidating Factors Levels with a List (list_approach) 195
Benchmarking each approach 196
Factors 196
Changing and reordering factors 197
Rebuilding factors from zero 202
Problem 202
Solution 203
Chapter 36: Fault-tolerant/resilient code 204
Parameters 204
Remarks 204
tryCatch 204
Implications of choosing specific return values of the handler functions 204
"Undesired" warning message 205
Examples 205
Using tryCatch() 205
Function definition using tryCatch 205
Testing things out 206
Investigating the output 207

Chapter 37: Feature Selection in R -- Removing Extraneous Features 208
Examples 208
Removing features with zero or near-zero variance 208
Removing features with high numbers of NA 208
Removing closely correlated features 208
Chapter 38: Formula 210
Examples 210
The basics of formula 210
Create Linear, Quadratic and Second Order Interaction Terms 211
Chapter 39: Fourier Series and Transformations 213
Remarks 213
Examples 214
Fourier Series 214
Chapter 40: Functional programming 221
Examples 221
Built-in Higher Order Functions 221
Chapter 41: Generalized linear models 222
Examples 222
Logistic regression on Titanic dataset 222
Chapter 42: Get user input 225
Syntax 225
Examples 225
User input in R 225
Chapter 43: ggplot2 226
Remarks 226
Examples 226
Scatter Plots 226
Displaying multiple plots 227
Prepare your data for plotting 231
Add horizontal and vertical lines to plot 233
Add one common horizontal line for all categorical variables 233
Add one horizontal line for each categorical variable 233
Add horizontal line over grouped bars 233
Add vertical line 233
Vertical and Horizontal Bar Chart 233
Violin plot 233
Produce basic plots with qplot 233
Chapter 44: GPU-accelerated computing 236
Remarks 236
Examples 236
gpuR gpuMatrix objects 236
gpuR vclMatrix objects 236
Chapter 45: Hashmaps 238
Examples 238
Environments as hash maps 238
Introduction 238
Insertion 238
Key Lookup 239
Inspecting the Hash Map 239
Flexibility 240
Limitations 241
package:hash 242
package:listenv 243
Chapter 46: heatmap and heatmap.2 244
Examples 244
Examples from the official documentation 244
stats::heatmap 244
Example 1 (Basic usage) 244
Example 2 (no column dendrogram (nor reordering) at all) 245
Example 3 ("no nothing") 245
Example 4 (with reorder()) 246
Example 5 (NO reorder()) 247

Example 6 (slightly artificial with color bar, without ordering) 248
Example 7 (slightly artificial with color bar, with ordering) 249
Example 8 (For variable clustering, rather use distance based on cor()) 250
Tuning parameters in heatmap.2 252
Chapter 47: Hierarchical clustering with hclust 258
Introduction 258
Remarks 258
Examples 258
Example 1 - Basic use of hclust, display of dendrogram, plot clusters 258
Example 2 - hclust and outliers 262
Chapter 48: Hierarchical Linear Modeling 265
Examples 265
basic model fitting 265
Chapter 49: I/O for database tables 266
Remarks 266
Examples 266
Reading Data from MySQL Databases 266
General 266
Using limits 266
Reading Data from MongoDB Databases 266
Chapter 50: I/O for foreign tables (Excel, SAS, SPSS, Stata) 268
Examples 268
Importing data with rio 268
Importing Excel files 268
Reading excel files with the xlsx package 269
Reading Excel files with the XLconnect package 269
Reading excel files with the openxlsx package 270
Reading excel files with the readxl package 270
Reading excel files with the RODBC package 271
Reading excel files with the gdata package 272

Read and write Stata, SPSS and SAS files 272
Import or Export of Feather file 273
Chapter 51: I/O for geographic data (shapefiles, etc.) 275
Introduction 275
Examples 275
Import and Export Shapefiles 275
Chapter 52: I/O for raster images 276
Introduction 276
Examples 276
Load a multilayer raster 276
Chapter 53: I/O for R's binary format 278
Examples 278
Rds and RData (Rda) files 278
Enviromments 278
Chapter 54: Implement State Machine Pattern using S4 Class 280
Introduction 280
Examples 280
Parsing Lines using State Machine 280
Chapter 55: Input and output 294
Remarks 294
Examples 294
Reading and writing data frames 294
Writing 294
Reading 294
Further resources 295
Chapter 56: Inspecting packages 296
Introduction 296
Remarks 296
Examples 296
View package information 296
View package's built-in data sets 296

List a package's exported functions 296
View Package Version 296
View Loaded packages in Current Session 297
Chapter 57: Installing packages 298
Syntax 298
Parameters 298
Remarks 298
Related Docs 298
Examples 298
Download and install packages from repositories 298
Using CRAN 298
Using Bioconductor 299
Install package from local source 299
Install packages from GitHub 300
Using a CLI package manager -- basic pacman usage 301
Install local development version of a package 302
Chapter 58: Introduction to Geographical Maps 304
Introduction 304
Examples 304
Basic map-making with map() from the package maps 304
50 State Maps and Advanced Choropleths with Google Viz 308
Interactive plotly maps 309
Making Dynamic HTML Maps with Leaflet 311
Dynamic Leaflet maps in Shiny applications 313
Chapter 59: Introspection 315
Examples 315
Functions for Learning about Variables 315
Chapter 60: JSON 317
Examples 317
JSON to / from R objects 317
Chapter 61: Linear Models (Regression) 319

Syntax 319
Parameters 319
Examples 320
Linear regression on the mtcars dataset 320
Plotting The Regression (base) 321
Weighting 323
Checking for nonlinearity with polynomial regression 325
Quality assessment 328
Using the 'predict' function 329
Chapter 62: Lists 331
Examples 331
Quick Introduction to Lists 331
Introduction to lists 333
Reasons for using lists 333
Convert a list to a vector while keeping empty list elements 334
Serialization: using lists to pass informations 335
Chapter 63: lubridate 337
Syntax 337
Remarks 337
Examples 337
Parsing dates and datetimes from strings with lubridate 338
Dates 338
Datetimes 338
Utility functions 338
Parser functions 339
Parsing date and time in lubridate 339
Manipulating date and time in lubridate 340
Instants 340
Intervals, Durations and Periods 341
Rounding dates 342
Difference between period and duration 343
Time Zones 343

Chapter 64: Machine learning 345
Examples 345
Creating a Random Forest model 345
Chapter 65: Matrices 346
Introduction 346
Examples 346
Creating matrices 346
Chapter 66: Meta: Documentation Guidelines 348
Remarks 348
Examples 348
Making good examples 348
Style 348
Prompts 348
Console output 348
Assignment 348
Code comments 349
Sections 349
Chapter 67: Missing values 350
Introduction 350
Remarks 350
Examples 350
Examining missing data 350
Reading and writing data with NA values 350
Using NAs of different classes 351
TRUE/FALSE and/or NA 351
Omitting or replacing missing values 352
Recoding missing values 352
Removing missing values 353
Excluding missing values from calculations 353
Chapter 68: Modifying strings by substitution 354
Introduction 354
Examples 354
Rearrange character strings using capture groups 354
Eliminate duplicated consecutive elements 354
Chapter 69: Natural language processing 356
Introduction 356
Examples 356
Create a term frequency matrix 356
Chapter 70: Network analysis with the igraph package 358
Examples 358
Simple Directed and Non-directed Network Graphing 358
Chapter 71: Non-standard evaluation and standard evaluation 360
Introduction 360
Examples 360
Examples with standard dplyr verbs 360
Chapter 72: Numeric classes and storage modes 362
Examples 362
Numeric 362
Chapter 73: Object-Oriented Programming in R 364
Introduction 364
Examples 364
S3 364
Chapter 74: Parallel processing 366
Remarks 366
Examples 366
Parallel processing with foreach package 366
Parallel processing with parallel package 367
Random Number Generation 368
mcparallelDo 369
Example 369
Other Examples 369
Chapter 75: Pattern Matching and Replacement 371

Introduction 371
Syntax 371
Remarks 371
Differences from other languages 371
Examples 371
Making substitutions 371
Finding Matches 372
Is there a match? 372
Match locations 372
Matched values 372
Details 373
Summary of matches 373
Single and Global match. 373
Find matches in big data sets 375
Chapter 76: Performing a Permutation Test 376
Examples 376
A fairly general function 376
Chapter 77: Pipe operators (%>% and others) 379
Introduction 379
Syntax 379
Parameters 379
Remarks 379
Packages that use %>% 379
Finding documentation 380
Hotkeys 380
Performance Considerations 380
Examples 380
Basic use and chaining 380
Functional sequences 381
Assignment with %<>% 382

Exposing contents with %$% 382
Using the pipe with dplyr and ggplot2 383
Creating side effects with %T>% 383
Chapter 78: Pivot and unpivot with data.table 385
Syntax 385
Parameters 385
Remarks 385
Examples 385
Pivot and unpivot tabular data with data.table - I 385
Pivot and unpivot tabular data with data.table - II 387
Chapter 79: Probability Distributions with R 389
Examples 389
PDF and PMF for different distributions in R 389
Chapter 80: Publishing 390
Introduction 390
Remarks 390
Examples 390
Formatting tables 390
Printing to plain text 390
Printing delimited tables 390
Further resources 390
Formatting entire documents 391
Further Resources 391
Chapter 81: R code vectorization best practices 392
Examples 392
By row operations 392
Chapter 82: R in LaTeX with knitr 396
Syntax 396
Parameters 396
Remarks 396
Examples 397
R in Latex with Knitr and Code Externalization 397
R in Latex with Knitr and Inline Code Chunks 398
R in LaTex with Knitr and Internal Code Chunks 398
Chapter 83: R Markdown Notebooks (from RStudio) 399
Introduction 399
Examples 399
Creating a Notebook 399
Inserting Chunks 400
Executing Chunk Code 401
Splitting Code into Chunks 401
Execution Progress 402
Executing Multiple Chunks 403
Preview Output 404
Saving and Sharing 404
Chapter 84: R memento by examples 406
Introduction 406
Examples 406
Data types 406
Vectors 406
Matrices 406
Dataframes 406
Lists 406
Environments 407
Plotting (using plot) 407
Commonly used functions 407
Chapter 85: Random Forest Algorithm 409
Introduction 409
Examples 409
Basic examples - Classification and Regression 409
Chapter 86: Random Numbers Generator 411
Examples 411
Random permutations 411
Random number generator's reproducibility 411
Generating random numbers using various density functions 412
Uniform distribution between 0 and 10 412
Normal distribution with 0 mean and standard deviation of 1 412
Binomial distribution with 10 trials and success probability of 0.5 412
Geometric distribution with 0.2 success probability 412
Hypergeometric distribution with 3 white balls, 10 black balls and 5 draws 413
Negative Binomial distribution with 10 trials and success probability of 0.8 413
Poisson distribution with mean and variance (lambda) of 2 413
Exponential distribution with the rate of 1.5 413
Logistic distribution with 0 location and scale of 1 413
Chi-squared distribution with 15 degrees of freedom 413
Beta distribution with shape parameters a=1 and b=0.5 413
Gamma distribution with shape parameter of 3 and scale=0.5 413
Cauchy distribution with 0 location and scale of 1 414
Log-normal distribution with 0 mean and standard deviation of 1 (on log scale) 414
Weibull distribution with shape parameter of 0.5 and scale of 1 414
Wilcoxon distribution with 10 observations in the first sample and 20 in second. 414
Multinomial distribution with 5 object and 3 boxes using the specified probabilities 414
Chapter 87: Randomization 415
Introduction 415
Remarks 415
Examples 415
Random draws and permutations 415
Random permutation 415
Draws without Replacement 416
Draws with Replacement 416
Changing Draw Probabilities 417
Setting the seed 418
Chapter 88: Raster and Image Analysis 419

Introduction 419
Examples 419
Calculating GLCM Texture 419
Mathematical Morphologies 421
Chapter 89: Rcpp 424
Examples 424
Inline Code Compile 424
Rcpp Attributes 424
Extending Rcpp with Plugins 425
Specifying Additional Build Dependencies 426
Chapter 90: Reading and writing strings 427
Remarks 427
Examples 427
Printing and displaying strings 427
Reading from or writing to a file connection 429
Capture output of operating system command 429
Functions which return a character vector 429
Functions which return a data frame 430
Chapter 91: Reading and writing tabular data in plain-text files (CSV, TSV, etc.) 431
Syntax 431
Parameters 431
Remarks 431
Examples 432
Importing .csv files 432
Importing using base R 432
Notes 432
Importing using packages 432
Importing with data.table 433
Notes 434
Importing .tsv files as matrices (basic R) 434
Exporting .csv files 435

Exporting using base R 435
Exporting using packages 435
Import multiple csv files 435
Importing fixed-width files 435
Importing with base R 436
Importing with readr 436
Chapter 92: Recycling 437
Remarks 437
Examples 437
Recycling use in subsetting 437
Chapter 93: Regular Expression Syntax in R 439
Introduction 439
Examples 439
Use `grep` to find a string in a character vector 439
Chapter 94: Regular Expressions (regex) 441
Introduction 441
Remarks 441
Character classes 441
Quantifiers 441
Start and end of line indicators 441
Differences from other languages 441
Additional Resources 442
Examples 442
Eliminating Whitespace 442
Trimming Whitespace 442
Removing Leading Whitespace 442
Removing Trailing Whitespace 443
Removing All Whitespace 443
Validate a date in a "YYYYMMDD" format 443
Validate US States postal abbreviations 444
Validate US phone numbers 444

Escaping characters in R regex patterns 445
Differences between Perl and POSIX regex 446
Look-ahead/look-behind 446
Chapter 95: Reproducible R 447
Introduction 447
Remarks 447
References 447
Examples 447
Data reproducibility 447
dput() and dget() 447
Package reproducibility 448
Chapter 96: Reshape using tidyr 449
Introduction 449
Examples 449
Reshape from long to wide format with spread() 449
Reshape from wide to long format with gather() 450
h21 450
Chapter 97: Reshaping data between long and wide forms 451
Introduction 451
Remarks 451
Helpful packages 451
Examples 451
The reshape function 451
Long to Wide 452
Wide to Long 452
Reshaping data 453
Base R 453
The tidyr package 454
The data.table package 454
Chapter 98: RESTful R Services 455
Introduction 455
Examples 455
opencpu Apps 455
Chapter 99: RMarkdown and knitr presentation 456
Syntax 456
Parameters 456
Remarks 456
Sub options parameters: 456
Examples 460
Rstudio example 460
Adding a footer to an ioslides presentation 460
Chapter 100: RODBC 463
Examples 463
Connecting to Excel Files via RODBC 463
SQL Server Management Database connection to get individual table 463
Connecting to relational databases 463
Chapter 101: roxygen2 464
Parameters 464
Examples 464
Documenting a package with roxygen2 464
Writing with roxygen2 464
Building the documentation 465
Chapter 102: Run-length encoding 466
Remarks 466
Extensions 466
Examples 466
Run-length Encoding with `rle` 466
Identifying and grouping by runs in base R 467
Identifying and grouping by runs in data.table 467
Run-length encoding to compress and decompress vectors 468
Chapter 103: Scope of variables 470
Remarks 470
Examples 470
Environments and Functions 470
Sub functions 471
Global Assignment 471
Explicit Assignment of Environments and Variables 472
Function Exit 472
Packages and Masking 473
Chapter 104: Set operations 474
Remarks 474
Examples 474
Set operators for pairs of vectors 474
Comparing sets 474
Combining sets 474
Set membership for vectors 475
Cartesian or "cross" products of vectors 475
Applying functions to combinations 475
Make unique / drop duplicates / select distinct elements from a vector 476
Measuring set overlaps / Venn diagrams for vectors 476
Chapter 105: Shiny 478
Examples 478
Create an app 478
One file 478
Two files 478
Create ui.R file 478
Create server.R file 479
Radio Button 479
Checkbox Group 479
Select box 480
Launch a Shiny app 481
1. Two files app 481
2. One file app 482

Control widgets 482
Debugging 484
Showcase mode 484
Reactive Log Visualizer 484
Chapter 106: Solving ODEs in R 485
Syntax 485
Parameters 485
Remarks 485
Examples 485
The Lorenz model 485
Lotka-Volterra or: Prey vs. predator 487
ODEs in compiled languages - definition in R 488
ODEs in compiled languages - definition in C 489
ODEs in compiled languages - definition in fortran 490
ODEs in compiled languages - a benchmark test 492
Chapter 107: Spark API (SparkR) 494
Remarks 494
Examples 494
Setup Spark context 494
Setup Spark context in R 494
Get Spark Cluster 494
Cache data 494
Create RDDs (Resilient Distributed Datasets) 495
From dataframe: 495
From csv: 495
Chapter 108: spatial analysis 496
Examples 496
Create spatial points from XY data set 496
Importing a shape file (.shp) 497
rgdal 497
raster 497
tmap 498
Chapter 109: Speeding up tough-to-vectorize code 499
Examples 499
Speeding tough-to-vectorize for loops with Rcpp 499
Speeding tough-to-vectorize for loops by byte compiling 500
Chapter 110: Split function 502
Examples 502
Basic usage of split 502
Using split in the split-apply-combine paradigm 504
Chapter 111: sqldf 506
Examples 506
Basic Usage Examples 506
Chapter 112: Standardize analyses by writing standalone R scripts 508
Introduction 508
Remarks 508
Examples 508
The basic structure of standalone R program and how to call it 508
The first standalone R script 508
Preparing a standalone R script 509
Linux/Mac 509
Windows 509
Using littler to execute R scripts 510
Installing littler 510
From R: 510
Using apt-get (Debian, Ubuntu): 510
Using littler with standard .r scripts 510
Using littler on shebanged scripts 511
Chapter 113: String manipulation with stringi package 512
Remarks 512
Examples 512
Count pattern inside string 512

Duplicating strings 513
Paste vectors 513
Splitting text by some fixed pattern 513
Chapter 114: strsplit function 515
Syntax 515
Examples 515
Introduction 515
Chapter 115: Subsetting 517
Introduction 517
Remarks 517
Examples 518
Atomic vectors 518
Lists 519
Matrices 521
Selecting individual matrix entries by their positions 522
Data frames 523
Other objects 524
Vector indexing 525
Elementwise Matrix Operations 525
Some Functions used with Matrices 526
Chapter 116: Survival analysis 528
Examples 528
Random Forest Survival Analysis with randomForestSRC 528
Introduction - basic fitting and plotting of parametric survival models with the survival 529
Kaplan Meier estimates of survival curves and risk set tables with survminer 530
Chapter 117: Text mining 533
Examples 533
Scraping Data to build N-gram Word Clouds 533
Chapter 118: The character class 537
Introduction 537
Remarks 537
Related topics 537

Examples 537
Coercion 537
Chapter 119: The Date class 538
Remarks 538
Related topics 538
Jumbled notes 538
More notes 538
Examples 538
Formatting Dates 538
Dates 539
Parsing Strings into Date Objects 541
Chapter 120: The logical class 542
Introduction 542
Remarks 542
Shorthand 542
Examples 542
Logical operators 542
Coercion 543
Interpretation of NAs 543
Chapter 121: tidyverse 544
Examples 544
Creating tbl_df’s 544
tidyverse: an overview 544
What is tidyverse? 544
How to use it? 545
What are those packages? 545
Chapter 122: Time Series and Forecasting 547
Remarks 547
Examples 547
Exploratory Data Analysis with time-series data 547
Creating a ts object 548

Chapter 123: Updating R and the package library 550
Examples 550
On Windows 550
Chapter 124: Updating R version 551
Introduction 551
Examples 551
Installing from R Website 551
Updating from within R using installr Package 551
Deciding on the old packages 552
Updating Packages 555
Check R Version 556
Chapter 125: Using pipe assignment in your own package %<>%: How to ? 557
Introduction 557
Examples 557
Putting the pipe in a utility-functions file 557
Chapter 126: Using texreg to export models in a paper-ready way 558
Introduction 558
Remarks 558
Links 558
Examples 558
Printing linear regression results 558
Chapter 127: Variables 560
Examples 560
Variables, data structures and basic Operations 560
Types of data structures 561
Common operations and some cautionary advice 561
Example objects 561
Some vector operations 562
Some vector operation Warnings! 562
Some Matrix operations Warning! 562
"Private" variables 563

Chapter 128: Web Crawling in R 564
Examples 564
Standard scraping approach using the RCurl package 564
Chapter 129: Web scraping and parsing 565
Remarks 565
Legality 565
Examples 565
Basic scraping with rvest 565
Using rvest when login is required 566
Chapter 130: Writing functions in R 568
Examples 568
Named functions 568
Anonymous functions 569
RStudio code snippets 569
Passing column names as argument of a function 570
Chapter 131: xgboost 572
Examples 572
Cross Validation and Tuning with xgboost 572
Credits 575
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https://riptutorial.com/ 1
Chapter 1: Getting started with R Language
Remarks
Editing R Docs on Stack Overflow

See the documentation guidelines for general rules when creating documentation.
A few features of R that immigrants from

other language may find unusual
• Unlike other languages variables in R need not require type declaration.
• The same variable can be assigned different data types at different instances of time, if
required.
• Indexing of atomic vectors and lists starts from 1, not 0.
• R arrays (and the special case of matrices) have a dim attribute that sets them apart from R's
"atomic vectors" which have no attributes.
• A list in R allows you to gather a variety of objects under one name (that is, the name of the
list) in an ordered way. These objects can be matrices, vectors, data frames, even other
lists, etc. It is not even required that these objects are related to each other in any way.
• Recycling
• Missing values
Examples
Installing R
You might wish to install RStudio after you have installed R. RStudio is a development
environment for R that simplifies many programming tasks.
Windows only:
Visual Studio (starting from version 2015 Update 3) now features a development environment for
R called R Tools, that includes a live interpreter, IntelliSense, and a debugging module. If you
choose this method, you won't have to install R as specified in the following section.
For Windows
1. Go to the CRAN website, click on download R for Windows, and download the latest version
of R.
2. Right-click the installer file and RUN as administrator.
3. Select the operational language for installation.
4. Follow the instructions for installation.
For OSX / macOS

Alternative 1
(0. Ensure XQuartz is installed )
1. Go to the CRAN website and download the latest version of R.

2. Open the disk image and run the installer.
3. Follow the instructions for installation.
This will install both R and the R-MacGUI. It will put the GUI in the /Applications/ Folder as R.app
where it can either be double-clicked or dragged to the Doc. When a new version is released, the
(re)-installation process will overwrite R.app but prior major versions of R will be maintained. The
actual R code will be in the /Library/Frameworks/R.Framework/Versions/ directory. Using R within
RStudio is also possible and would be using the same R code with a different GUI.
Alternative 2
1. Install homebrew (the missing package manager for macOS) by following the instructions on
https://brew.sh/
2. brew install R
Those choosing the second method should be aware that the maintainer of the Mac fork advises
against it, and will not respond to questions about difficulties on the R-SIG-Mac Mailing List.
For Debian, Ubuntu and derivatives

You can get the version of R corresponding to your distro via apt-get. However, this version will
frequently be quite far behind the most recent version available on CRAN. You can add CRAN to
your list of recognized "sources".
sudo apt-get install r-base
You can get a more recent version directly from CRAN by adding CRAN to your sources list.
Follow the directions from CRAN for more details. Note in particular the need to also execute this
so that you can use install.packages(). Linux packages are usually distributed as source files and
need compilation:
sudo apt-get install r-base-dev
For Red Hat and Fedora
sudo dnf install R
For Archlinux
R is directly available in the Extra package repo.
sudo pacman -S r
More info on using R under Archlinux can be found on the ArchWiki R page.
Hello World!
"Hello World!"
Also, check out the detailed discussion of how, when, whether and why to print a string.
Getting Help
You can use function help() or ? to access documentations and search for help in R. For even
more general searches, you can use help.search() or ??.
#For help on the help function of R

help()
#For help on the paste function

help(paste) #OR
help("paste") #OR
?paste #OR
?"paste"
Visit https://www.r-project.org/help.html for additional information
Interactive mode and R scripts
The interactive mode

The most basic way to use R is the interactive mode. You type commands and immediately get
the result from R.
Using R as a calculator
Start R by typing R at the command prompt of your operating system or by executing RGui on
Windows. Below you can see a screenshot of an interactive R session on Linux:
This is RGui on Windows, the most basic working environment for R under Windows:
After the > sign, expressions can be typed in. Once an expression is typed, the result is shown by
R. In the screenshot above, R is used as a calculator: Type
1+1
to immediately see the result, 2. The leading [1] indicates that R returns a vector. In this case, the
vector contains only one number (2).
The first plot

R can be used to generate plots. The following example uses the data set PlantGrowth, which
comes as an example data set along with R
Type int the following all lines into the R prompt which do not start with ##. Lines starting with ##
are meant to document the result which R will return.
data(PlantGrowth)
str(PlantGrowth)
## 'data.frame': 30 obs. of 2 variables:
## $ weight: num 4.17 5.58 5.18 6.11 4.5 4.61 5.17 4.53 5.33 5.14 ...
## $ group : Factor w/ 3 levels "ctrl","trt1",..: 1 1 1 1 1 1 1 1 1 1 ...
anova(lm(weight ~ group, data = PlantGrowth))
## Analysis of Variance Table
##
## Response: weight
## Df Sum Sq Mean Sq F value Pr(>F)
## group 2 3.7663 1.8832 4.8461 0.01591 *
## Residuals 27 10.4921 0.3886
## ---
## Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
boxplot(weight ~ group, data = PlantGrowth, ylab = "Dry weight")
The following plot is created:
data(PlantGrowth) loads the example data set PlantGrowth, which is records of dry masses of plants
which were subject to two different treatment conditions or no treatment at all (control group). The
data set is made available under the name PlantGrowth. Such a name is also called a Variable.
To load your own data, the following two documentation pages might be helpful:
• Reading and writing tabular data in plain-text files (CSV, TSV, etc.)
• I/O for foreign tables (Excel, SAS, SPSS, Stata)
str(PlantGrowth) shows information about the data set which was loaded. The output indicates that
PlantGrowth is a data.frame, which is R's name for a table. The data.frame contains of two columns
and 30 rows. In this case, each row corresponds to one plant. Details of the two columns are
shown in the lines starting with $: The first column is called weight and contains numbers (num, the
dry weight of the respective plant). The second column, group, contains the treatment that the plant
was subjected to. This is categorial data, which is called factor in R. Read more information about
data frames.
To compare the dry masses of the three different groups, a one-way ANOVA is performed using
anova(lm( ... )). weight ~ group means "Compare the values of the column weight, grouping by
the values of the column group". This is called a Formula in R. data = ... specifies the name of the
table where the data can be found.
The result shows, among others, that there exists a significant difference (Column Pr(>F)), p =
0.01591) between some of the three groups. Post-hoc tests, like Tukey's Test, must be performed
to determine which groups' means differ significantly.
boxplot(...) creates a box plot of the data. where the values to be plotted come from. weight ~
group means: "Plot the values of the column weight versus the values of the column group. ylab =
... specifies the label of the y axis. More information: Base plotting
Type q() or Ctrl-D to exit from the R session.
R scripts
To document your research, it is favourable to save the commands you use for calculation in a file.
For that effect, you can create R scripts. An R script is a simple text file, containing R commands.
Create a text file with the name plants.R, and fill it with the following text, where some commands
are familiar from the code block above:
data(PlantGrowth)
anova(lm(weight ~ group, data = PlantGrowth))
png("plant_boxplot.png", width = 400, height = 300)

boxplot(weight ~ group, data = PlantGrowth, ylab = "Dry weight")
dev.off()
Execute the script by typing into your terminal (The terminal of your operating system, not an
interactive R session like in the previous section!)
R --no-save <plant.R >plant_result.txt
The file plant_result.txt contains the results of your calculation, as if you had typed them into the
interactive R prompt. Thereby, your calculations are documented.
The new commands png and dev.off are used for saving the boxplot to disk. The two commands
must enclose the plotting command, as shown in the example above. png("FILENAME", width = ...,
height = ...) opens a new PNG file with the specified file name, width and height in pixels.
dev.off() will finish plotting and saves the plot to disk. No output is saved until dev.off() is called.
Read Getting started with R Language online: https://riptutorial.com/r/topic/360/getting-started-

with-r-language
Chapter 2: *apply family of functions
(functionals)
Remarks
A function in the *apply family is an abstraction of a for loop. Compared with the for loops *apply
functions have the following advantages:
1. Require less code to write.

2. Doesn't have an iteration counter.
3. Doesn't use temporary variables to store intermediate results.
However for loops are more general and can give us more control allowing to achieve complex
computations that are not always trivial to do using *apply functions.
The relationship between for loops and *apply functions is explained in the documentation for for
loops.
Members of the *apply Family

The *apply family of functions contains several variants of the same principle that differ based
primarily on the kind of output they return.
function Input Output
matrix, data.frame, or vector or matrix (depending on the length of each

apply
array element returned)
vector or matrix (depending on the length of each

sapply vector or list
element returned)
lapply vector or list list
vector or matrix (depending on the length of each

vapply vector or `list
element returned) of the user-designated class
multiple vectors, lists or

mapply list
a combination
See "Examples" to see how each of these functions is used.
Examples
Use anonymous functions with apply
apply is used to evaluate a function (maybe an anonymous one) over the margins of an array or
matrix.
Let's use the iris dataset to illustrate this idea. The iris dataset has measurements of 150
flowers from 3 species. Let's see how this dataset is structured:
> head(iris)
Sepal.Length Sepal.Width Petal.Length Petal.Width Species

1 5.1 3.5 1.4 0.2 setosa
2 4.9 3.0 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
5 5.0 3.6 1.4 0.2 setosa
6 5.4 3.9 1.7 0.4 setosa
Now, imagine that you want to know the mean of each of these variables. One way to solve this
might be to use a for loop, but R programmers will often prefer to use apply (for reasons why, see
Remarks):
> apply(iris[1:4], 2, mean)
Sepal.Length Sepal.Width Petal.Length Petal.Width

5.843333 3.057333 3.758000 1.199333
• In the first parameter, we subset iris to include only the first 4 columns, because mean only
works on numeric data.
• The second parameter value of 2 indicates that we want to work on the columns only (the
second subscript of the r×c array); 1 would give the row means.
In the same way we can calculate more meaningful values:
# standard deviation
apply(iris[1:4], 2, sd)
# variance
apply(iris[1:4], 2, var)
Caveat: R has some built-in functions which are better for calculating column and row sums and
means: colMeans and rowMeans.
Now, let's do a different and more meaningful task: let's calculate the mean only for those values
which are bigger than 0.5. For that, we will create our own mean function.
> our.mean.function <- function(x) { mean(x[x > 0.5]) }

> apply(iris[1:4], 2, our.mean.function)

5.843333 3.057333 3.758000 1.665347
(Note the difference in the mean of Petal.Width)
But, what if we don't want to use this function in the rest of our code? Then, we can use an
anonymous function, and write our code like this:
apply(iris[1:4], 2, function(x) { mean(x[x > 0.5]) })
So, as we have seen, we can use apply to execute the same operation on columns or rows of a
dataset using only one line.
Caveat: Since apply returns very different kinds of output depending on the length of the results of
the specified function, it may not be the best choice in cases where you are not working
interactively. Some of the other *apply family functions are a bit more predictable (see Remarks).
Bulk File Loading
for a large number of files which may need to be operated on in a similar process and with well
structured file names.
firstly a vector of the file names to be accessed must be created, there are multiple options for this:
• Creating the vector manually with paste0()
files <- paste0("file_", 1:100, ".rds")
• Using list.files() with a regex search term for the file type, requires knowledge of regular
expressions (regex) if other files of same type are in the directory.
files <- list.files("./", pattern = "\\.rds$", full.names = TRUE)
where X is a vector of part of the files naming format used.
lapply will output each response as element of a list.
readRDS is specific to .rds files and will change depending on the application of the process.
my_file_list <- lapply(files, readRDS)
This is not necessarily faster than a for loop from testing but allows all files to be an element of a
list without assigning them explicitly.
Finally, we often need to load multiple packages at once. This trick can do it quite easily by
applying library() to all libraries that we wish to import:
lapply(c("jsonlite","stringr","igraph"),library,character.only=TRUE)
Combining multiple `data.frames` (`lapply`, `mapply`)
In this exercise, we will generate four bootstrap linear regression models and combine the
summaries of these models into a single data frame.
library(broom)
#* Create the bootstrap data sets

BootData <- lapply(1:4,
function(i) mtcars[sample(1:nrow(mtcars),
size = nrow(mtcars),
replace = TRUE), ])
#* Fit the models

Models <- lapply(BootData,
function(BD) lm(mpg ~ qsec + wt + factor(am),
data = BD))
#* Tidy the output into a data.frame

Tidied <- lapply(Models,
tidy)
#* Give each element in the Tidied list a name

Tidied <- setNames(Tidied, paste0("Boot", seq_along(Tidied)))
At this point, we can take two approaches to inserting the names into the data.frame.
#* Insert the element name into the summary with `lapply`

#* Requires passing the names attribute to `lapply` and referencing `Tidied` within
#* the applied function.
Described_lapply <-
lapply(names(Tidied),
function(nm) cbind(nm, Tidied[[nm]]))
Combined_lapply <- do.call("rbind", Described_lapply)
#* Insert the element name into the summary with `mapply`

#* Allows us to pass the names and the elements as separate arguments.
Described_mapply <-
mapply(
function(nm, dframe) cbind(nm, dframe),
names(Tidied),
Tidied,
SIMPLIFY = FALSE)
Combined_mapply <- do.call("rbind", Described_mapply)
If you're a fan of magrittr style pipes, you can accomplish the entire task in a single chain (though
it may not be prudent to do so if you need any of the intermediary objects, such as the model
objects themselves):
library(magrittr)
library(broom)
Combined <- lapply(1:4,
function(i) mtcars[sample(1:nrow(mtcars),
size = nrow(mtcars),
replace = TRUE), ]) %>%
lapply(function(BD) lm( mpg ~ qsec + wt + factor(am), data = BD)) %>%
lapply(tidy) %>%
setNames(paste0("Boot", seq_along(.))) %>%
mapply(function(nm, dframe) cbind(nm, dframe),
nm = names(.),
dframe = .,
SIMPLIFY = FALSE) %>%
do.call("rbind", .)
Using built-in functionals
Built-in functionals: lapply(), sapply(), and

mapply()
R comes with built-in functionals, of which perhaps the most well-known are the apply family of
functions. Here is a description of some of the most common apply functions:
• = takes a list as an argument and applies the specified function to the list.
lapply()
• sapply() = the same as lapply() but attempts to simplify the output to a vector or a matrix.
vapply() = a variant of sapply() in which the output object's type must be specified.
○
• mapply() = like lapply() but can pass multiple vectors as input to the specified function. Can
be simplified like sapply().
Map() is an alias to mapply() with SIMPLIFY = FALSE.
○
lapply()
lapply() can be used with two different iterations:
• lapply(variable, FUN)
• lapply(seq_along(variable), FUN)
# Two ways of finding the mean of x

set.seed(1)
df <- data.frame(x = rnorm(25), y = rnorm(25))
lapply(df, mean)
lapply(seq_along(df), function(x) mean(df[[x]))
sapply()
sapply() will attempt to resolve its output to either a vector or a matrix.
# Two examples to show the different outputs of sapply()

sapply(letters, print) ## produces a vector
x <- list(a = 1:10, beta = exp(-3:3), logic = c(TRUE,FALSE,FALSE,TRUE))
sapply(x, quantile) ## produces a matrix
mapply()
mapply() works much like lapply() except it can take multiple vectors as input (hence the m for
multivariate).
mapply(sum, 1:5, 10:6, 3) # 3 will be "recycled" by mapply
Using user-defined functionals
User-defined functionals
Users can create their own functionals to varying degrees of complexity. The following examples
are from Functionals by Hadley Wickham:
randomise <- function(f) f(runif(1e3))
lapply2 <- function(x, f, ...) {

out <- vector("list", length(x))
for (i in seq_along(x)) {
out[[i]] <- f(x[[i]], ...)
}
out
}
In the first case, randomise accepts a single argument f, and calls it on a sample of Uniform
random variables. To demonstrate equivalence, we call set.seed below:
set.seed(123)
randomise(mean)
#[1] 0.4972778
set.seed(123)
mean(runif(1e3))
#[1] 0.4972778
set.seed(123)
randomise(max)
#[1] 0.9994045
set.seed(123)
max(runif(1e3))
#[1] 0.9994045
The second example is a re-implementation of base::lapply, which uses functionals to apply an

operation (f) to each element in a list (x). The ... parameter allows the user to pass additional
arguments to f, such as the na.rm option in the mean function:
lapply(list(c(1, 3, 5), c(2, NA, 6)), mean)

# [[1]]
# [1] 3
#
# [[2]]
# [1] NA
lapply2(list(c(1, 3, 5), c(2, NA, 6)), mean)
# [[1]]
# [1] 3
#
# [[2]]
# [1] NA
lapply(list(c(1, 3, 5), c(2, NA, 6)), mean, na.rm = TRUE)

# [[1]]
# [1] 3
#
# [[2]]
# [1] 4
lapply2(list(c(1, 3, 5), c(2, NA, 6)), mean, na.rm = TRUE)

# [[1]]
# [1] 3
#
# [[2]]
# [1] 4
Read *apply family of functions (functionals) online: https://riptutorial.com/r/topic/3567/-apply-

family-of-functions--functionals-
Chapter 3: .Rprofile
Remarks
There is a nice chapter on the matter in Efficient R programming
Examples
.Rprofile - the first chunk of code executed
.Rprofile is a file containing R code that is executed when you launch R from the directory
containing the .Rprofile file. The similarly named Rprofile.site, located in R's home directory, is
executed by default every time you load R from any directory. Rprofile.site and to a greater
extend .Rprofile can be used to initialize an R session with personal preferences and various
utility functions that you have defined.
Important note: if you use RStudio, you can have a separate .Rprofile in every RStudio
project directory.
Here are some examples of code that you might include in an .Rprofile file.
Setting your R home directory

# set R_home
Sys.setenv(R_USER="c:/R_home") # just an example directory
# but don't confuse this with the $R_HOME environment variable.
Setting page size options

options(papersize="a4")
options(editor="notepad")
options(pager="internal")
set the default help type

options(help_type="html")
set a site library
.Library.site <- file.path(chartr("\\", "/", R.home()), "site-library")
Set a CRAN mirror

local({r <- getOption("repos")
r["CRAN"] <- "http://my.local.cran"
options(repos=r)})
Setting the location of your library

This will allow you to not have to install all the packages again with each R version update.
# library location
.libPaths("c:/R_home/Rpackages/win")
Custom shortcuts or functions

Sometimes it is useful to have a shortcut for a long R expression. A common example of this
setting an active binding to access the last top-level expression result without having to type out
.Last.value:
makeActiveBinding(".", function(){.Last.value}, .GlobalEnv)
Because .Rprofile is just an R file, it can contain any arbitrary R code.
Pre-loading the most useful packages

This is bad practice and should generally be avoided because it separates package loading code
from the scripts where those packages are actually used.
See Also
See help(Startup) for all the different startup scripts, and further aspects. In particular, two system-
wide Profile files can be loaded as well. The first, Rprofile, may contain global settings, the other
file Profile.site may contain local choices the system administrator can make for all users. Both
files are found in the ${RHOME}/etc directory of the R installation. This directory also contains global
files Renviron and Renviron.site which both can be completemented with a local file ~/.Renviron in
the user's home directory.
.Rprofile example
Startup
# Load library setwidth on start - to set the width automatically.

.First <- function() {
library(setwidth)
# If 256 color terminal - use library colorout.
if (Sys.getenv("TERM") %in% c("xterm-256color", "screen-256color")) {
library("colorout")
}
}
Options
# Select default CRAN mirror for package installation.

options(repos=c(CRAN="https://cran.gis-lab.info/"))
# Print maximum 1000 elements.

options(max.print=1000)
# No scientific notation.
options(scipen=10)
# No graphics in menus.
options(menu.graphics=FALSE)
# Auto-completion for package names.

utils::rc.settings(ipck=TRUE)
Custom Functions
# Invisible environment to mask defined functions

.env = new.env()
# Quit R without asking to save.

.env$q <- function (save="no", ...) {
quit(save=save, ...)
}
# Attach the environment to enable functions.

attach(.env, warn.conflicts=FALSE)
Read .Rprofile online: https://riptutorial.com/r/topic/4166/-rprofile
Chapter 4: Aggregating data frames
Introduction
Aggregation is one of the most common uses for R. There are several ways to do so in R, which
we will illustrate here.
Examples
Aggregating with base R
For this, we will use the function aggregate, which can be used as follows:
aggregate(formula,function,data)
The following code shows various ways of using the aggregate function.
CODE:
df = data.frame(group=c("Group 1","Group 1","Group 2","Group 2","Group 2"), subgroup =

c("A","A","A","A","B"),value = c(2,2.5,1,2,1.5))
# sum, grouping by one column

aggregate(value~group, FUN=sum, data=df)
# mean, grouping by one column

aggregate(value~group, FUN=mean, data=df)
# sum, grouping by multiple columns

aggregate(value~group+subgroup,FUN=sum,data=df)
# custom function, grouping by one column

# in this example we want the sum of all values larger than 2 per group.
aggregate(value~group, FUN=function(x) sum(x[x>2]), data=df)
OUTPUT:
> df = data.frame(group=c("Group 1","Group 1","Group 2","Group 2","Group 2"), subgroup =

c("A","A","A","A","B"),value = c(2,2.5,1,2,1.5))
> print(df)
group subgroup value
1 Group 1 A 2.0
2 Group 1 A 2.5
3 Group 2 A 1.0
4 Group 2 A 2.0
5 Group 2 B 1.5
>
> # sum, grouping by one column
> aggregate(value~group, FUN=sum, data=df)
group value
1 Group 1 4.5
2 Group 2 4.5
>
> # mean, grouping by one column
> aggregate(value~group, FUN=mean, data=df)
group value
1 Group 1 2.25
2 Group 2 1.50
>
> # sum, grouping by multiple columns
> aggregate(value~group+subgroup,FUN=sum,data=df)
1 Group 1 A 4.5
2 Group 2 A 3.0
3 Group 2 B 1.5
>
> # custom function, grouping by one column
> # in this example we want the sum of all values larger than 2 per group.
> aggregate(value~group, FUN=function(x) sum(x[x>2]), data=df)
group value
1 Group 1 2.5
2 Group 2 0.0
Aggregating with dplyr
Aggregating with dplyr is easy! You can use the group_by() and the summarize() functions for this.
Some examples are given below.
CODE:
# Aggregating with dplyr

library(dplyr)
df = data.frame(group=c("Group 1","Group 1","Group 2","Group 2","Group 2"), subgroup =

c("A","A","A","A","B"),value = c(2,2.5,1,2,1.5))
print(df)

df %>% group_by(group) %>% summarize(value = sum(value)) %>% as.data.frame()

df %>% group_by(group) %>% summarize(value = mean(value)) %>% as.data.frame()

df %>% group_by(group,subgroup) %>% summarize(value = sum(value)) %>% as.data.frame()

df %>% group_by(group) %>% summarize(value = sum(value[value>2])) %>% as.data.frame()
OUTPUT:
> library(dplyr)
>
> df = data.frame(group=c("Group 1","Group 1","Group 2","Group 2","Group 2"), subgroup =
c("A","A","A","A","B"),value = c(2,2.5,1,2,1.5))
> print(df)
1 Group 1 A 2.0
2 Group 1 A 2.5
3 Group 2 A 1.0
4 Group 2 A 2.0
5 Group 2 B 1.5
>
> df %>% group_by(group) %>% summarize(value = sum(value)) %>% as.data.frame()
group value
1 Group 1 4.5
2 Group 2 4.5
>
> df %>% group_by(group) %>% summarize(value = mean(value)) %>% as.data.frame()
group value
1 Group 1 2.25
2 Group 2 1.50
>
> df %>% group_by(group,subgroup) %>% summarize(value = sum(value)) %>% as.data.frame()
1 Group 1 A 4.5
2 Group 2 A 3.0
3 Group 2 B 1.5
>
> df %>% group_by(group) %>% summarize(value = sum(value[value>2])) %>% as.data.frame()
group value
1 Group 1 2.5
2 Group 2 0.0
Aggregating with data.table
Grouping with the data.table package is done using the syntax dt[i, j, by] Which can be read out
loud as: "Take dt, subset rows using i, then calculate j, grouped by by." Within the dt statement,
multiple calculations or groups should be put in a list. Since an alias for list() is .(), both can be
used interchangeably. In the examples below we use .().
CODE:
# Aggregating with data.table

library(data.table)
dt = data.table(group=c("Group 1","Group 1","Group 2","Group 2","Group 2"), subgroup =

c("A","A","A","A","B"),value = c(2,2.5,1,2,1.5))
print(dt)

dt[,.(value=sum(value)),group]

dt[,.(value=mean(value)),group]

dt[,.(value=sum(value)),.(group,subgroup)]
dt[,.(value=sum(value[value>2])),group]
OUTPUT:
> # Aggregating with data.table

> library(data.table)
>
> dt = data.table(group=c("Group 1","Group 1","Group 2","Group 2","Group 2"), subgroup =
c("A","A","A","A","B"),value = c(2,2.5,1,2,1.5))
> print(dt)
1: Group 1 A 2.0
2: Group 1 A 2.5
3: Group 2 A 1.0
4: Group 2 A 2.0
5: Group 2 B 1.5
>
> dt[,.(value=sum(value)),group]
group value
1: Group 1 4.5
2: Group 2 4.5
>
> dt[,.(value=mean(value)),group]
group value
1: Group 1 2.25
2: Group 2 1.50
>
> dt[,.(value=sum(value)),.(group,subgroup)]
1: Group 1 A 4.5
2: Group 2 A 3.0
3: Group 2 B 1.5
>
> dt[,.(value=sum(value[value>2])),group]
group value
1: Group 1 2.5
2: Group 2 0.0
Read Aggregating data frames online: https://riptutorial.com/r/topic/10792/aggregating-data-

frames
Chapter 5: Analyze tweets with R
Introduction
(Optional) Every topic has a focus. Tell the readers what they will find here and let future
contributors know what belongs.
Examples
Download Tweets
The first think you need to do is to download tweets. You need to Setup your tweeter account.
Much Information can be found in Internet on how to do it. The following two links were useful for
my Setup (last checked in May 2017)
In particular I found the following two links useful (last checked in May 2017):
Link 1
Link 2
R Libraries
You will need the following R packages
library("devtools")
library("twitteR")
library("ROAuth")
Supposing you have your keys You have to run the following code
api_key <- XXXXXXXXXXXXXXXXXXXXXX

api_secret <- XXXXXXXXXXXXXXXXXXXXXX
access_token <- XXXXXXXXXXXXXXXXXXXXXX
access_token_secret <- XXXXXXXXXXXXXXXXXXXXXX
setup_twitter_oauth(api_key,api_secret)
Change XXXXXXXXXXXXXXXXXXXXXX to your keys (if you have Setup your tweeter account you know
which keys I mean).
Let's now suppose we want to download tweets on coffee. The following code will do it
search.string <- "#coffee"

no.of.tweets <- 1000
c_tweets <- searchTwitter(search.string, n=no.of.tweets, lang="en")
You will get 1000 tweets on "coffee".
Get text of tweets
Now we need to access the text of the tweets. So we do it in this way (we also need to clean up
the tweets from special characters that for now we don't need, like emoticons with the sapply
function.)
coffee_tweets = sapply(c_tweets, function(t) t$getText())
coffee_tweets <- sapply(coffee_tweets,function(row) iconv(row, "latin1", "ASCII", sub=""))
and you can check your tweets with the head function.
head(coffee_tweets)
Read Analyze tweets with R online: https://riptutorial.com/r/topic/10086/analyze-tweets-with-r
Chapter 6: ANOVA
Examples
Basic usage of aov()
Analysis of Variance (aov) is used to determine if the means of two or more groups differ
significantly from each other. Responses are assumed to be independent of each other, Normally
distributed (within each group), and the within-group variances are assumed equal.
In order to complete the analysis data must be in long format (see reshaping data topic). aov() is a
wrapper around the lm() function, using Wilkinson-Rogers formula notation y~f where y is the
response (independent) variable and f is a factor (categorical) variable representing group
membership. If f is numeric rather than a factor variable, aov() will report the results of a linear
regression in ANOVA format, which may surprise inexperienced users.
The aov() function uses Type I (sequential) Sum of Squares. This type of Sum of Squares tests all
of the (main and interaction) effects sequentially. The result is that the first effect tested is also
assigned shared variance between it and other effects in the model. For the results from such a
model to be reliable, data should be balanced (all groups are of the same size).
When the assumptions for Type I Sum of Squares do not hold, Type II or Type III Sum of Squares
may be applicable. Type II Sum of Squares test each main effect after every other main effect, and
thus controls for any overlapping variance. However, Type II Sum of Squares assumes no
interaction between the main effects.
Lastly, Type III Sum of Squares tests each main effect after every other main effect and every
interaction. This makes Type III Sum of Squares a necessity when an interaction is present.
Type II and Type III Sums of Squares are implemented in the Anova() function.
Using the mtcars data set as an example.
mtCarsAnovaModel <- aov(wt ~ factor(cyl), data=mtcars)
To view summary of ANOVA model:
summary(mtCarsAnovaModel)
One can also extract the coefficients of the underlying lm() model:
coefficients(mtCarsAnovaModel)
Basic usage of Anova()
When dealing with an unbalanced design and/or non-orthogonal contrasts, Type II or Type III Sum
of Squares are necessary. The Anova() function from the car package implements these. Type II
Sum of Squares assumes no interaction between main effects. If interactions are assumed, Type
III Sum of Squares is appropriate.
The Anova() function wraps around the lm() function.
Using the mtcars data sets as an example, demonstrating the difference between Type II and Type
III when an interaction is tested.
> Anova(lm(wt ~ factor(cyl)*factor(am), data=mtcars), type = 2)

Anova Table (Type II tests)
Response: wt
Sum Sq Df F value Pr(>F)
factor(cyl) 7.2278 2 11.5266 0.0002606 ***
factor(am) 3.2845 1 10.4758 0.0032895 **
factor(cyl):factor(am) 0.0668 2 0.1065 0.8993714
Residuals 8.1517 26
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> Anova(lm(wt ~ factor(cyl)*factor(am), data=mtcars), type = 3)

Anova Table (Type III tests)
Response: wt
Sum Sq Df F value Pr(>F)
(Intercept) 25.8427 1 82.4254 1.524e-09 ***
factor(cyl) 4.0124 2 6.3988 0.005498 **
factor(am) 1.7389 1 5.5463 0.026346 *
factor(cyl):factor(am) 0.0668 2 0.1065 0.899371
Residuals 8.1517 26
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Read ANOVA online: https://riptutorial.com/r/topic/3610/anova
Chapter 7: Arima Models
Remarks
The Arima function in the forecast package is more explicit in how it deals with constants, which
may make it easier for some users relative to the arima function in base R.
ARIMA is a general framework for modeling and making predictions from time series data using
(primarily) the series itself. The purpose of the framework is to differentiate short- and long-term
dynamics in a series to improve the accuracy and certainty of forecasts. More poetically, ARIMA
models provide a method for describing how shocks to a system transmit through time.
From an econometric perspective, ARIMA elements are necessary to correct serial correlation and
ensure stationarity.
Examples
Modeling an AR1 Process with Arima
We will model the process
#Load the forecast package

library(forecast)
#Generate an AR1 process of length n (from Cowpertwait & Meltcalfe)

# Set up variables
set.seed(1234)
n <- 1000
x <- matrix(0,1000,1)
w <- rnorm(n)
# loop to create x
for (t in 2:n) x[t] <- 0.7 * x[t-1] + w[t]
plot(x,type='l')
We will fit an Arima model with autoregressive order 1, 0 degrees of differencing, and an MA order
of 0.
#Fit an AR1 model using Arima

fit <- Arima(x, order = c(1, 0, 0))
summary(fit)
# Series: x
# ARIMA(1,0,0) with non-zero mean
#
# Coefficients:
# ar1 intercept
# 0.7040 -0.0842
# s.e. 0.0224 0.1062
#
# sigma^2 estimated as 0.9923: log likelihood=-1415.39
# AIC=2836.79 AICc=2836.81 BIC=2851.51
#
# Training set error measures:
# ME RMSE MAE MPE MAPE MASE ACF1
# Training set -8.369365e-05 0.9961194 0.7835914 Inf Inf 0.91488 0.02263595
# Verify that the model captured the true AR parameter
Notice that our coefficient is close to the true value from the generated data
fit$coef[1]
# ar1
# 0.7040085
#Verify that the model eliminates the autocorrelation

acf(x)
acf(fit$resid)
#Forecast 10 periods
fcst <- forecast(fit, h = 100)
fcst
Point Forecast Lo 80 Hi 80 Lo 95 Hi 95
1001 0.282529070 -0.9940493 1.559107 -1.669829 2.234887
1002 0.173976408 -1.3872262 1.735179 -2.213677 2.561630
1003 0.097554408 -1.5869850 1.782094 -2.478726 2.673835
1004 0.043752667 -1.6986831 1.786188 -2.621073 2.708578
1005 0.005875783 -1.7645535 1.776305 -2.701762 2.713514
...
#Call the point predictions

fcst$mean
# Time Series:
# Start = 1001
# End = 1100
# Frequency = 1
[1] 0.282529070 0.173976408 0.097554408 0.043752667 0.005875783 -0.020789866 -
0.039562711 -0.052778954
[9] -0.062083302
...
#Plot the forecast

plot(fcst)
Read Arima Models online: https://riptutorial.com/r/topic/1725/arima-models
Chapter 8: Arithmetic Operators
Remarks
Nearly all operators in R are really functions. For example, + is a function defined as function (e1,
e2) .Primitive("+") where e1 is the left-hand side of the operator and e2 is the right-hand side of
the operator. This means it is possible to accomplish rather counterintuitive effects by masking the
+ in base with a user defined function.
For example:
`+` <- function(e1, e2) {e1-e2}
> 3+10
[1] -7
Examples
Range and addition
Let's take an example of adding a value to a range (as it could be done in a loop for example):
3+1:5
Gives:
[1] 4 5 6 7 8
This is because the range operator : has higher precedence than addition operator +.
What happens during evaluation is as follows:
• 3+1:5
• 3+c(1, 2, 3, 4, 5) expansion of the range operator to make a vector of integers.
• c(4, 5, 6, 7, 8) Addition of 3 to each member of the vector.
To avoid this behavior you have to tell the R interpreter how you want it to order the operations
with ( ) like this:
(3+1):5
Now R will compute what is inside the parentheses before expanding the range and gives:
[1] 4 5
Addition and subtraction
The basic math operations are performed mainly on numbers or on vectors (lists of numbers).
1. Using single numbers
We can simple enter the numbers concatenated with + for adding and - for subtracting:
> 3 + 4.5
# [1] 7.5
> 3 + 4.5 + 2
# [1] 9.5
> 3 + 4.5 + 2 - 3.8
# [1] 5.7
> 3 + NA
#[1] NA
> NA + NA
#[1] NA
> NA - NA
#[1] NA
> NaN - NA
#[1] NaN
> NaN + NA
#[1] NaN
We can assign the numbers to variables (constants in this case) and do the same operations:
> a <- 3; B <- 4.5; cc <- 2; Dd <- 3.8 ;na<-NA;nan<-NaN

> a + B
# [1] 7.5
> a + B + cc
# [1] 9.5
> a + B + cc - Dd
# [1] 5.7
> B-nan
#[1] NaN
> a+na-na
#[1] NA
> a + na
#[1] NA
> B-nan
#[1] NaN
> a+na-na
#[1] NA
2. Using vectors
In this case we create vectors of numbers and do the operations using those vectors, or
combinations with single numbers. In this case the operation is done considering each element of
the vector:
> A <- c(3, 4.5, 2, -3.8);

> A
# [1] 3.0 4.5 2.0 -3.8
> A + 2 # Adding a number
# [1] 5.0 6.5 4.0 -1.8
> 8 - A # number less vector
# [1] 5.0 3.5 6.0 11.8
> n <- length(A) #number of elements of vector A
> n
# [1] 4
> A[-n] + A[n] # Add the last element to the same vector without the last element
# [1] -0.8 0.7 -1.8
> A[1:2] + 3 # vector with the first two elements plus a number
# [1] 6.0 7.5
> A[1:2] - A[3:4] # vector with the first two elements less the vector with elements 3 and 4
# [1] 1.0 8.3
We can also use the function sum to add all elements of a vector:
> sum(A)
# [1] 5.7
> sum(-A)
# [1] -5.7
> sum(A[-n]) + A[n]
# [1] 5.7
We must take care with recycling, which is one of the characteristics of R, a behavior that happens
when doing math operations where the length of vectors is different. Shorter vectors in the
expression are recycled as often as need be (perhaps fractionally) until they match the length of
the longest vector. In particular a constant is simply repeated. In this case a Warning is show.
> B <- c(3, 5, -3, 2.7, 1.8)

> B
# [1] 3.0 5.0 -3.0 2.7 1.8
> A
# [1] 3.0 4.5 2.0 -3.8
> A + B # the first element of A is repeated
# [1] 6.0 9.5 -1.0 -1.1 4.8
Warning message:
In A + B : longer object length is not a multiple of shorter object length
> B - A # the first element of A is repeated
# [1] 0.0 0.5 -5.0 6.5 -1.2
Warning message:
In B - A : longer object length is not a multiple of shorter object length
In this case the correct procedure will be to consider only the elements of the shorter vector:
> B[1:n] + A
# [1] 6.0 9.5 -1.0 -1.1
> B[1:n] - A
# [1] 0.0 0.5 -5.0 6.5
When using the sum function, again all the elements inside the function are added.
> sum(A, B)
# [1] 15.2
> sum(A, -B)
# [1] -3.8
> sum(A)+sum(B)
# [1] 15.2
> sum(A)-sum(B)
# [1] -3.8
Read Arithmetic Operators online: https://riptutorial.com/r/topic/4389/arithmetic-operators
Chapter 9: Bar Chart
Introduction
The purpose of the bar plot is to display the frequencies (or proportions) of levels of a factor
variable. For example, a bar plot is used to pictorially display the frequencies (or proportions) of
individuals in various socio-economic (factor) groups(levels-high, middle, low). Such a plot will
help to provide a visual comparison among the various factor levels.
Examples
barplot() function
In barplot, factor-levels are placed on the x-axis and frequencies (or proportions) of various factor-
levels are considered on the y-axis. For each factor-level one bar of uniform width with heights
being proportional to factor level frequency (or proportion) is constructed.
The barplot() function is in the graphics package of the R's System Library. The barplot() function
must be supplied at least one argument. The R help calls this as heights, which must be either
vector or a matrix. If it is vector, its members are the various factor-levels.
To illustrate barplot(), consider the following data preparation:
> grades<-c("A+","A-","B+","B","C")
> Marks<-sample(grades,40,replace=T,prob=c(.2,.3,.25,.15,.1))
> Marks
[1] "A+" "A-" "B+" "A-" "A+" "B" "A+" "B+" "A-" "B" "A+" "A-"
[13] "A-" "B+" "A-" "A-" "A-" "A-" "A+" "A-" "A+" "A+" "C" "C"
[25] "B" "C" "B+" "C" "B+" "B+" "B+" "A+" "B+" "A-" "A+" "A-"
[37] "A-" "B" "C" "A+"
>
A bar chart of the Marks vector is obtained from
> barplot(table(Marks),main="Mid-Marks in Algorithms")
Notice that, the barplot() function places the factor levels on the x-axis in the lexicographical order
of the levels. Using the parameter names.arg, the bars in plot can be placed in the order as stated
in the vector, grades.
# plot to the desired horizontal axis labels

> barplot(table(Marks),names.arg=grades ,main="Mid-Marks in Algorithms")
Colored bars can be drawn using the col= parameter.
> barplot(table(Marks),names.arg=grades,col = c("lightblue",
"lightcyan", "lavender", "mistyrose", "cornsilk"),
main="Mid-Marks in Algorithms")
A bar chart with horizontal bars can be obtained as follows:
> barplot(table(Marks),names.arg=grades,horiz=TRUE,col = c("lightblue",

A bar chart with proportions on the y-axis can be obtained as follows:
> barplot(prop.table(table(Marks)),names.arg=grades,col = c("lightblue",

The sizes of the factor-level names on the x-axis can be increased using cex.names parameter.
> barplot(prop.table(table(Marks)),names.arg=grades,col = c("lightblue",
main="Mid-Marks in Algorithms",cex.names=2)
The heights parameter of the barplot() could be a matrix. For example it could be matrix, where
the columns are the various subjects taken in a course, the rows could be the labels of the grades.
Consider the following matrix:
> gradTab
Algorithms Operating Systems Discrete Math
A- 13 10 7
A+ 10 7 2
B 4 2 14
B+ 8 19 12
C 5 2 5
To draw a stacked bar, simply use the command:
> barplot(gradTab,col = c("lightblue","lightcyan",

"lavender", "mistyrose", "cornsilk"),legend.text = grades,
To draw a juxtaposed bars, use the besides parameter, as given under:
> barplot(gradTab,beside = T,col = c("lightblue","lightcyan",

A horizontal bar chart can be obtained using horiz=T parameter:
> barplot(gradTab,beside = T,horiz=T,col = c("lightblue","lightcyan",

cex.names=.75,main="Mid-Marks in Algorithms")
Read Bar Chart online: https://riptutorial.com/r/topic/8091/bar-chart
Chapter 10: Base Plotting
Parameters
Parameter Details
x x-axis variable. May supply either data$variablex or data[,x]
y y-axis variable. May supply either data$variabley or data[,y]
main Main title of plot
sub Optional subtitle of plot
xlab Label for x-axis
ylab Label for y-axis
pch Integer or character indicating plotting symbol
col Integer or string indicating color
Type of plot. "p" for points, "l" for lines, "b" for both, "c" for the lines part alone
type of "b", "o" for both ‘overplotted’, "h" for ‘histogram’-like (or ‘high-density’) vertical
lines, "s" for stair steps, "S" for other steps, "n" for no plotting
Remarks
The items listed in the "Parameters" section is a small fraction of hte possible parameters that can
be modified or set by the par function. See par for a more complete list. In addition all the graphics
devices, including the system specific interactive graphics devices will have a set of parameters
that can customize the output.
Examples
Basic Plot
A basic plot is created by calling plot(). Here we use the built-in cars data frame that contains the
speed of cars and the distances taken to stop in the 1920s. (To find out more about the dataset,
use help(cars)).
plot(x = cars$speed, y = cars$dist, pch = 1, col = 1,

main = "Distance vs Speed of Cars",
xlab = "Speed", ylab = "Distance")
We can use many other variations in the code to get the same result. We can also change the
parameters to obtain different results.
with(cars, plot(dist~speed, pch = 2, col = 3,

main = "Distance to stop vs Speed of Cars",
xlab = "Speed", ylab = "Distance"))
Additional features can be added to this plot by calling points(), text(), mtext(), lines(), grid(),
etc.
plot(dist~speed, pch = "*", col = "magenta", data=cars,

main = "Distance to stop vs Speed of Cars",
xlab = "Speed", ylab = "Distance")
mtext("In the 1920s.")
grid(,col="lightblue")
Matplot
matplotis useful for quickly plotting multiple sets of observations from the same object, particularly
from a matrix, on the same graph.
Here is an example of a matrix containing four sets of random draws, each with a different mean.
xmat <- cbind(rnorm(100, -3), rnorm(100, -1), rnorm(100, 1), rnorm(100, 3))
head(xmat)
# [,1] [,2] [,3] [,4]
# [1,] -3.072793 -2.53111494 0.6168063 3.780465
# [2,] -3.702545 -1.42789347 -0.2197196 2.478416
# [3,] -2.890698 -1.88476126 1.9586467 5.268474
# [4,] -3.431133 -2.02626870 1.1153643 3.170689
# [5,] -4.532925 0.02164187 0.9783948 3.162121
# [6,] -2.169391 -1.42699116 0.3214854 4.480305
One way to plot all of these observations on the same graph is to do one plot call followed by
three more points or lines calls.
plot(xmat[,1], type = 'l')

lines(xmat[,2], col = 'red')
lines(xmat[,3], col = 'green')
lines(xmat[,4], col = 'blue')
However, this is both tedious, and causes problems because, among other things, by default the
axis limits are fixed by plot to fit only the first column.
Much more convenient in this situation is to use the matplot function, which only requires one call
and automatically takes care of axis limits and changing the aesthetics for each column to make
them distinguishable.
matplot(xmat, type = 'l')
Note that, by default, matplot varies both color (col) and linetype (lty) because this increases the
number of possible combinations before they get repeated. However, any (or both) of these
aesthetics can be fixed to a single value...
matplot(xmat, type = 'l', col = 'black')
...or a custom vector (which will recycle to the number of columns, following standard R vector
recycling rules).
matplot(xmat, type = 'l', col = c('red', 'green', 'blue', 'orange'))
Standard graphical parameters, including main, xlab, xmin, work exactly the same way as for plot.
For more on those, see ?par.
Like plot, if given only one object, matplot assumes it's the y variable and uses the indices for x.
However, x and y can be specified explicitly.
matplot(x = seq(0, 10, length.out = 100), y = xmat, type='l')
In fact, both x and y can be matrices.
xes <- cbind(seq(0, 10, length.out = 100),

seq(2.5, 12.5, length.out = 100),
seq(5, 15, length.out = 100),
seq(7.5, 17.5, length.out = 100))
matplot(x = xes, y = xmat, type = 'l')
Histograms
Histograms allow for a pseudo-plot of the underlying distribution of the data.
hist(ldeaths)
hist(ldeaths, breaks = 20, freq = F, col = 3)
Combining Plots
It's often useful to combine multiple plot types in one graph (for example a Barplot next to a
Scatterplot.) R makes this easy with the help of the functions par() and layout().
par()
par uses the arguments mfrow or mfcol to create a matrix of nrows and ncols c(nrows, ncols) which
will serve as a grid for your plots. The following example shows how to combine four plots in one
graph:
par(mfrow=c(2,2))
plot(cars, main="Speed vs. Distance")
hist(cars$speed, main="Histogram of Speed")
boxplot(cars$dist, main="Boxplot of Distance")
boxplot(cars$speed, main="Boxplot of Speed")
layout()
The layout() is more flexible and allows you to specify the location and the extent of each plot
within the final combined graph. This function expects a matrix object as an input:
layout(matrix(c(1,1,2,3), 2,2, byrow=T))

hist(cars$speed, main="Histogram of Speed")
boxplot(cars$dist, main="Boxplot of Distance")
boxplot(cars$speed, main="Boxplot of Speed")
Density plot
A very useful and logical follow-up to histograms would be to plot the smoothed density function of
a random variable. A basic plot produced by the command
plot(density(rnorm(100)),main="Normal density",xlab="x")
would look like
You can overlay a histogram and a density curve with
x=rnorm(100)
hist(x,prob=TRUE,main="Normal density + histogram")
lines(density(x),lty="dotted",col="red")
which gives
Empirical Cumulative Distribution Function
A very useful and logical follow-up to histograms and density plots would be the Empirical
Cumulative Distribution Function. We can use the function ecdf() for this purpose. A basic plot
produced by the command
plot(ecdf(rnorm(100)),main="Cumulative distribution",xlab="x")
would look like
Getting Started with R_Plots
• Scatterplot
You have two vectors and you want to plot them.
x_values <- rnorm(n = 20 , mean = 5 , sd = 8) #20 values generated from Normal(5,8)

y_values <- rbeta(n = 20 , shape1 = 500 , shape2 = 10) #20 values generated from Beta(500,10)
If you want to make a plot which has the y_values in vertical axis and the x_valuesin horizontal axis,
you can use the following commands:
plot(x = x_values, y = y_values, type = "p") #standard scatter-plot

plot(x = x_values, y = y_values, type = "l") # plot with lines
plot(x = x_values, y = y_values, type = "n") # empty plot
You can type ?plot() in the console to read about more options.
• Boxplot
You have some variables and you want to examine their Distributions
#boxplot is an easy way to see if we have some outliers in the data.
z<- rbeta(20 , 500 , 10) #generating values from beta distribution

z[c(19 , 20)] <- c(0.97 , 1.05) # replace the two last values with outliers
boxplot(z) # the two points are the outliers of variable z.
• Histograms
Easy way to draw histograms
hist(x = x_values) # Histogram for x vector

hist(x = x_values, breaks = 3) #use breaks to set the numbers of bars you want
• Pie_charts
If you want to visualize the frequencies of a variable just draw pie
First we have to generate data with frequencies, for example :
P <- c(rep('A' , 3) , rep('B' , 10) , rep('C' , 7) )

t <- table(P) # this is a frequency matrix of variable P
pie(t) # And this is a visual version of the matrix above
Read Base Plotting online: https://riptutorial.com/r/topic/1377/base-plotting
Chapter 11: Bibliography in RMD
Parameters
Parameter in YAML header Detail
toc table of contents
number_sections numbering the sections automatically
bibliography path to the bibliography file
csl path to the style file
Remarks
• The purpose of this documentation is integrating an academic bibliography in a RMD file.
• To use the documentation given above, you have to install rmarkdown in R via
install.packages("rmarkdown").
• Sometimes Rmarkdown removes the hyperlinks of the citations. The solution for this is
adding the following code to your YAML header: link-citations: true
• The bibliography may have any of these formats:
Format File extension
MODS .mods
BibLaTeX .bib
BibTeX .bibtex
RIS .ris
EndNote .enl
EndNote XML .xml
ISI .wos
MEDLINE .medline
Copac .copac
JSON citeproc .json
Examples
Specifying a bibliography and cite authors
The most important part of your RMD file is the YAML header. For writing an academic paper, I
suggest to use PDF output, numbered sections and a table of content (toc).
---
title: "Writing an academic paper in R"
author: "Author"
date: "Date"
output:
pdf_document:
number_sections: yes
toc: yes
bibliography: bibliography.bib
---
In this example, our file bibliography.bib looks like this:
@ARTICLE{Meyer2000,
AUTHOR="Bernd Meyer",
TITLE="A constraint-based framework for diagrammatic reasoning",
JOURNAL="Applied Artificial Intelligence",
VOLUME= "14",
ISSUE = "4",
PAGES= "327--344",
YEAR=2000
}
To cite an author mentioned in your .bib file write @ and the bibkey, e.g. Meyer2000.
# Introduction
`@Meyer2000` results in @Meyer2000.
`@Meyer2000 [p. 328]` results in @Meyer2000 [p. 328]
`[@Meyer2000]` results in [@Meyer2000]
`[-@Meyer2000]` results in [-@Meyer2000]
# Summary
# References
Rendering the RMD file via RStudio (Ctrl+Shift+K) or via console rmarkdown::render("<path-to-
your-RMD-file">) results in the following output:
will use a Chicago author-date format for citations and references. To use another style, you will
need to specify a CSL 1.0 style file in the csl metadata field. In the following a often used citation
style, the elsevier style, is presented (download at https://github.com/citation-style-language/styles
). The style-file has to be stored in the same directory as the RMD file OR the absolute path to the
file has to be submitted.
To use another style then the default one, the following code is used:
---
title: "Writing an academic paper in R"
author: "Author"
date: "Date"
output:
pdf_document:
number_sections: yes
toc: yes
bibliography: bibliography.bib
csl: elsevier-harvard.csl
---
# Introduction
`@Meyer2000` results in @Meyer2000.
`@Meyer2000 [p. 328]` results in @Meyer2000 [p. 328]
`[@Meyer2000]` results in [@Meyer2000]
`[-@Meyer2000]` results in [-@Meyer2000]
# Summary
# Reference
Notice the differences to the output of example "Specifying a bibliography and cite authors"
Read Bibliography in RMD online: https://riptutorial.com/r/topic/7606/bibliography-in-rmd
Chapter 12: boxplot
Syntax
• boxplot(x, ...) # generic function
• boxplot(formula, data = NULL, ..., subset, na.action = NULL) ## S3 method for class
'formula'
• boxplot(x, ..., range = 1.5, width = NULL, varwidth = FALSE, notch = FALSE, outline =
TRUE, names, plot = TRUE, border = par("fg"), col = NULL, log = "", pars = list(boxwex =
0.8, staplewex = 0.5, outwex = 0.5), horizontal = FALSE, add = FALSE, at = NULL) ##
Default S3 method
Parameters
Parameters Details (source R Documentation)
a formula, such as y ~ grp, where y is a numeric vector of data values to be

formula
split into groups according to the grouping variable grp (usually a factor).
data a data.frame (or list) from which the variables in formula should be taken.
subset an optional vector specifying a subset of observations to be used for plotting.
a function which indicates what should happen when the data contain NAs.
na.action
The default is to ignore missing values in either the response or the group.
a scale factor to be applied to all boxes. When there are only a few groups, the
boxwex
appearance of the plot can be improved by making the boxes narrower.
if TRUE (the default) then a boxplot is produced. If not, the summaries which
plot
the boxplots are based on are returned.
if col is non-null it is assumed to contain colors to be used to colour the bodies

col
of the box plots. By default they are in the background colour.
Examples
Create a box-and-whisker plot with boxplot() {graphics}
This example use the default boxplot() function and the irisdata frame.
> head(iris)
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3.0 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
5 5.0 3.6 1.4 0.2 setosa
6 5.4 3.9 1.7 0.4 setosa
Simple boxplot (Sepal.Length)

Create a box-and-whisker graph of a numerical variable
boxplot(iris[,1],xlab="Sepal.Length",ylab="Length(in centemeters)",
main="Summary Charateristics of Sepal.Length(Iris Data)")
Boxplot of sepal length grouped by species

Create a boxplot of a numerical variable grouped by a categorical variable
boxplot(Sepal.Length~Species,data = iris)
Bring order
To change order of the box in the plot you have to change the order of the categorical variable's
levels.
For example if we want to have the order virginica - versicolor - setosa
newSpeciesOrder <- factor(iris$Species, levels=c("virginica","versicolor","setosa"))

boxplot(Sepal.Length~newSpeciesOrder,data = iris)
Change groups names
If you want to specifie a better name to your groups you can use the Names parameter. It take a
vector of the size of the levels of categorical variable
boxplot(Sepal.Length~newSpeciesOrder,data = iris,names= c("name1","name2","name3"))
Small improvements
Color
col : add a vector of the size of the levels of categorical variable
boxplot(Sepal.Length~Species,data = iris,col=c("green","yellow","orange"))
Proximity of the box
boxwex: set the margin between boxes.
Left boxplot(Sepal.Length~Species,data = iris,boxwex = 0.1)
Right boxplot(Sepal.Length~Species,data = iris,boxwex = 1)
See the summaries which the boxplots are

based plot=FALSE
To see a summary you have to put the paramater plot to FALSE.

Various results are given
> boxplot(Sepal.Length~newSpeciesOrder,data = iris,plot=FALSE)
$stats #summary of the numerical variable for the 3 groups
[,1] [,2] [,3]
[1,] 5.6 4.9 4.3 # extreme value
[2,] 6.2 5.6 4.8 # first quartile limit
[3,] 6.5 5.9 5.0 # median limit
[4,] 6.9 6.3 5.2 # third quartile limit
[5,] 7.9 7.0 5.8 # extreme value
$n #number of observations in each groups

[1] 50 50 50
$conf #extreme value of the notchs

[,1] [,2] [,3]
[1,] 6.343588 5.743588 4.910622
[2,] 6.656412 6.056412 5.089378
$out #extreme value

[1] 4.9
$group #group in which are the extreme value

[1] 1
$names #groups names

[1] "virginica" "versicolor" "setosa"
Additional boxplot style parameters.
Box
• boxlty - box line type
• boxlwd - box line width
• boxcol - box line color
• boxfill - box fill colors
Median
• medlty - median line type ("blank" for no line)
• medlwd - median line widht
• medcol - median line color
• medpch - median point (NA for no symbol)
• medcex - median point size
• medbg - median point background color
Whisker
• whisklty - whisker line type
• whisklwd - whisker line width
• whiskcol - whisker line color
Staple
• staplelty - staple line type
• staplelwd - staple line width
• staplecol - staple line color
Outliers
• outlty - outlier line type ("blank" for no line)
• outlwd - outlier line width
• outcol - outlier line color
• outpch - outlier point type (NA for no symbol)
• outcex - outlier point size
• outbg - outlier point background color
Example
Default and heavily modified plots side by side
par(mfrow=c(1,2))
# Default
boxplot(Sepal.Length ~ Species, data=iris)
# Modified
boxplot(Sepal.Length ~ Species, data=iris,
boxlty=2, boxlwd=3, boxfill="cornflowerblue", boxcol="darkblue",
medlty=2, medlwd=2, medcol="red", medpch=21, medcex=1, medbg="white",
whisklty=2, whisklwd=3, whiskcol="darkblue",
staplelty=2, staplelwd=2, staplecol="red",
outlty=3, outlwd=3, outcol="grey", outpch=NA
)
Read boxplot online: https://riptutorial.com/r/topic/1005/boxplot
Chapter 13: caret
Introduction
caret is an R package that aids in data processing needed for machine learning problems. It
stands for classification and regression training. When building models for a real dataset, there are
some tasks other than the actual learning algorithm that need to be performed, such as cleaning
the data, dealing with incomplete observations, validating our model on a test set, and compare
different models.
caret helps in these scenarios, independent of the actual learning algorithms used.
Examples
Preprocessing
Pre-processing in caret is done through the preProcess() function. Given a matrix or data frame
type object x, preProcess() applies transformations on the training data which can then be applied
to testing data.
The heart of the preProcess() function is the method argument. Method operations are applied in
this order:
1. Zero-variance filter
2. Near-zero variance filter
3. Box-Cox/Yeo-Johnson/exponential transformation
4. Centering
5. Scaling
6. Range
7. Imputation
8. PCA
9. ICA
10. Spatial Sign
Below, we take the mtcars data set and perform centering, scaling, and a spatial sign transform.
auto_index <- createDataPartition(mtcars$mpg, p = .8,

list = FALSE,
times = 1)
mt_train <- mtcars[auto_index,]

mt_test <- mtcars[-auto_index,]
process_mtcars <- preProcess(mt_train, method = c("center","scale","spatialSign"))
mtcars_train_transf <- predict(process_mtcars, mt_train)

mtcars_test_tranf <- predict(process_mtcars,mt_test)
Read caret online: https://riptutorial.com/r/topic/4271/caret
Chapter 14: Classes
Introduction
The class of a data-object determines which functions will process its contents. The class-attribute
is a character vector, and objects can have zero, one or more classes. If there is no class-
attribute, there will still be an implicit class determined by an object's mode. The class can be
inspected with the function class and it can be set or modified by the class<- function. The S3
class system was established early in S's history. The more complex S4 class system was
established later
Remarks
There are several functions for inspecting the "type" of an object. The most useful such function is
class, although sometimes it is necessary to examine the mode of an object. Since we are
discussing "types", one might think that typeof would be useful, but generally the result from mode
will be more useful, because objects with no explicit "class"-attribute will have function dispatch
determined by the "implicit class" determined by their mode.
Examples
Vectors
The most simple data structure available in R is a vector. You can make vectors of numeric
values, logical values, and character strings using the c() function. For example:
c(1, 2, 3)
## [1] 1 2 3
c(TRUE, TRUE, FALSE)
## [1] TRUE TRUE FALSE
c("a", "b", "c")
## [1] "a" "b" "c"
You can also join to vectors using the c() function.
x <- c(1, 2, 5)
y <- c(3, 4, 6)
z <- c(x, y)
z
## [1] 1 2 5 3 4 6
A more elaborate treatment of how to create vectors can be found in the "Creating vectors" topic
Inspect classes
Every object in R is assigned a class. You can use class() to find the object's class and str() to
see its structure, including the classes it contains. For example:
class(iris)
[1] "data.frame"
str(iris)
'data.frame': 150 obs. of 5 variables:
$ Sepal.Length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
$ Sepal.Width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
$ Petal.Length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
$ Petal.Width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
$ Species : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 1 1 1 1 1 ...
class(iris$Species)
[1] "factor"
We see that iris has the class data.frame and using str() allows us to examine the data inside. The
variable Species in the iris data frame is of class factor, in contrast to the other variables which are
of class numeric. The str() function also provides the length of the variables and shows the first
couple of observations, while the class() function only provides the object's class.
Vectors and lists
Data in R are stored in vectors. A typical vector is a sequence of values all having the same
storage mode (e.g., characters vectors, numeric vectors). See ?atomic for details on the atomic
implicit classes and their corresponding storage modes: "logical", "integer", "numeric" (synonym
"double"), "complex", "character" and "raw". Many classes are simply an atomic vector with a
class attribute on top:
x <- 1826
class(x) <- "Date"
x
# [1] "1975-01-01"
x <- as.Date("1970-01-01")
class(x)
#[1] "Date"
is(x,"Date")
#[1] TRUE
is(x,"integer")
#[1] FALSE
is(x,"numeric")
#[1] FALSE
mode(x)
#[1] "numeric"
Lists are a special type of vector where each element can be anything, even another list, hence
the R term for lists: "recursive vectors":
mylist <- list( A = c(5,6,7,8), B = letters[1:10], CC = list( 5, "Z") )
Lists have two very important uses:
• Since functions can only return a single value, it is common to return complicated results in a
list:
f <- function(x) list(xplus = x + 10, xsq = x^2)
f(7)
# $xplus
# [1] 17
#
# $xsq
# [1] 49
• Lists are also the underlying fundamental class for data frames. Under the hood, a data
frame is a list of vectors all having the same length:
L <- list(x = 1:2, y = c("A","B"))

DF <- data.frame(L)
DF
# x y
# 1 1 A
# 2 2 B
is.list(DF)
# [1] TRUE
The other class of recursive vectors is R expressions, which are "language"- objects
Read Classes online: https://riptutorial.com/r/topic/3563/classes
Chapter 15: Cleaning data
Introduction
Cleaning data in R is paramount to make any analysis. whatever data you have, be it from
measurements taken in the field or scraped from the web it is most probable that you will have to
reshape it, transform it or filter it to make it suitable for your analysis. In this documentation, we will
cover the following topics: - Removing observations with missing data - Factorizing data -
Removing incomplete Rows
Examples
Removing missing data from a vector
First lets create a vector called Vector1:
set.seed(123)
Vector1 <- rnorm(20)
And add missing data to it:
set.seed(123)
Vector1[sample(1:length(Vector1), 5)] <- NA
Now we can use the is.na function to subset the Vector
Vector1 <- Vector1[!is.na(Vector1)]
Now the resulting vector will have removed the NAs of the original Vector1
Removing incomplete rows
There might be times where you have a data frame and you want to remove all the rows that might
contain an NA value, for that the function complete.cases is the best option.
We will use the first 6 rows of the airquality dataset to make an example since it already has NAs
x <- head(airquality)
This has two rows with NAs in the Solar.R column, to remove them we do the following
x_no_NA <- x[complete.cases(x),]
The resulting dataframe x_no_NA will only have complete rows without NAs
Read Cleaning data online: https://riptutorial.com/r/topic/8165/cleaning-data
Chapter 16: Code profiling
Examples
System.time
System time gives you the CPU time required to execute a R expression, for example:
system.time(print("hello world"))
# [1] "hello world"

# user system elapsed
# 0 0 0
You can add larger pieces of code through use of braces:
system.time({
library(numbers)
Primes(1,10^5)
})
Or use it to test functions:
fibb <- function (n) {

if (n < 3) {
return(c(0,1)[n])
} else {
return(fibb(n - 2) + fibb(n -1))
}
}
system.time(fibb(30))
proc.time()
At its simplest, proc.time() gives the total elapsed CPU time in seconds for the current process.
Executing it in the console gives the following type of output:
proc.time()

# 284.507 120.397 515029.305
This is particularly useful for benchmarking specific lines of code. For example:
t1 <- proc.time()
fibb <- function (n) {
if (n < 3) {
return(c(0,1)[n])
} else {
return(fibb(n - 2) + fibb(n -1))
}
}
print("Time one")
print(proc.time() - t1)
t2 <- proc.time()
fibb(30)
print("Time two")
print(proc.time() - t2)
This gives the following output:
source('~/.active-rstudio-document')
# [1] "Time one"

# 0 0 0
# [1] "Time two"

# 1.534 0.012 1.572
is a wrapper for proc.time() that returns the elapsed time for a particular
system.time()
command/expression.
print(t1 <- system.time(replicate(1000,12^2)))

## user system elapsed
## 0.000 0.000 0.002
Note that the returned object, of class proc.time, is slightly more complicated than it appears on
the surface:
str(t1)
## Class 'proc_time' Named num [1:5] 0 0 0.002 0 0
## ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" "user.child" ...
Line Profiling
One package for line profiling is lineprof which is written and maintained by Hadley Wickham. Here
is a quick demonstration of how it works with auto.arima in the forecast package:
library(lineprof)
library(forecast)
l <- lineprof(auto.arima(AirPassengers))
shine(l)
This will provide you with a shiny app, which allows you to delve deeper into every function call.
This enables you to see with ease what is causing your R code to slow down. There is a
screenshot of the shiny app below:
Microbenchmark
Microbenchmark is useful for estimating the time taking for otherwise fast procedures. For
example, consider estimating the time taken to print hello world.
system.time(print("hello world"))
# [1] "hello world"

# 0 0 0
This is because system.time is essentially a wrapper function for proc.time, which measures in
seconds. As printing "hello world" takes less than a second it appears that the time taken is less
than a second, however this is not true. To see this we can use the package microbenchmark:
library(microbenchmark)
microbenchmark(print("hello world"))
# Unit: microseconds
# expr min lq mean median uq max neval
# print("hello world") 26.336 29.984 44.11637 44.6835 45.415 158.824 100
Here we can see after running print("hello world") 100 times, the average time taken was in fact
44 microseconds. (Note that running this code will print "hello world" 100 times onto the console.)
We can compare this against an equivalent procedure, cat("hello world\n"), to see if it is faster
than print("hello world"):
microbenchmark(cat("hello world\n"))
# cat("hello world\\n") 14.093 17.6975 23.73829 19.319 20.996 119.382 100
In this case cat() is almost twice as fast as print().
Alternatively one can compare two procedures within the same microbenchmark call:
microbenchmark(print("hello world"), cat("hello world\n"))

# print("hello world") 29.122 31.654 39.64255 34.5275 38.852 192.779 100
# cat("hello world\\n") 9.381 12.356 13.83820 12.9930 13.715 52.564 100
Benchmarking using microbenchmark
You can use the microbenchmark package to conduct "sub-millisecond accurate timing of expression
evaluation".
In this example we are comparing the speeds of six equivalent data.table expressions for updating
elements in a group, based on a certain condition.
More specifically:
A data.table with 3 columns: id, time and status. For each id, I want to find the record
with the maximum time - then if for that record if the status is true, I want to set it to
false if the time is > 7
library(data.table)
set.seed(20160723)
dt <- data.table(id = c(rep(seq(1:10000), each = 10)),
time = c(rep(seq(1:10000), 10)),
status = c(sample(c(TRUE, FALSE), 10000*10, replace = TRUE)))
setkey(dt, id, time) ## create copies of the data so the 'updates-by-reference' don't affect
other expressions
dt1 <- copy(dt)
dt2 <- copy(dt)
dt3 <- copy(dt)
dt4 <- copy(dt)
dt5 <- copy(dt)
dt6 <- copy(dt)
microbenchmark(
expression_1 = {
dt1[ dt1[order(time), .I[.N], by = id]$V1, status := status * time < 7 ]
},
expression_2 = {
dt2[,status := c(.SD[-.N, status], .SD[.N, status * time > 7]), by = id]
},
expression_3 = {
dt3[dt3[,.N, by = id][,cumsum(N)], status := status * time > 7]
},
expression_4 = {
y <- dt4[,.SD[.N],by=id]
dt4[y, status := status & time > 7]
},
expression_5 = {
y <- dt5[, .SD[.N, .(time, status)], by = id][time > 7 & status]
dt5[y, status := FALSE]
},
expression_6 = {
dt6[ dt6[, .I == .I[which.max(time)], by = id]$V1 & time > 7, status := FALSE]
},
times = 10L ## specify the number of times each expression is evaluated

)
# Unit: milliseconds
# expression_1 11.646149 13.201670 16.808399 15.643384 18.78640 26.321346 10
# expression_2 8051.898126 8777.016935 9238.323459 8979.553856 9281.93377 12610.869058 10
# expression_3 3.208773 3.385841 4.207903 4.089515 4.70146 5.654702 10
# expression_4 15.758441 16.247833 20.677038 19.028982 21.04170 36.373153 10
# expression_5 7552.970295 8051.080753 8702.064620 8861.608629 9308.62842 9722.234921 10
# expression_6 18.403105 18.812785 22.427984 21.966764 24.66930 28.607064 10
The output shows that in this test expression_3 is the fastest.
References
data.table - Adding and modifying columns
data.table - special grouping symbols in data.table
Read Code profiling online: https://riptutorial.com/r/topic/2149/code-profiling
Chapter 17: Coercion
Introduction
Coercion happens in R when the type of objects are changed during computation either implicitly
or by using functions for explicit coercion (such as as.numeric, as.data.frame, etc.).
Examples
Implicit Coercion
Coercion happens with data types in R, often implicitly, so that the data can accommodate all the
values. For example,
x = 1:3
x
[1] 1 2 3
typeof(x)
#[1] "integer"
x[2] = "hi"
x
#[1] "1" "hi" "3"
typeof(x)
#[1] "character"
Notice that at first, x is of type integer. But when we assigned x[2] = "hi", all the elements of x
were coerced into character as vectors in R can only hold data of single type.
Read Coercion online: https://riptutorial.com/r/topic/9793/coercion
Chapter 18: Color schemes for graphics
Examples
viridis - print and colorblind friendly palettes
Viridis (named after the chromis viridis fish) is a recently developed color scheme for the Python
library matplotlib (the video presentation by the link explains how the color scheme was
developed and what are its main advantages). It is seamlessly ported to R.
There are 4 variants of color schemes: magma, plasma, inferno, and viridis (default). They are
chosen with the option parameter and are coded as A, B, C, and D, correspondingly. To have an
impression of the 4 color schemes, look at the maps:
(image souce)
The package can be installed from CRAN or github.
The vignette for viridis package is just brilliant.
Nice feature of the viridis color scheme is integration with ggplot2. Within the package two ggplot2
-specific functions are defined: scale_color_viridis() and scale_fill_viridis(). See the example
below:
library(viridis)
library(ggplot2)
gg1 <- ggplot(mtcars)+

geom_point(aes(x = mpg, y = hp, color = disp), size = 3)+
scale_color_viridis(option = "B")+
theme_minimal()+
theme(legend.position = c(.8,.8))
gg2 <- ggplot(mtcars)+

geom_violin(aes(x = factor(cyl), y = hp, fill = factor(cyl)))+
scale_fill_viridis(discrete = T)+
theme_minimal()+
theme(legend.position = 'none')
library(cowplot)
output <- plot_grid(gg1,gg2, labels = c('B','D'),label_size = 20)
print(output)
RColorBrewer is a port of the project for R and provides also colorblind-friendly palettes.
An example of use
colors_vec <- brewer.pal(5, name = 'BrBG')

print(colors_vec)
[1] "#A6611A" "#DFC27D" "#F5F5F5" "#80CDC1" "#018571"
RColorBrewer creates coloring options for ggplot2: scale_color_brewer and scale_fill_brewer.
library(ggplot2)
ggplot(mtcars)+
geom_point(aes(x = mpg, y = hp, color = factor(cyl)), size = 3)+
scale_color_brewer(palette = 'Greens')+
theme_minimal()+
theme(legend.position = c(.8,.8))
A handy function to glimse a vector of colors
Quite often there is a need to glimpse the chosen color palette. One elegant solution is the
following self defined function:
color_glimpse <- function(colors_string){
n <- length(colors_string)
hist(1:n,breaks=0:n,col=colors_string)
}
An example of use
color_glimpse(blues9)
colorspace - click&drag interface for colors
The package colorspace provides GUI for selecting a palette. On the call of choose_palette()
function the following window pops-up:
When the palette is chosen, just hit OK and do not forget to store the output in a variable, e.g. pal.
pal <- choose_palette()
The output is a function that takes n (number) as input and produces a color vector of length n
according to the selected palette.
pal(10)
[1] "#023FA5" "#6371AF" "#959CC3" "#BEC1D4" "#DBDCE0" "#E0DBDC" "#D6BCC0" "#C6909A" "#AE5A6D"
"#8E063B"
basic R color functions
Function colors() lists all the color names that are recognized by R. There is a nice PDF where
one can actually see those colors.
colorRampPalette creates a function that interpolate a set of given colors to create new color
palettes. This output function takes n (number) as input and produces a color vector of length n
interpolating the initial colors.
pal <- colorRampPalette(c('white','red'))

pal(5)
[1] "#FFFFFF" "#FFBFBF" "#FF7F7F" "#FF3F3F" "#FF0000"
Any specific color may be produced with an rgb() function:
rgb(0,1,0)
produces green color.
Colorblind-friendly palettes
Even though colorblind people can recognize a wide range of colors, it might be hard to
differentiate between certain colors.
RColorBrewer provides colorblind-friendly palettes:
library(RColorBrewer)
display.brewer.all(colorblindFriendly = T)
The Color Universal Design from the University of Tokyo proposes the following palettes:
#palette using grey
cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00",
"#CC79A7")
#palette using black

cbbPalette <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00",
"#CC79A7")
Read Color schemes for graphics online: https://riptutorial.com/r/topic/8005/color-schemes-for-

graphics
Chapter 19: Column wise operation
Examples
sum of each column
Suppose we need to do the sum of each column in a dataset
set.seed(20)
df1 <- data.frame(ID = rep(c("A", "B", "C"), each = 3), V1 = rnorm(9), V2 = rnorm(9))
m1 <- as.matrix(df1[-1])
There are many ways to do this. Using base R, the best option would be colSums
colSums(df1[-1], na.rm = TRUE)
Here, we removed the first column as it is non-numeric and did the sum of each column, specifying
the na.rm = TRUE (in case there are any NAs in the dataset)
This also works with matrix
colSums(m1, na.rm = TRUE)
This can be done in a loop with lapply/sapply/vapply
lapply(df1[-1], sum, na.rm = TRUE)
It should be noted that the output is a list. If we need a vector output
sapply(df1[-1], sum, na.rm = TRUE)
Or
vapply(df1[-1], sum, na.rm = TRUE, numeric(1))
For matrices, if we want to loop through columns, then use apply with MARGIN = 1
apply(m1, 2, FUN = sum, na.rm = TRUE)
There are ways to do this with packages like dplyr or data.table
library(dplyr)
df1 %>%
summarise_at(vars(matches("^V\\d+")), sum, na.rm = TRUE)
Here, we are passing a regular expression to match the column names that we need to get the sum
in summarise_at. The regex will match all columns that start with V followed by one or more numbers
(\\d+).
A data.table option is
library(data.table)
setDT(df1)[, lapply(.SD, sum, na.rm = TRUE), .SDcols = 2:ncol(df1)]
We convert the 'data.frame' to 'data.table' (setDT(df1)), specified the columns to be applied the
function in .SDcols and loop through the Subset of Data.table (.SD) and get the sum.
If we need to use a group by operation, we can do this easily by specifying the group by
column/columns
df1 %>%
group_by(ID) %>%
summarise_at(vars(matches("^V\\d+")), sum, na.rm = TRUE)
In cases where we need the sum of all the columns, summarise_each can be used instead of
summarise_at
df1 %>%
group_by(ID) %>%
summarise_each(funs(sum(., na.rm = TRUE)))
The data.table option is
setDT(df1)[, lapply(.SD, sum, na.rm = TRUE), by = ID]
Read Column wise operation online: https://riptutorial.com/r/topic/2212/column-wise-operation
Chapter 20: Combinatorics
Examples
Enumerating combinations of a specified length
Without replacement
With combn, each vector appears in a column:
combn(LETTERS, 3)
# Showing only first 10.

[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] "A" "A" "A" "A" "A" "A" "A" "A" "A" "A"
[2,] "B" "B" "B" "B" "B" "B" "B" "B" "B" "B"
[3,] "C" "D" "E" "F" "G" "H" "I" "J" "K" "L"
With replacement
With expand.grid, each vector appears in a row:
expand.grid(LETTERS, LETTERS, LETTERS)

# or
do.call(expand.grid, rep(list(LETTERS), 3))
# Showing only first 10.

Var1 Var2 Var3
1 A A A
2 B A A
3 C A A
4 D A A
5 E A A
6 F A A
7 G A A
8 H A A
9 I A A
10 J A A
For the special case of pairs, outer can be used, putting each vector into a cell:
# FUN here is used as a function executed on each resulting pair.

# in this case it's string concatenation.
outer(LETTERS, LETTERS, FUN=paste0)
# Showing only first 10 rows and columns

[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] "AA" "AB" "AC" "AD" "AE" "AF" "AG" "AH" "AI" "AJ"
[2,] "BA" "BB" "BC" "BD" "BE" "BF" "BG" "BH" "BI" "BJ"
[3,] "CA" "CB" "CC" "CD" "CE" "CF" "CG" "CH" "CI" "CJ"
[4,] "DA" "DB" "DC" "DD" "DE" "DF" "DG" "DH" "DI" "DJ"
[5,] "EA" "EB" "EC" "ED" "EE" "EF" "EG" "EH" "EI" "EJ"
[6,] "FA" "FB" "FC" "FD" "FE" "FF" "FG" "FH" "FI" "FJ"
[7,] "GA" "GB" "GC" "GD" "GE" "GF" "GG" "GH" "GI" "GJ"
[8,] "HA" "HB" "HC" "HD" "HE" "HF" "HG" "HH" "HI" "HJ"
[9,] "IA" "IB" "IC" "ID" "IE" "IF" "IG" "IH" "II" "IJ"
[10,] "JA" "JB" "JC" "JD" "JE" "JF" "JG" "JH" "JI" "JJ"
Counting combinations of a specified length
Without replacement
choose(length(LETTERS), 5)
[1] 65780
With replacement
length(letters)^5
[1] 11881376
Read Combinatorics online: https://riptutorial.com/r/topic/5836/combinatorics
Chapter 21: Control flow structures
Remarks
For loops are a flow control method for repeating a task or set of tasks over a domain. The core
structure of a for loop is
for ( [index] in [domain]){

[body]
}
Where
1. [index] is a name takes exactly one value of [domain] over each iteration of the loop.
2. [domain] is a vector of values over which to iterate.
3. [body] is the set of instructions to apply on each iteration.
As a trivial example, consider the use of a for loop to obtain the cumulative sum of a vector of
values.
x <- 1:4
cumulative_sum <- 0
for (i in x){
cumulative_sum <- cumulative_sum + x[i]
}
cumulative_sum
Optimizing Structure of For Loops

For loops can be useful for conceptualizing and executing tasks to repeat. If not constructed
carefully, however, they can be very slow to execute compared to the preferred used of the apply
family of functions. Nonetheless, there are a handful of elements you can include in your for loop
construction to optimize the loop. In many cases, good construction of the for loop will yield
computational efficiency very close to that of an apply function.
A 'properly constructed' for loop builds on the core structure and includes a statement declaring
the object that will capture each iteration of the loop. This object should have both a class and a
length declared.
[output] <- [vector_of_length]

for ([index] in [length_safe_domain]){
[output][index] <- [body]
}
To illustrate, let us write a loop to square each value in a numeric vector (this is a trivial example
for illustration only. The 'correct' way of completing this task would be x_squared <- x^2).
x <- 1:100
x_squared <- vector("numeric", length = length(x))
for (i in seq_along(x)){
x_squared[i] <- x[i]^2
}
Again, notice that we first declared a receptacle for the output x_squared, and gave it the class
"numeric" with the same length as x. Additionally, we declared a "length safe domain" using the
seq_along function. seq_along generates a vector of indices for an object that is suited for use in for
loops. While it seems intuitive to use for (i in 1:length(x)), if x has 0 length, the loop will attempt
to iterate over the domain of 1:0, resulting in an error (the 0th index is undefined in R).
Receptacle objects and length safe domains are handled internally by the apply family of functions
and users are encouraged to adopt the apply approach in place of for loops as much as possible.
However, if properly constructed, a for loop may occasionally provide greater code clarity with
minimal loss of efficiency.
Vectorizing For Loops

For loops can often be a useful tool in conceptualizing the tasks that need to be completed within
each iteration. When the loop is completely developed and conceptualized, there may be
advantages to turning the loop into a function.
In this example, we will develop a for loop to calculate the mean of each column in the mtcars
dataset (again, a trivial example as it could be accomplished via the colMeans function).
column_mean_loop <- vector("numeric", length(mtcars))

for (k in seq_along(mtcars)){
column_mean_loop[k] <- mean(mtcars[[k]])
}
The for loop can be converted to an apply function by rewriting the body of the loop as a function.
col_mean_fn <- function(x) mean(x)

column_mean_apply <- vapply(mtcars, col_mean_fn, numeric(1))
And to compare the results:
identical(column_mean_loop,
unname(column_mean_apply)) #* vapply added names to the elements
#* remove them for comparison
The advantages of the vectorized form is that we were able to eliminate a few lines of code. The
mechanics of determining the length and type of the output object and iterating over a length safe
domain are handled for us by the apply function. Additionally, the apply function is a little bit faster
than the loop. The difference of speed is often negligible in human terms depending on the
number of iterations and the complexity of the body.
Examples
Basic For Loop Construction
In this example we will calculate the squared deviance for each column in a data frame, in this
case the mtcars.
Option A: integer index
squared_deviance <- vector("list", length(mtcars))

for (i in seq_along(mtcars)){
squared_deviance[[i]] <- (mtcars[[i]] - mean(mtcars[[i]]))^2
}
squared_deviance is an 11 elements list, as expected.
class(squared_deviance)
length(squared_deviance)
Option B: character index
squared_deviance <- vector("list", length(mtcars))

Squared_deviance <- setNames(squared_deviance, names(mtcars))
for (k in names(mtcars)){
squared_deviance[[k]] <- (mtcars[[k]] - mean(mtcars[[k]]))^2
}
What if we want a data.frame as a result? Well, there are many options for transforming a list into
other objects. However, and maybe the simplest in this case, will be to store the for results in a
data.frame.
squared_deviance <- mtcars #copy the original

squared_deviance[TRUE]<-NA #replace with NA or do squared_deviance[,]<-NA
squared_deviance[[i]] <- (mtcars[[i]] - mean(mtcars[[i]]))^2
}
dim(squared_deviance)
[1] 32 11
The result will be the same event though we use the character option (B).
Optimal Construction of a For Loop
To illustrate the effect of good for loop construction, we will calculate the mean of each column in
four different ways:
1. Using a poorly optimized for loop

2. Using a well optimized for for loop
3. Using an *apply family of functions
4. Using the colMeans function
Each of these options will be shown in code; a comparison of the computational time to execute
each option will be shown; and lastly a discussion of the differences will be given.
Poorly optimized for loop
column_mean_poor <- NULL

for (i in 1:length(mtcars)){
column_mean_poor[i] <- mean(mtcars[[i]])
}
Well optimized for loop
column_mean_optimal <- vector("numeric", length(mtcars))

column_mean_optimal <- mean(mtcars[[i]])
}
vapply Function
column_mean_vapply <- vapply(mtcars, mean, numeric(1))
colMeans Function
column_mean_colMeans <- colMeans(mtcars)
Efficiency comparison
The results of benchmarking these four approaches is shown below (code not displayed)
Unit: microseconds
expr min lq mean median uq max neval cld
poor 240.986 262.0820 287.1125 275.8160 307.2485 442.609 100 d
optimal 220.313 237.4455 258.8426 247.0735 280.9130 362.469 100 c
vapply 107.042 109.7320 124.4715 113.4130 132.6695 202.473 100 a
colMeans 155.183 161.6955 180.2067 175.0045 194.2605 259.958 100 b
Notice that the optimized for loop edged out the poorly constructed for loop. The poorly
constructed for loop is constantly increasing the length of the output object, and at each change of
the length, R is reevaluating the class of the object.
Some of this overhead burden is removed by the optimized for loop by declaring the type of output
object and its length before starting the loop.
In this example, however, the use of an vapply function doubles the computational efficiency,
largely because we told R that the result had to be numeric (if any one result were not numeric, an
error would be returned).
Use of the colMeans function is a touch slower than the vapply function. This difference is
attributable to some error checks performed in colMeans and mainly to the as.matrix conversion
(because mtcars is a data.frame) that weren't performed in the vapply function.
The Other Looping Constructs: while and repeat
R provides two additional looping constructs, while and repeat, which are typically used in
situations where the number of iterations required is indeterminate.
The while loop

The general form of a while loop is as follows,
while (condition) {
## do something
## in loop body
}
where condition is evaluated prior to entering the loop body. If condition evaluates to TRUE, the
code inside of the loop body is executed, and this process repeats until condition evaluates to
FALSE (or a break statement is reached; see below). Unlike the for loop, if a while loop uses a
variable to perform incremental iterations, the variable must be declared and initialized ahead of
time, and must be updated within the loop body. For example, the following loops accomplish the
same task:
for (i in 0:4) {
cat(i, "\n")
}
# 0
# 1
# 2
# 3
# 4
i <- 0
while (i < 5) {
cat(i, "\n")
i <- i + 1
}
# 0
# 1
# 2
# 3
# 4
In the while loop above, the line i <- i + 1 is necessary to prevent an infinite loop.
Additionally, it is possible to terminate a while loop with a call to break from inside the loop body:
iter <- 0
while (TRUE) {
if (runif(1) < 0.25) {
break
} else {
iter <- iter + 1
}
}
iter
#[1] 4
In this example, condition is always TRUE, so the only way to terminate the loop is with a call to
break inside the body. Note that the final value of iter will depend on the state of your PRNG when
this example is run, and should produce different results (essentially) each time the code is
executed.
The repeat loop

The repeat construct is essentially the same as while (TRUE) { ## something }, and has the
following form:
repeat ({
## do something
## in loop body
})
The extra {} are not required, but the () are. Rewriting the previous example using repeat,
iter <- 0
repeat ({
if (runif(1) < 0.25) {
break
} else {
iter <- iter + 1
}
})
iter
#[1] 2
More on break
It's important to note that break will only terminate the immediately enclosing loop. That is, the
following is an infinite loop:
while (TRUE) {
while (TRUE) {
cat("inner loop\n")
break
}
cat("outer loop\n")
}
With a little creativity, however, it is possible to break entirely from within a nested loop. As an
example, consider the following expression, which, in its current state, will loop infinitely:
while (TRUE) {
cat("outer loop body\n")
while (TRUE) {
cat("inner loop body\n")
x <- runif(1)
if (x < .3) {
break
} else {
cat(sprintf("x is %.5f\n", x))
}
}
}
One possibility is to recognize that, unlike break, the return expression does have the ability to
return control across multiple levels of enclosing loops. However, since return is only valid when
used within a function, we cannot simply replace break with return() above, but also need to wrap
the entire expression as an anonymous function:
(function() {
while (TRUE) {
while (TRUE) {
x <- runif(1)
if (x < .3) {
return()
} else {
}
}
}
})()
Alternatively, we can create a dummy variable (exit) prior to the expression, and activate it via <<-
from the inner loop when we are ready to terminate:
exit <- FALSE

while (TRUE) {
while (TRUE) {
x <- runif(1)
if (x < .3) {
exit <<- TRUE
break
} else {
}
}
if (exit) break
}
Read Control flow structures online: https://riptutorial.com/r/topic/2201/control-flow-structures
Chapter 22: Creating packages with devtools
Introduction
This topic will cover the creation of R packages from scratch with the devtools package.
Remarks
1. Official R manual for creating packages
2. roxygen2 reference manual
3. devtools reference manual
Examples
Creating and distributing packages
This is a compact guide about how to quickly create an R package from your code. Exhaustive
documentations will be linked when available and should be read if you want a deeper knowledge
of the situation. See Remarks for more resources.
The directory where your code stands will be refered as ./, and all the commands are meant to be
executed from a R prompt in this folder.
Creation of the documentation

The documentation for your code has to be in a format which is very similar to LaTeX.
However, we will use a tool named roxygen in order to simplify the process:
install.packages("devtools")
library("devtools")
install.packages("roxygen2")
library("roxygen2")
The full man page for roxygen is available here. It is very similar to doxygen.
Here is a practical sample about how to document a function with roxygen:
#' Increment a variable.

#'
#' Note that the behavior of this function
#' is undefined if `x` is not of class `numeric`.
#'
#' @export
#' @author another guy
#' @name Increment Function
#' @title increment
#'
#' @param x Variable to increment
#' @return `x` incremented of 1
#'
#' @seealso òther_function`
#'
#' @examples
#' increment(3)
#' > 4
increment <- function(x) {
return (x+1)
}
And here will be the result.
It is also recommanded to create a vignette (see the topic Creating vignettes), which is a full guide
about your package.
Construction of the package skeleton

Assuming that your code is written for instance in files ./script1.R and ./script2.R, launch the
following command in order to create the file tree of your package:
package.skeleton(name="MyPackage", code_files=c("script1.R","script2.R"))
Then delete all the files in ./MyPackage/man/. You have now to compile the documentation:
roxygenize("MyPackage")
You should also generate a reference manual from your documentation using R CMD Rd2pdf
MyPackage from a command prompt started in ./.
Edition of the package properties

1. Package description
Modify ./MyPackage/DESCRIPTION according to your needs. The fields Package, Version, License,
Description, Title, Author and Maintainer are mandatory, the other are optional.
If your package depends on others packages, specify them in a field named Depends (R version <
3.2.0) or Imports (R version > 3.2.0).
2. Optional folders
Once you launched the skeleton build, ./MyPackage/ only had R/ and man/ subfolders. However, it
can have some others:
• data/:
here you can place the data that your library needs and that isn't code. It must be
saved as dataset with the .RData extension, and you can load it at runtime with data() and
load()
• tests/:all the code files in this folder will be ran at install time. If there is any error, the
installation will fail.
• src/: for C/C++/Fortran source files you need (using Rcpp...).
• exec/: for other executables.
• misc/: for barely everything else.
Finalization and build

You can delete ./MyPackage/Read-and-delete-me.
As it is now, your package is ready to be installed.
You can install it with devtools::install("MyPackage").
To build your package as a source tarball, you need to execute the following command, from a
command prompt in ./ : R CMD build MyPackage
Distribution of your package

Through Github
Simply create a new repository called MyPackage and upload everything in MyPackage/ to the
master branch. Here is an example.
Then anyone can install your package from github with devtools:
install_package("MyPackage", "your_github_usename")
Through CRAN
Your package needs to comply to the CRAN Repository Policy. Including but not limited to: your
package must be cross-platforms (except some very special cases), it should pass the R CMD check
test.
Here is the submission form. You must upload the source tarball.
Creating vignettes
A vignette is a long-form guide to your package. Function documentation is great if you
know the name of the function you need, but it’s useless otherwise. A vignette is like a
book chapter or an academic paper: it can describe the problem that your package is
designed to solve, and then show the reader how to solve it.
Vignettes will be created entirely in markdown.
Requirements
• Rmarkdown: install.packages("rmarkdown")
• Pandoc
Vignette creation
devtools::use_vignette("MyVignette", "MyPackage")
You can now edit your vignette at ./vignettes/MyVignette.Rmd.
The text in your vignette is formatted as Markdown.
The only addition to the original Markdown, is a tag that takes R code, runs it, captures the output,
and translates it into formatted Markdown:
```{r}
# Add two numbers together
add <- function(a, b) a + b
add(10, 20)
```
Will display as:
# Add two numbers together

add <- function(a, b) a + b
add(10, 20)
## [1] 30
Thus, all the packages you will use in your vignettes must be listed as dependencies in
./DESCRIPTION.
Read Creating packages with devtools online: https://riptutorial.com/r/topic/10884/creating-

packages-with-devtools
Chapter 23: Creating reports with RMarkdown
Examples
Printing tables
There are several packages that allow the output of data structures in form of HTML or LaTeX
tables. They mostly differ in flexibility.
Here I use the packages:
• knitr
• xtable
• pander
For HTML documents
---
title: "Printing Tables"
author: "Martin Schmelzer"
date: "29 Juli 2016"
output: html_document
---
```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = TRUE)
library(knitr)
library(xtable)
library(pander)
df <- mtcars[1:4,1:4]
```
# Print tables using `kable`

```{r, 'kable'}
kable(df)
```
# Print tables using `xtable`

```{r, 'xtable', results='asis'}
print(xtable(df), type="html")
```
# Print tables using `pander`

```{r, 'pander'}
pander(df)
```
For PDF documents
---
title: "Printing Tables"
output: pdf_document
---

knitr::opts_chunk$set(echo = TRUE)
library(knitr)
library(xtable)
library(pander)
df <- mtcars[1:4,1:4]
```
# Print tables using `kable`

```{r, 'kable'}
kable(df)
```
# Print tables using `xtable`

```{r, 'xtable', results='asis'}
print(xtable(df, caption="My Table"))
```
# Print tables using `pander`

```{r, 'pander'}
pander(df)
```
How can I stop xtable printing the comment ahead of each table?
options(xtable.comment = FALSE)
Including LaTeX Preample Commands
There are two possible ways of including LaTeX preamble commands (e.g. \usepackage) in a
RMarkdown document.
1. Using the YAML option header-includes:
---
title: "Including LaTeX Preample Commands in RMarkdown"
header-includes:
- \renewcommand{\familydefault}{cmss}
- \usepackage[cm, slantedGreek]{sfmath}
- \usepackage[T1]{fontenc}
---

knitr::opts_chunk$set(echo = TRUE, external=T)
```
# Section 1
As you can see, this text uses the Computer Moden Font!
2. Including External Commands with includes, in_header
---
title: "Including LaTeX Preample Commands in RMarkdown"
output:
pdf_document:
includes:
in_header: includes.tex
---

knitr::opts_chunk$set(echo = TRUE, external=T)
```
# Section 1
As you can see, this text uses the Computer Modern Font!
Here, the content of includes.tex are the same three commands we included with header-includes.
Writing a whole new template
A possible third option is to write your own LaTex template and include it with template. But this
covers a lot more of the structure than only the preamble.
---
title: "My Template"
output:
pdf_document:
template: myTemplate.tex
---
Including bibliographies
A bibtex catalogue cna easily be included with the YAML option bibliography:. A certain style for
the bibliography can be added with biblio-style:. The references are added at the end of the
document.
---
title: "Including Bibliography"
author: "John Doe"
bibliography: references.bib
---
# Abstract
@R_Core_Team_2016
# References
Basic R-markdown document structure
R-markdown code chunks

R-markdown is a markdown file with embedded blocks of R code called chunks. There are two
types of R code chunks: inline and block.
Inline chunks are added using the following syntax:
`r 2*2`
They are evaluated and inserted their output answer in place.
Block chunks have a different syntax:
```{r name, echo=TRUE, include=TRUE, ...}
2*2
````
And they come with several possible options. Here are the main ones (but there are many others):
• echo (boolean) controls wether the code inside chunk will be included in the document
• include (boolean) controls wether the output should be included in the document
• fig.width (numeric) sets the width of the output figures
• fig.height (numeric) sets the height of the output figures
• fig.cap (character) sets the figure captions
They are written in a simple tag=value format like in the example above.
R-markdown document example

Below is a basic example of R-markdown file illustrating the way R code chunks are embedded
inside r-markdown.
# Title #
This is **plain markdown** text.
```{r code, include=FALSE, echo=FALSE}
# Just declare variables
income <- 1000

taxes <- 125
```
My income is: `r income ` dollars and I payed `r taxes ` dollars in taxes.
Below is the sum of money I will have left:
```{r gain, include=TRUE, echo=FALSE}
gain <- income-taxes
gain
```
```{r plotOutput, include=TRUE, echo=FALSE, fig.width=6, fig.height=6}
pie(c(income,taxes), label=c("income", "taxes"))
```
Converting R-markdown to other formats

The R knitr package can be used to evaluate R chunks inside R-markdown file and turn it into a
regular markdown file.
The following steps are needed in order to turn R-markdown file into pdf/html:
1. Convert R-markdown file to markdown file using knitr.

2. Convert the obtained markdown file to pdf/html using specialized tools like pandoc.
In addition to the above knitr package has wrapper functions knit2html() and knit2pdf() that can
be used to produce the final document without the intermediate step of manually converting it to
the markdown format:
If the above example file was saved as income.Rmd it can be converted to a pdf file using the
following R commands:
library(knitr)
knit2pdf("income.Rmd", "income.pdf")
The final document will be similar to the one below.
Read Creating reports with RMarkdown online: https://riptutorial.com/r/topic/4572/creating-reports-
with-rmarkdown
Chapter 24: Creating vectors
Examples
Sequence of numbers
Use the : operator to create sequences of numbers, such as for use in vectorizing larger chunks of
your code:
x <- 1:5
x
## [1] 1 2 3 4 5
This works both ways
10:4
# [1] 10 9 8 7 6 5 4
and even with floating point numbers
1.25:5
# [1] 1.25 2.25 3.25 4.25
or negatives
-4:4
#[1] -4 -3 -2 -1 0 1 2 3 4
seq()
seq is a more flexible function than the : operator allowing to specify steps other than 1.
The function creates a sequence from the start (default is 1) to the end including that number.
You can supply only the end (to) parameter
seq(5)
# [1] 1 2 3 4 5
As well as the start
seq(2, 5) # or seq(from=2, to=5)

# [1] 2 3 4 5
And finally the step (by)
seq(2, 5, 0.5) # or seq(from=2, to=5, by=0.5)
# [1] 2.0 2.5 3.0 3.5 4.0 4.5 5.0
seqcan optionally infer the (evenly spaced) steps when alternatively the desired length of the
output (length.out) is supplied
seq(2,5, length.out = 10)

# [1] 2.0 2.3 2.6 2.9 3.2 3.5 3.8 4.1 4.4 4.7 5.0
If the sequence needs to have the same length as another vector we can use the along.with as a
shorthand for length.out = length(x)
x = 1:8
seq(2,5,along.with = x)
# [1] 2.000000 2.428571 2.857143 3.285714 3.714286 4.142857 4.571429 5.000000
There are two useful simplified functions in the seq family: seq_along, seq_len, and seq.int.
seq_along and seq_len functions construct the natural (counting) numbers from 1 through N where
N is determined by the function argument, the length of a vector or list with seq_along, and the
integer argument with seq_len.
seq_along(x)
# [1] 1 2 3 4 5 6 7 8
Note that seq_along returns the indices of an existing object.
# counting numbers 1 through 10

seq_len(10)
[1] 1 2 3 4 5 6 7 8 9 10
# indices of existing vector (or list) with seq_along
letters[1:10]
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j"
seq_along(letters[1:10])
[1] 1 2 3 4 5 6 7 8 9 10
seq.intis the same as seq maintained for ancient compatibility.
There is also an old function sequencethat creates a vector of sequences from a non negative
argument.
sequence(4)
# [1] 1 2 3 4
sequence(c(3, 2))
# [1] 1 2 3 1 2
sequence(c(3, 2, 5))
# [1] 1 2 3 1 2 1 2 3 4 5
Vectors
Vectors in R can have different types (e.g. integer, logical, character). The most general way of
defining a vector is by using the function vector().
vector('integer',2) # creates a vector of integers of size 2.

vector('character',2) # creates a vector of characters of size 2.
vector('logical',2) # creates a vector of logicals of size 2.
However, in R, the shorthand functions are generally more popular.
integer(2) # is the same as vector('integer',2) and creates an integer vector with two
elements
character(2) # is the same as vector('integer',2) and creates an character vector with two
elements
logical(2) # is the same as vector('logical',2) and creates an logical vector with two
elements
Creating vectors with values, other than the default values, is also possible. Often the function c()
is used for this. The c is short for combine or concatenate.
c(1, 2) # creates a integer vector of two elements: 1 and 2.

c('a', 'b') # creates a character vector of two elements: a and b.
c(T,F) # creates a logical vector of two elements: TRUE and FALSE.
Important to note here is that R interprets any integer (e.g. 1) as an integer vector of size one. The
same holds for numerics (e.g. 1.1), logicals (e.g. T or F), or characters (e.g. 'a'). Therefore, you
are in essence combining vectors, which in turn are vectors.
Pay attention that you always have to combine similar vectors. Otherwise, R will try to convert the
vectors in vectors of the same type.
c(1,1.1,'a',T) # all types (integer, numeric, character and logical) are converted to the
'lowest' type which is character.
Finding elements in vectors can be done with the [ operator.
vec_int <- c(1,2,3)

vec_char <- c('a','b','c')
vec_int[2] # accessing the second element will return 2
vec_char[2] # accessing the second element will return 'b'
This can also be used to change values
vec_int[2] <- 5 # change the second value from 2 to 5

vec_int # returns [1] 1 5 3
Finally, the : operator (short for the function seq()) can be used to quickly create a vector of
numbers.
vec_int <- 1:10

vec_int # returns [1] 1 2 3 4 5 6 7 8 9 10
This can also be used to subset vectors (from easy to more complex subsets)
vec_char <- c('a','b','c','d','e')

vec_char[2:4] # returns [1] "b" "c" "d"
vec_char[c(1,3,5)] # returns [1] "a" "c" "e"
Creating named vectors
Named vector can be created in several ways. With c:
xc <- c('a' = 5, 'b' = 6, 'c' = 7, 'd' = 8)
which results in:
> xc
a b c d
5 6 7 8
with list:
xl <- list('a' = 5, 'b' = 6, 'c' = 7, 'd' = 8)
which results in:
> xl
$a
[1] 5
$b
[1] 6
$c
[1] 7
$d
[1] 8
With the setNames function, two vectors of the same length can be used to create a named vector:
x <- 5:8
y <- letters[1:4]
xy <- setNames(x, y)
which results in a named integer vector:
> xy
a b c d
5 6 7 8
As can be seen, this gives the same result as the c method.
You may also use the names function to get the same result:
xy <- 5:8
names(xy) <- letters[1:4]
With such a vector it is also possibly to select elements by name:
> xy["c"]
c
7
This feature makes it possible to use such a named vector as a look-up vector/table to match the
values to values of another vector or column in dataframe. Considering the following dataframe:
mydf <- data.frame(let = c('c','a','b','d'))
> mydf
let
1 c
2 a
3 b
4 d
Suppose you want to create a new variable in the mydf dataframe called num with the correct values
from xy in the rows. Using the match function the appropriate values from xy can be selected:
mydf$num <- xy[match(mydf$let, names(xy))]
which results in:
> mydf
let num
1 c 7
2 a 5
3 b 6
4 d 8
Expanding a vector with the rep() function
The rep function can be used to repeat a vector in a fairly flexible manner.
# repeat counting numbers, 1 through 5 twice

rep(1:5, 2)
[1] 1 2 3 4 5 1 2 3 4 5
# repeat vector with incomplete recycling

rep(1:5, 2, length.out=7)
[1] 1 2 3 4 5 1 2
The each argument is especially useful for expanding a vector of statistics of

observational/experimental units into a vector of data.frame with repeated observations of these
units.
# same except repeat each integer next to each other

rep(1:5, each=2)
[1] 1 1 2 2 3 3 4 4 5 5
A nice feature of rep regarding involving expansion to such a data structure is that expansion of a
vector to an unbalanced panel can be accomplished by replacing the length argument with a
vector that dictates the number of times to repeat each element in the vector:
# automated length repetition

rep(1:5, 1:5)
[1] 1 2 2 3 3 3 4 4 4 4 5 5 5 5 5
# hand-fed repetition length vector
rep(1:5, c(1,1,1,2,2))
[1] 1 2 3 4 4 5 5
This should expose the possibility of allowing an external function to feed the second argument of
rep in order to dynamically construct a vector that expands according to the data.
As with seq, faster, simplified versions of rep are rep_len and rep.int. These drop some attributes
that rep maintains and so may be most useful in situations where speed is a concern and
additional aspects of the repeated vector are unnecessary.
# repeat counting numbers, 1 through 5 twice

rep.int(1:5, 2)
[1] 1 2 3 4 5 1 2 3 4 5
# repeat vector with incomplete recycling

rep_len(1:5, length.out=7)
[1] 1 2 3 4 5 1 2
Vectors from build in constants: Sequences of letters & month names
R has a number of build in constants. The following constants are available:
• LETTERS: the 26 upper-case letters of the Roman alphabet

• letters: the 26 lower-case letters of the Roman alphabet
• month.abb: the three-letter abbreviations for the English month names
• month.name: the English names for the months of the year
• pi: the ratio of the circumference of a circle to its diameter
From the letters and month constants, vectors can be created.
1) Sequences of letters:
> letters
[1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s" "t" "u" "v"
"w" "x" "y" "z"
> LETTERS[7:9]
[1] "G" "H" "I"
> letters[c(1,5,3,2,4)]
[1] "a" "e" "c" "b" "d"
2) Sequences of month abbreviations or month names:
> month.abb
[1] "Jan" "Feb" "Mar" "Apr" "May" "Jun" "Jul" "Aug" "Sep" "Oct" "Nov" "Dec"
> month.name[1:4]
[1] "January" "February" "March" "April"
> month.abb[c(3,6,9,12)]
[1] "Mar" "Jun" "Sep" "Dec"
Read Creating vectors online: https://riptutorial.com/r/topic/1088/creating-vectors
Chapter 25: Data acquisition
Introduction
Get data directly into an R session. One of the nice features of R is the ease of data acquisition.
There are several ways data dissemination using R packages.
Examples
Built-in datasets
Rhas a vast collection of built-in datasets. Usually, they are used for teaching purposes to create
quick and easily reproducible examples. There is a nice web-page listing the built-in datasets:
https://vincentarelbundock.github.io/Rdatasets/datasets.html
Example
Swiss Fertility and Socioeconomic Indicators (1888) Data. Let's check the difference in fertility
based of rurality and domination of Catholic population.
library(tidyverse)
swiss %>%
ggplot(aes(x = Agriculture, y = Fertility,
color = Catholic > 50))+
geom_point()+
stat_ellipse()
, it does not find all the relevant datasets available. This, it's more convenient to browse the code
of a dataset manually at the Eurostat website: Countries Database, or Regional Database. If the
automated download does not work, the data can be grabbed manually at via Bulk Download
Facility.
library(tidyverse)
library(lubridate)
library(forcats)
library(eurostat)
library(geofacet)
library(viridis)
library(ggthemes)
library(extrafont)
# download NEET data for countries

neet <- get_eurostat("edat_lfse_22")
neet %>%
filter(geo %>% paste %>% nchar == 2,
sex == "T", age == "Y18-24") %>%
group_by(geo) %>%
mutate(avg = values %>% mean()) %>%
ungroup() %>%
ggplot(aes(x = time %>% year(),
y = values))+
geom_path(aes(group = 1))+
geom_point(aes(fill = values), pch = 21)+
scale_x_continuous(breaks = seq(2000, 2015, 5),
labels = c("2000", "'05", "'10", "'15"))+
scale_y_continuous(expand = c(0, 0), limits = c(0, 40))+
scale_fill_viridis("NEET, %", option = "B")+
facet_geo(~ geo, grid = "eu_grid1")+
labs(x = "Year",
y = "NEET, %",
title = "Young people neither in employment nor in education and training in
Europe",
subtitle = "Data: Eurostat Regional Database, 2000-2016",
caption = "ikashnitsky.github.io")+
theme_few(base_family = "Roboto Condensed", base_size = 15)+
theme(axis.text = element_text(size = 10),
panel.spacing.x = unit(1, "lines"),
legend.position = c(0, 0),
legend.justification = c(0, 0))
that gathers and pre-process human mortality data for those countries, where more or less reliable
statistics is available.
# load required packages

library(tidyverse)
library(extrafont)
library(HMDHFDplus)
country <- getHMDcountries()
exposures <- list()

for (i in 1: length(country)) {
cnt <- country[i]
exposures[[cnt]] <- readHMDweb(cnt, "Exposures_1x1", user_hmd, pass_hmd)
# let's print the progress
paste(i,'out of',length(country))
} # this will take quite a lot of time
Please note, the arguments user_hmd and pass_hmd are the login credentials at the website of
Human Mortality Database. In order to access the data, one needs to create an account at
http://www.mortality.org/ and provide their own credentials to the readHMDweb() function.
sr_age <- list()
for (i in 1:length(exposures)) {
di <- exposures[[i]]
sr_agei <- di %>% select(Year,Age,Female,Male) %>%
filter(Year %in% 2012) %>%
select(-Year) %>%
transmute(country = names(exposures)[i],
age = Age, sr_age = Male / Female * 100)
sr_age[[i]] <- sr_agei
}
sr_age <- bind_rows(sr_age)
# remove optional populations

sr_age <- sr_age %>% filter(!country %in% c("FRACNP","DEUTE","DEUTW","GBRCENW","GBR_NP"))
# summarize all ages older than 90 (too jerky)

sr_age_90 <- sr_age %>% filter(age %in% 90:110) %>%
group_by(country) %>% summarise(sr_age = mean(sr_age, na.rm = T)) %>%
ungroup() %>% transmute(country, age=90, sr_age)
df_plot <- bind_rows(sr_age %>% filter(!age %in% 90:110), sr_age_90)
# finaly - plot
df_plot %>%
ggplot(aes(age, sr_age, color = country, group = country))+
geom_hline(yintercept = 100, color = 'grey50', size = 1)+
geom_line(size = 1)+
scale_y_continuous(limits = c(0, 120), expand = c(0, 0), breaks = seq(0, 120, 20))+
scale_x_continuous(limits = c(0, 90), expand = c(0, 0), breaks = seq(0, 80, 20))+
xlab('Age')+
ylab('Sex ratio, males per 100 females')+
facet_wrap(~country, ncol=6)+
theme_minimal(base_family = "Roboto Condensed", base_size = 15)+
theme(legend.position='none',
panel.border = element_rect(size = .5, fill = NA))
Chapter 26: Data frames
Syntax
• data.frame(..., row.names = NULL, check.rows = FALSE, check.names = TRUE,
stringsAsFactors = default.stringsAsFactors())
• as.data.frame(x, row.names = NULL, optional = FALSE, ...) # generic function
• as.data.frame(x, ..., stringsAsFactors = default.stringsAsFactors()) # S3 method for class

'character'
• as.data.frame(x, row.names = NULL, optional = FALSE, ..., stringsAsFactors =

default.stringsAsFactors()) # S3 method for class 'matrix'
• is.data.frame(x)
Examples
Create an empty data.frame
A data.frame is a special kind of list: it is rectangular. Each element (column) of the list has same
length, and where each row has a "row name". Each column has its own class, but the class of
one column can be different from the class of another column (unlike a matrix, where all elements
must have the same class).
In principle, a data.frame could have no rows and no columns:
> structure(list(character()), class = "data.frame")

NULL
<0 rows> (or 0-length row.names)
But this is unusual. It is more common for a data.frame to have many columns and many rows.
Here is a data.frame with three rows and two columns (a is numeric class and b is character class):
> structure(list(a = 1:3, b = letters[1:3]), class = "data.frame")

[1] a b
<0 rows> (or 0-length row.names)
In order for the data.frame to print, we will need to supply some row names. Here we use just the
numbers 1:3:
> structure(list(a = 1:3, b = letters[1:3]), class = "data.frame", row.names = 1:3)

a b
1 1 a
2 2 b
3 3 c
Now it becomes obvious that we have a data.frame with 3 rows and 2 columns. You can check
this using nrow(), ncol(), and dim():
> x <- structure(list(a = numeric(3), b = character(3)), class = "data.frame", row.names =

1:3)
> nrow(x)
[1] 3
> ncol(x)
[1] 2
> dim(x)
[1] 3 2
R provides two other functions (besides structure()) that can be used to create a data.frame. The
first is called, intuitively, data.frame(). It checks to make sure that the column names you supplied
are valid, that the list elements are all the same length, and supplies some automatically
generated row names. This means that the output of data.frame() might now always be exactly
what you expect:
> str(data.frame("a a a" = numeric(3), "b-b-b" = character(3)))

$ a.a.a: num 0 0 0
$ b.b.b: Factor w/ 1 level "": 1 1 1
The other function is called as.data.frame(). This can be used to coerce an object that is not a
data.frame into being a data.frame by running it through data.frame(). As an example, consider a
matrix:
> m <- matrix(letters[1:9], nrow = 3)

> m
[,1] [,2] [,3]
[1,] "a" "d" "g"
[2,] "b" "e" "h"
[3,] "c" "f" "i"
And the result:
> as.data.frame(m)
V1 V2 V3
1 a d g
2 b e h
3 c f i
> str(as.data.frame(m))
$ V1: Factor w/ 3 levels "a","b","c": 1 2 3
$ V2: Factor w/ 3 levels "d","e","f": 1 2 3
$ V3: Factor w/ 3 levels "g","h","i": 1 2 3
Subsetting rows and columns from a data frame
Syntax for accessing rows and columns: , , [ [[
and $
This topic covers the most common syntax to access specific rows and columns of a data frame.
These are
• Like a matrix with single brackets data[rows, columns]

○Using row and column numbers
○Using column (and row) names
• Like a list:
○With single brackets data[columns] to get a data frame
○With double brackets data[[one_column]] to get a vector
• With $ for a single column data$column_name
We will use the built-in mtcars data frame to illustrate.
Like a matrix: data[rows, columns]
With numeric indexes
Using the built in data frame mtcars, we can extract rows and columns using [] brackets with a
comma included. Indices before the comma are rows:
# get the first row

mtcars[1, ]
# get the first five rows
mtcars[1:5, ]
Similarly, after the comma are columns:
# get the first column

mtcars[, 1]
# get the first, third and fifth columns:
mtcars[, c(1, 3, 5)]
As shown above, if either rows or columns are left blank, all will be selected. mtcars[1, ] indicates
the first row with all the columns.
With column (and row) names
So far, this is identical to how rows and columns of matrices are accessed. With data.frames, most
of the time it is preferable to use a column name to a column index. This is done by using a
character with the column name instead of numeric with a column number:
# get the mpg column

mtcars[, "mpg"]
# get the mpg, cyl, and disp columns
mtcars[, c("mpg", "cyl", "disp")]
Though less common, row names can also be used:
mtcars["Mazda Rx4", ]
Rows and columns together
The row and column arguments can be used together:
# first four rows of the mpg column

mtcars[1:4, "mpg"]
# 2nd and 5th row of the mpg, cyl, and disp columns
mtcars[c(2, 5), c("mpg", "cyl", "disp")]
A warning about dimensions:
When using these methods, if you extract multiple columns, you will get a data frame back.
However, if you extract a single column, you will get a vector, not a data frame under the default
options.
## multiple columns returns a data frame

class(mtcars[, c("mpg", "cyl")])
# [1] "data.frame"
## single column returns a vector
class(mtcars[, "mpg"])
# [1] "numeric"
There are two ways around this. One is to treat the data frame as a list (see below), the other is to
add a drop = FALSE argument. This tells R to not "drop the unused dimensions":
class(mtcars[, "mpg", drop = FALSE])

# [1] "data.frame"
Note that matrices work the same way - by default a single column or row will be a vector, but if
you specify drop = FALSE you can keep it as a one-column or one-row matrix.
Like a list
Data frames are essentially lists, i.e., they are a list of column vectors (that all must have the
same length). Lists can be subset using single brackets [ for a sub-list, or double brackets [[ for a
single element.
With single brackets data[columns]
When you use single brackets and no commas, you will get column back because data frames are
lists of columns.
mtcars["mpg"]
mtcars[c("mpg", "cyl", "disp")]
my_columns <- c("mpg", "cyl", "hp")
mtcars[my_columns]
Single brackets like a list vs. single brackets like a matrix
The difference between data[columns] and data[, columns] is that when treating the data.frame as a
list (no comma in the brackets) the object returned will be a data.frame. If you use a comma to
treat the data.frame like a matrix then selecting a single column will return a vector but selecting
multiple columns will return a data.frame.
## When selecting a single column

## like a list will return a data frame
class(mtcars["mpg"])
# [1] "data.frame"
## like a matrix will return a vector
class(mtcars[, "mpg"])
# [1] "numeric"
With double brackets data[[one_column]]
To extract a single column as a vector when treating your data.frame as a list, you can use
double brackets [[. This will only work for a single column at a time.
# extract a single column by name as a vector

mtcars[["mpg"]]
# extract a single column by name as a data frame (as above)

mtcars["mpg"]
Using $ to access columns

A single column can be extracted using the magical shortcut $ without using a quoted column
name:
# get the column "mpg"

mtcars$mpg
Columns accessed by $ will always be vectors, not data frames.
Drawbacks of $ for accessing columns
The $ can be a convenient shortcut, especially if you are working in an environment (such as
RStudio) that will auto-complete the column name in this case. However, $ has drawbacks as
well: it uses non-standard evaluation to avoid the need for quotes, which means it will not work if
your column name is stored in a variable.
my_column <- "mpg"

# the below will not work
mtcars$my_column
# but these will work
mtcars[, my_column] # vector
mtcars[my_column] # one-column data frame
mtcars[[my_column]] # vector
Due to these concerns, $ is best used in interactive R sessions when your column names are
constant. For programmatic use, for example in writing a generalizable function that will be used
on different data sets with different column names, $ should be avoided.
Also note that the default behaviour is to use partial matching only when extracting from recursive
objects (except environments) by $
# give you the values of "mpg" column

# as "mtcars" has only one column having name starting with "m"
mtcars$m
# will give you "NULL"
# as "mtcars" has more than one columns having name starting with "d"
mtcars$d
Advanced indexing: negative and logical

indices
Whenever we have the option to use numbers for a index, we can also use negative numbers to
omit certain indices or a boolean (logical) vector to indicate exactly which items to keep.
Negative indices omit elements
mtcars[1, ] # first row

mtcars[ -1, ] # everything but the first row
mtcars[-(1:10), ] # everything except the first 10 rows
Logical vectors indicate specific elements to keep

We can use a condition such as < to generate a logical vector, and extract only the rows that meet
the condition:
# logical vector indicating TRUE when a row has mpg less than 15
# FALSE when a row has mpg >= 15
test <- mtcars$mpg < 15
# extract these rows from the data frame

mtcars[test, ]
We can also bypass the step of saving the intermediate variable
# extract all columns for rows where the value of cyl is 4.

mtcars[mtcars$cyl == 4, ]
# extract the cyl, mpg, and hp columns where the value of cyl is 4
mtcars[mtcars$cyl == 4, c("cyl", "mpg", "hp")]
Convenience functions to manipulate data.frames
Some convenience functions to manipulate data.frames are subset(), transform(), with() and
within().
subset
The subset() function allows you to subset a data.frame in a more convenient way (subset also
works with other classes):
subset(mtcars, subset = cyl == 6, select = c("mpg", "hp"))

mpg hp
Mazda RX4 21.0 110
Mazda RX4 Wag 21.0 110
Hornet 4 Drive 21.4 110
Valiant 18.1 105
Merc 280 19.2 123
Merc 280C 17.8 123
Ferrari Dino 19.7 175
In the code above we asking only for the lines in which cyl == 6 and for the columns mpg and hp.
You could achieve the same result using [] with the following code:
mtcars[mtcars$cyl == 6, c("mpg", "hp")]
transform
The transform() function is a convenience function to change columns inside a data.frame. For
instance the following code adds another column named mpg2 with the result of mpg^2 to the mtcars
data.frame:
mtcars <- transform(mtcars, mpg2 = mpg^2)
with and within

Both with() and within() let you to evaluate expressions inside the data.frame environment,
allowing a somewhat cleaner syntax, saving you the use of some $ or [].
For example, if you want to create, change and/or remove multiple columns in the airquality
data.frame:
aq <- within(airquality, {
lOzone <- log(Ozone) # creates new column
Month <- factor(month.abb[Month]) # changes Month Column
cTemp <- round((Temp - 32) * 5/9, 1) # creates new column
S.cT <- Solar.R / cTemp # creates new column
rm(Day, Temp) # removes columns
})
Introduction
Data frames are likely the data structure you will used most in your analyses. A data frame is a
special kind of list that stores same-length vectors of different classes. You create data frames
using the data.frame function. The example below shows this by combining a numeric and a
character vector into a data frame. It uses the : operator, which will create a vector containing all
integers from 1 to 3.
df1 <- data.frame(x = 1:3, y = c("a", "b", "c"))

df1
## x y
## 1 1 a
## 2 2 b
## 3 3 c
class(df1)
## [1] "data.frame"
Data frame objects do not print with quotation marks, so the class of the columns is not always
obvious.
df2 <- data.frame(x = c("1", "2", "3"), y = c("a", "b", "c"))

df2
## x y
## 1 1 a
## 2 2 b
## 3 3 c
Without further investigation, the "x" columns in df1 and df2 cannot be differentiated. The str
function can be used to describe objects with more detail than class.
str(df1)
## $ x: int 1 2 3
## $ y: Factor w/ 3 levels "a","b","c": 1 2 3
str(df2)
## $ x: Factor w/ 3 levels "1","2","3": 1 2 3
## $ y: Factor w/ 3 levels "a","b","c": 1 2 3
Here you see that df1 is a data.frame and has 3 observations of 2 variables, "x" and "y." Then you
are told that "x" has the data type integer (not important for this class, but for our purposes it
behaves like a numeric) and "y" is a factor with three levels (another data class we are not
discussing). It is important to note that, by default, data frames coerce characters to factors.
The default behavior can be changed with the stringsAsFactors parameter:
df3 <- data.frame(x = 1:3, y = c("a", "b", "c"), stringsAsFactors = FALSE)

str(df3)
## $ x: int 1 2 3
## $ y: chr "a" "b" "c"
Now the "y" column is a character. As mentioned above, each "column" of a data frame must have
the same length. Trying to create a data.frame from vectors with different lengths will result in an
error. (Try running data.frame(x = 1:3, y = 1:4) to see the resulting error.)
As test-cases for data frames, some data is provided by R by default. One of them is iris, loaded
as follows:
mydataframe <- iris

str(mydataframe)
Convert data stored in a list to a single data frame using do.call
If you have your data stored in a list and you want to convert this list to a data frame the do.call
function is an easy way to achieve this. However, it is important that all list elements have the
same length in order to prevent unintended recycling of values.
dataList <- list(1:3,4:6,7:9)

dataList
# [[1]]
# [1] 1 2 3
#
# [[2]]
# [1] 4 5 6
#
# [[3]]
# [1] 7 8 9
dataframe <- data.frame(do.call(rbind, dataList))

dataframe
# X1 X2 X3
# 1 1 2 3
# 2 4 5 6
# 3 7 8 9
It also works if your list consists of data frames itself.
dataframeList <- list(data.frame(a = 1:2, b = 1:2, c = 1:2),

data.frame(a = 3:4, b = 3:4, c = 3:4))
dataframeList
# [[1]]
# a b c
# 1 1 1 1
# 2 2 2 2
# [[2]]
# a b c
# 1 3 3 3
# 2 4 4 4
dataframe <- do.call(rbind, dataframeList)

dataframe
# a b c
# 1 1 1 1
# 2 2 2 2
# 3 3 3 3
# 4 4 4 4
Convert all columns of a data.frame to character class
A common task is to convert all columns of a data.frame to character class for ease of
manipulation, such as in the cases of sending data.frames to a RDBMS or merging data.frames
containing factors where levels may differ between input data.frames.
The best time to do this is when the data is read in - almost all input methods that create data
frames have an options stringsAsFactors which can be set to FALSE.
If the data has already been created, factor columns can be converted to character columns as
shown below.
bob <- data.frame(jobs = c("scientist", "analyst"),

pay = c(160000, 100000), age = c(30, 25))
str(bob)

$ jobs: Factor w/ 2 levels "analyst","scientist": 2 1
$ pay : num 160000 100000
$ age : num 30 25
# Convert *all columns* to character

bob[] <- lapply(bob, as.character)
str(bob)

$ jobs: chr "scientist" "analyst"
$ pay : chr "160000" "1e+05"
$ age : chr "30" "25"
# Convert only factor columns to character

bob[] <- lapply(bob, function(x) {
if is.factor(x) x <- as.character(x)
return(x)
})
Subsetting Rows by Column Values
Built in functions can subset rows with columns that meet conditions.
df <- data.frame(item = c(1:10),

price_Elasticity = c(-0.57667, 0.03205, -0.04904, 0.10342, 0.04029,
0.0742, 0.1669, 0.0313, 0.22204, 0.06158),
total_Margin = c(-145062, 98671, 20576, -56382, 207623, 43463, 1235,
34521, 146553, -74516))
To find rows with price_Elasticity > 0:
df[df$price_Elasticity > 0, ]
item price_Elasticity total_Margin

2 2 0.03205 98671
4 4 0.10342 -56382
5 5 0.04029 207623
6 6 0.07420 43463
7 7 0.16690 1235
8 8 0.03130 34521
9 9 0.22204 146553
10 10 0.06158 -74516
subset based on price_Elasticity > 0 and total_Margin > 0:
df[df$price_Elasticity > 0 & df$total_Margin > 0, ]
item price_Elasticity total_Margin

2 2 0.03205 98671
5 5 0.04029 207623
6 6 0.07420 43463
7 7 0.16690 1235
8 8 0.03130 34521
9 9 0.22204 146553
Read Data frames online: https://riptutorial.com/r/topic/438/data-frames
Chapter 27: data.table
Introduction
Data.table is a package that extends the functionality of data frames from base R, particularly
improving on their performance and syntax. See the package's Docs area at Getting started with
data.table for details.
Syntax
• DT[i, j, by]
# DT[where, select|update|do, by]
• DT[...][...]
# chaining
• ################# Shortcuts, special functions and special symbols inside DT[...]
• .()
# in several arguments, replaces list()
• J()
# in i, replaces list()
• :=
# in j, a function used to add or modify columns
• .N
# in i, the total number of rows
# in j, the number of rows in a group
• .I
# in j, the vector of row numbers in the table (filtered by i)
• .SD
# in j, the current subset of the data
# selected by the .SDcols argument
• .GRP
# in j, the current index of the subset of the data
• .BY
# in j, the list of by values for the current subset of data
• V1, V2, ...
# default names for unnamed columns created in j
• ################# Joins inside DT[...]
• DT1[DT2, on, j]
# join two tables
• i.*
# special prefix on DT2's columns after the join
• by=.EACHI
# special option available only with a join
• DT1[!DT2, on, j]
# anti-join two tables
• DT1[DT2, on, roll, j]
# join two tables, rolling on the last column in on=
• ################# Reshaping, stacking and splitting
• melt(DT, id.vars, measure.vars)
# transform to long format
# for multiple columns, use measure.vars = patterns(...)
• dcast(DT, formula)
# transform to wide format
• rbind(DT1, DT2, ...)
# stack enumerated data.tables
• rbindlist(DT_list, idcol)
# stack a list of data.tables
• split(DT, by)
# split a data.table into a list
• ################# Some other functions specialized for data.tables
• foverlaps
# overlap joins
• merge
# another way of joining two tables
• set
# another way of adding or modifying columns
• fintersect, fsetdiff, funion, fsetequal, unique, duplicated, anyDuplicated
# set-theory operations with rows as elements
• uniqueN
# the number of distinct rows
• rowidv(DT, cols)
# row ID (1 to .N) within each group determined by cols
• rleidv(DT, cols)
# group ID (1 to .GRP) within each group determined by runs of cols
• shift(DT, n, type=c("lag", "lead"))
# apply a shift operator to every column
• setorder, setcolorder, setnames, setkey, setindex, setattr
# modify attributes and order by reference
Remarks
Installation and support

To install the data.table package:
# install from CRAN

install.packages("data.table")
# or install development version

install.packages("data.table", type = "source", repos =
"http://Rdatatable.github.io/data.table")
# and to revert from devel to CRAN, the current version must first be removed
remove.packages("data.table")
install.packages("data.table")
The package's official site has wiki pages providing help getting started, and lists of presentations
and articles from around the web. Before asking a question -- here on StackOverflow or anywhere
else -- please read the support page.
Loading the package

Many of the functions in the examples above exist in the data.table namespace. To use them, you
will need to add a line like library(data.table) first or to use their full path, like data.table::fread
instead of simply fread. For help on individual functions, the syntax is help("fread") or ?fread.
Again, if the package is not loaded, use the full name like ?data.table::fread.
Examples
Creating a data.table
A data.table is an enhanced version of the data.frame class from base R. As such, its class()
attribute is the vector "data.table" "data.frame" and functions that work on a data.frame will also
work with a data.table. There are many ways to create, load or coerce to a data.table.
Build
Don't forget to install and activate the data.table package
library(data.table)
There is a constructor of the same name:
DT <- data.table(
x = letters[1:5],
y = 1:5,
z = (1:5) > 3
)
# x y z
# 1: a 1 FALSE
# 2: b 2 FALSE
# 3: c 3 FALSE
# 4: d 4 TRUE
# 5: e 5 TRUE
Unlike data.frame, data.table will not coerce strings to factors:
sapply(DT, class)
# x y z
# "character" "integer" "logical"
Read in
We can read from a text file:
dt <- fread("my_file.csv")
Unlike read.csv, fread will read strings as strings, not as factors.
Modify a data.frame
For efficiency, data.table offers a way of altering a data.frame or list to make a data.table in-place
(without making a copy or changing its memory location):
# example data.frame
DF <- data.frame(x = letters[1:5], y = 1:5, z = (1:5) > 3)
# modification
setDT(DF)
Note that we do not <- assign the result, since the object DF has been modified in-place. The class
attributes of the data.frame will be retained:
sapply(DF, class)
# x y z
# "factor" "integer" "logical"
Coerce object to data.table

If you have a list, data.frame, or data.table, you should use the setDT function to convert to a
data.table because it does the conversion by reference instead of making a copy (which
as.data.table does). This is important if you are working with large datasets.
If you have another R object (such as a matrix), you must use as.data.table to coerce it to a
data.table.
mat <- matrix(0, ncol = 10, nrow = 10)
DT <- as.data.table(mat)
# or
DT <- data.table(mat)
Adding and modifying columns
DT[where, select|update|do, by] syntax is used to work with columns of a data.table.
• The "where" part is the i argument
• The "select|update|do" part is the j argument
These two arguments are usually passed by position instead of by name.
Our example data below is
mtcars = data.table(mtcars, keep.rownames = TRUE)
Editing entire columns

Use the := operator inside j to assign new columns:
mtcars[, mpg_sq := mpg^2]
Remove columns by setting to NULL:
mtcars[, mpg_sq := NULL]
Add multiple columns by using the := operator's multivariate format:
mtcars[, `:=`(mpg_sq = mpg^2, wt_sqrt = sqrt(wt))]

# or
mtcars[, c("mpg_sq", "wt_sqrt") := .(mpg^2, sqrt(wt))]
If the columns are dependent and must be defined in sequence, one way is:
mtcars[, c("mpg_sq", "mpg2_hp") := .(temp1 <- mpg^2, temp1/hp)]
The .() syntax is used when the right-hand side of LHS := RHS is a list of columns.
For dynamically-determined column names, use parentheses:
vn = "mpg_sq"
mtcars[, (vn) := mpg^2]
Columns can also be modified with set, though this is rarely necessary:
set(mtcars, j = "hp_over_wt", v = mtcars$hp/mtcars$wt)
Editing subsets of columns

Use the i argument to subset to rows "where" edits should be made:
mtcars[1:3, newvar := "Hello"]

# or
set(mtcars, j = "newvar", i = 1:3, v = "Hello")
As in a data.frame, we can subset using row numbers or logical tests. It is also possible to use a
"join" in i, but that more complicated task is covered in another example.
Editing column attributes

Functions that edit attributes, such as levels<- or names<-, actually replace an object with a
modified copy. Even if only used on one column in a data.table, the entire object is copied and
replaced.
To modify an object without copies, use setnames to change the column names of a data.table or
data.frame and setattr to change an attribute for any object.
# Print a message to the console whenever the data.table is copied

tracemem(mtcars)
mtcars[, cyl2 := factor(cyl)]
# Neither of these statements copy the data.table

setnames(mtcars, old = "cyl2", new = "cyl_fac")
setattr(mtcars$cyl_fac, "levels", c("four", "six", "eight"))
# Each of these statements copies the data.table

names(mtcars)[names(mtcars) == "cyl_fac"] <- "cf"
levels(mtcars$cf) <- c("IV", "VI", "VIII")
Be aware that these changes are made by reference, so they are global. Changing them within
one environment affects the object in all environments.
# This function also changes the levels in the global environment

edit_levels <- function(x) setattr(x, "levels", c("low", "med", "high"))
edit_levels(mtcars$cyl_factor)
Special symbols in data.table
.SD
.SD refers to the subset of the data.table for each group, excluding all columns used in by.
.SD along with lapply can be used to apply any function to multiple columns by group in a
data.table
We will continue using the same built-in dataset, mtcars:
mtcars = data.table(mtcars) # Let's not include rownames to keep things simpler
Mean of all columns in the dataset by number of cylinders, cyl:
mtcars[ , lapply(.SD, mean), by = cyl]
# cyl mpg disp hp drat wt qsec vs am gear

carb
#1: 6 19.74286 183.3143 122.28571 3.585714 3.117143 17.97714 0.5714286 0.4285714 3.857143
3.428571
#2: 4 26.66364 105.1364 82.63636 4.070909 2.285727 19.13727 0.9090909 0.7272727 4.090909
1.545455
#3: 8 15.10000 353.1000 209.21429 3.229286 3.999214 16.77214 0.0000000 0.1428571 3.285714
3.500000
Apart from cyl, there are other categorical columns in the dataset such as vs, am, gear and carb. It
doesn't really make sense to take the mean of these columns. So let's exclude these columns. This
is where .SDcols comes into the picture.
.SDcols
.SDcols specifies the columns of the data.table that are included in .SD.
Mean of all columns (continuous columns) in the dataset by number of gears gear, and number of
cylinders, cyl, arranged by gear and cyl:
# All the continuous variables in the dataset

cols_chosen <- c("mpg", "disp", "hp", "drat", "wt", "qsec")
mtcars[order(gear, cyl), lapply(.SD, mean), by = .(gear, cyl), .SDcols = cols_chosen]
# gear cyl mpg disp hp drat wt qsec

#1: 3 4 21.500 120.1000 97.0000 3.700000 2.465000 20.0100
#2: 3 6 19.750 241.5000 107.5000 2.920000 3.337500 19.8300
#3: 3 8 15.050 357.6167 194.1667 3.120833 4.104083 17.1425
#4: 4 4 26.925 102.6250 76.0000 4.110000 2.378125 19.6125
#5: 4 6 19.750 163.8000 116.5000 3.910000 3.093750 17.6700
#6: 5 4 28.200 107.7000 102.0000 4.100000 1.826500 16.8000
#7: 5 6 19.700 145.0000 175.0000 3.620000 2.770000 15.5000
#8: 5 8 15.400 326.0000 299.5000 3.880000 3.370000 14.5500
Maybe we don't want to calculate the mean by groups. To calculate the mean for all the cars in the
dataset, we don't specify the by variable.
mtcars[ , lapply(.SD, mean), .SDcols = cols_chosen]
# mpg disp hp drat wt qsec

#1: 20.09062 230.7219 146.6875 3.596563 3.21725 17.84875
Note:
• It is not necessary to define cols_chosen beforehand. .SDcols can directly take column names
• .SDcols can also directly take a vector of columnnumbers. In the above example this would
be mtcars[ , lapply(.SD, mean), .SDcols = c(1,3:7)]
.N
.N is shorthand for the number of rows in a group.
iris[, .(count=.N), by=Species]
# Species count
#1: setosa 50
#2: versicolor 50
#3: virginica 50
Writing code compatible with both data.frame and data.table
Differences in subsetting syntax

A data.table is one of several two-dimensional data structures available in R, besides data.frame,
matrix and (2D) array. All of these classes use a very similar but not identical syntax for subsetting,
the A[rows, cols] schema.
Consider the following data stored in a matrix, a data.frame and a data.table:
ma <- matrix(rnorm(12), nrow=4, dimnames=list(letters[1:4], c('X', 'Y', 'Z')))

df <- as.data.frame(ma)
dt <- as.data.table(ma)
ma[2:3] #---> returns the 2nd and 3rd items, as if 'ma' were a vector (because it is!)
df[2:3] #---> returns the 2nd and 3rd columns
dt[2:3] #---> returns the 2nd and 3rd rows!
If you want to be sure of what will be returned, it is better to be explicit.
To get specific rows, just add a comma after the range:
ma[2:3, ] # \
df[2:3, ] # }---> returns the 2nd and 3rd rows
dt[2:3, ] # /
But, if you want to subset columns, some cases are interpreted differently. All three can be subset
the same way with integer or character indices not stored in a variable.
ma[, 2:3] # \
df[, 2:3] # \
dt[, 2:3] # }---> returns the 2nd and 3rd columns
ma[, c("Y", "Z")] # /
df[, c("Y", "Z")] # /
dt[, c("Y", "Z")] # /
However, they differ for unquoted variable names
mycols <- 2:3
ma[, mycols] # \
df[, mycols] # }---> returns the 2nd and 3rd columns
dt[, mycols, with = FALSE] # /
dt[, mycols] # ---> Raises an error
In the last case, mycols is evaluated as the name of a column. Because dt cannot find a column
named mycols, an error is raised.
Note: For versions of the data.table package priorto 1.9.8, this behavior was slightly different.
Anything in the column index would have been evaluated using dt as an environment. So both
dt[, 2:3] and dt[, mycols] would return the vector 2:3. No error would be raised for the second
case, because the variable mycols does exist in the parent environment.
Strategies for maintaining compatibility with

data.frame and data.table
There are many reasons to write code that is guaranteed to work with data.frame and data.table.
Maybe you are forced to use data.frame, or you may need to share some code that you don't know
how will be used. So, there are some main strategies for achieving this, in order of convenience:
1. Use syntax that behaves the same for both classes.

2. Use a common function that does the same thing as the shortest syntax.
3. Force data.table to behave as data.frame (ex.: call the specific method print.data.frame).
4. Treat them as list, which they ultimately are.
5. Convert the table to a data.frame before doing anything (bad idea if it is a huge table).
6. Convert the table to data.table, if dependencies are not a concern.
Subset rows. Its simple, just use the [, ] selector, with the comma:
A[1:10, ]
A[A$var > 17, ] # A[var > 17, ] just works for data.table
Subset columns. If you want a single column, use the $ or the [[ ]] selector:
A$var
colname <- 'var'
A[[colname]]
A[[1]]
If you want a uniform way to grab more than one column, it's necessary to appeal a bit:
B <- `[.data.frame`(A, 2:4)
# We can give it a better name

select <- `[.data.frame`
B <- select(A, 2:4)
C <- select(A, c('foo', 'bar'))
Subset 'indexed' rows. While data.frame has row.names, data.table has its unique key feature. The
best thing is to avoid row.names entirely and take advantage of the existing optimizations in the
case of data.table when possible.
B <- A[A$var != 0, ]
# or...
B <- with(A, A[var != 0, ]) # data.table will silently index A by var before subsetting
stuff <- c('a', 'c', 'f')

C <- A[match(stuff, A$name), ] # really worse than: setkey(A); A[stuff, ]
Get a 1-column table, get a row as a vector. These are easy with what we have seen until now:
B <- select(A, 2) #---> a table with just the second column

C <- unlist(A[1, ]) #---> the first row as a vector (coerced if necessary)
Setting keys in data.table
Yes, you need to SETKEY pre 1.9.6
In the past (pre 1.9.6), your data.table was sped up by setting columns as keys to the table,
particularly for large tables. [See intro vignette page 5 of September 2015 version, where speed of
search was 544 times better.] You may find older code making use of this setting keys with
'setkey' or setting a 'key=' column when setting up the table.
library(data.table)
DT <- data.table(
x = letters[1:5],
y = 5:1,
z = (1:5) > 3
)
#> DT
# x y z
#1: a 5 FALSE
#2: b 4 FALSE
#3: c 3 FALSE
#4: d 2 TRUE
#5: e 1 TRUE
Set your key with the setkey command. You can have a key with multiple columns.
setkey(DT, y)
Check your table's key in tables()
tables()
> tables()
NAME NROW NCOL MB COLS KEY
[1,] DT 5 3 1 x,y,z y
Total: 1MB
Note this will re-sort your data.
#> DT
# x y z
#1: e 1 TRUE
#2: d 2 TRUE
#3: c 3 FALSE
#4: b 4 FALSE
#5: a 5 FALSE
Now it is unnecessary
Prior to v1.9.6 you had to have set a key for certain operations especially joining tables. The
developers of data.table have sped up and introduced a "on=" feature that can replace the
dependency on keys. See SO answer here for a detailed discussion.
In Jan 2017, the developers have written a vignette around secondary indices which explains the
"on" syntax and allows for other columns to be identified for fast indexing.
Creating secondary indices?
In a manner similar to key, you can setindex(DT, key.col) or setindexv(DT, "key.col.string"),

where DT is your data.table. Remove all indices with setindex(DT, NULL).
See your secondary indices with indices(DT).
Why secondary indices?
This does not sort the table (unlike key), but does allow for quick indexing using the "on" syntax.
Note there can be only one key, but you can use multiple secondary indices, which saves having
to rekey and resort the table. This will speed up your subsetting when changing the columns you
want to subset on.
Recall, in example above y was the key for table DT:
DT
# x y z
# 1: e 1 TRUE
# 2: d 2 TRUE
# 3: c 3 FALSE
# 4: b 4 FALSE
# 5: a 5 FALSE
# Let us set x as index

setindex(DT, x)
# Use indices to see what has been set

indices(DT)
# [1] "x"
# fast subset using index and not keyed column
DT["c", on ="x"]
#x y z
#1: c 3 FALSE
# old way would have been rekeying DT from y to x, doing subset and
# perhaps keying back to y (now we save two sorts)
# This is a toy example above but would have been more valuable with big data sets
Read data.table online: https://riptutorial.com/r/topic/849/data-table
Chapter 28: Date and Time
Introduction
R comes with classes for dates, date-times and time differences; see ?Dates, ?DateTimeClasses,
?difftime and follow the "See Also" section of those docs for further documentation. Related Docs:
Dates and Date-Time Classes.
Remarks
Classes
• POSIXct
A date-time class, POSIXct stores time as seconds since UNIX epoch on 1970-01-01 00:00:00
UTC. It is the format returned when pulling the current time with Sys.Time().
• POSIXlt
A date-time class, stores a list of day, month, year, hour, minute, second, and so on. This is
the format returned by strptime.
• Date The only date class, stores the date as a floating-point number.
Selecting a date-time format

POSIXct is the sole option in the tidyverse and world of UNIX. It is faster and takes up less
memory than POSIXlt.
origin = as.POSIXct("1970-01-01 00:00:00", format ="%Y-%m-%d %H:%M:%S", tz = "UTC")
origin
## [1] "1970-01-01 UTC"
origin + 47
## [1] "1970-01-01 00:00:47 UTC"
as.numeric(origin) # At epoch
## 0
as.numeric(Sys.time()) # Right now (output as of July 21, 2016 at 11:47:37 EDT)

## 1469116057
posixlt = as.POSIXlt(Sys.time(), format ="%Y-%m-%d %H:%M:%S", tz = "America/Chicago")
# Conversion to POISXct
posixct = as.POSIXct(posixlt)
posixct
# Accessing components
posixlt$sec # Seconds 0-61
posixlt$min # Minutes 0-59
posixlt$hour # Hour 0-23
posixlt$mday # Day of the Month 1-31
posixlt$mon # Months after the first of the year 0-11
posixlt$year # Years since 1900.
ct = as.POSIXct("2015-05-25")
lt = as.POSIXlt("2015-05-25")
object.size(ct)
# 520 bytes
object.size(lt)
# 1816 bytes
Specialized packages
• anytime
• data.table IDate and ITime
• fasttime
• lubridate
• nanotime
Examples
Current Date and Time
R is able to access the current date, time and time zone:
Sys.Date() # Returns date as a Date object
## [1] "2016-07-21"
Sys.time() # Returns date & time at current locale as a POSIXct object
## [1] "2016-07-21 10:04:39 CDT"
as.numeric(Sys.time()) # Seconds from UNIX Epoch (1970-01-01 00:00:00 UTC)
## [1] 1469113479
Sys.timezone() # Time zone at current location
## [1] "Australia/Melbourne"
Use OlsonNames() to view the time zone names in Olson/IANA database on the current system:
str(OlsonNames())
## chr [1:589] "Africa/Abidjan" "Africa/Accra" "Africa/Addis_Ababa" "Africa/Algiers"
"Africa/Asmara" "Africa/Asmera" "Africa/Bamako" ...
Go to the End of the Month
Let's say we want to go to the last day of the month, this function will help on it:
eom <- function(x, p=as.POSIXlt(x)) as.Date(modifyList(p, list(mon=p$mon + 1, mday=0)))
Test:
x <- seq(as.POSIXct("2000-12-10"),as.POSIXct("2001-05-10"),by="months")
> data.frame(before=x,after=eom(x))
before after
1 2000-12-10 2000-12-31
2 2001-01-10 2001-01-31
3 2001-02-10 2001-02-28
4 2001-03-10 2001-03-31
5 2001-04-10 2001-04-30
6 2001-05-10 2001-05-31
>
Using a date in a string format:
> eom('2000-01-01')
[1] "2000-01-31"
Go to First Day of the Month
Let's say we want to go to the first day of a given month:
date <- as.Date("2017-01-20")
> as.POSIXlt(cut(date, "month"))

[1] "2017-01-01 EST"
Move a date a number of months consistently by months
Let's say we want to move a given date a numof months. We can define the following function, that
uses the mondate package:
moveNumOfMonths <- function(date, num) {

as.Date(mondate(date) + num)
}
It moves consistently the month part of the date and adjusting the day, in case the date refers to
the last day of the month.
For example:
Back one month:
> moveNumOfMonths("2017-10-30",-1)
[1] "2017-09-30"
Back two months:
> moveNumOfMonths("2017-10-30",-2)
[1] "2017-08-30"
Forward two months:
> moveNumOfMonths("2017-02-28", 2)
[1] "2017-04-30"
It moves two months from the last day of February, therefore the last day of April.
Let's se how it works for backward and forward operations when it is the last day of the month:
[1] "2017-01-31"
> moveNumOfMonths("2017-01-31", -2)
[1] "2016-11-30"
Because November has 30 days, we get the same date in the backward operation, but:
> moveNumOfMonths("2017-01-30", -2)

[1] "2016-11-30"
[1] "2017-01-31"
Because January has 31 days, then moving two months from last day of November will get the
last day of January.
Read Date and Time online: https://riptutorial.com/r/topic/1157/date-and-time
Chapter 29: Date-time classes (POSIXct and
POSIXlt)
Introduction
R includes two date-time classes -- POSIXct and POSIXlt -- see ?DateTimeClasses.
Remarks
Pitfalls
With POSIXct, midnight will display only the date and time zone, though the full time is still stored.
Related topics
• Date and Time
• lubridate
Examples
Formatting and printing date-time objects
# test date-time object

options(digits.secs = 3)
d = as.POSIXct("2016-08-30 14:18:30.58", tz = "UTC")
format(d,"%S") # 00-61 Second as integer

## [1] "30"
format(d,"%OS") # 00-60.99… Second as fractional

## [1] "30.579"
format(d,"%M") # 00-59 Minute

## [1] "18"
format(d,"%H") # 00-23 Hours

## [1] "14"
format(d,"%I") # 01-12 Hours

## [1] "02"
format(d,"%p") # AM/PM Indicator
## [1] "PM"
format(d,"%z") # Signed offset

## [1] "+0000"
format(d,"%Z") # Time Zone Abbreviation

## [1] "UTC"
See ?strptime for details on the format strings here, as well as other formats.
Parsing strings into date-time objects
The functions for parsing a string into POSIXct and POSIXlt take similar parameters and return a
similar-looking result, but there are differences in how that date-time is stored; see "Remarks."
as.POSIXct("11:38", # time string

format = "%H:%M") # formatting string
## [1] "2016-07-21 11:38:00 CDT"
strptime("11:38", # identical, but makes a POSIXlt object
format = "%H:%M")
## [1] "2016-07-21 11:38:00 CDT"
as.POSIXct("11 AM",
format = "%I %p")
## [1] "2016-07-21 11:00:00 CDT"
Note that date and timezone are imputed.
as.POSIXct("11:38:22", # time string without timezone

format = "%H:%M:%S",
tz = "America/New_York") # set time zone
## [1] "2016-07-21 11:38:22 EDT"
as.POSIXct("2016-07-21 00:00:00",
format = "%F %T") # shortcut tokens for "%Y-%m-%d" and "%H:%M:%S"
See ?strptime for details on the format strings here.
Notes
Missing elements
• If a date element is not supplied, then that from the current date is used.
• If a time element is not supplied, then that from midnight is used, i.e. 0s.
• If no timezone is supplied in either the string or the tz parameter, the local timezone is used.
Time zones
• The accepted values of tz depend on the location.
CST is given with "CST6CDT" or "America/Chicago"
○
• For supported locations and time zones use:

In R: OlsonNames()
○
Alternatively, try in R: system("cat $R_HOME/share/zoneinfo/zone.tab")

○
• These locations are given by Internet Assigned Numbers Authority (IANA)

List of tz database time zones (Wikipedia)
○
IANA TZ Data (2016e)

○
Date-time arithmetic
To add/subtract time, use POSIXct, since it stores times in seconds
## adding/subtracting times - 60 seconds

as.POSIXct("2016-01-01") + 60
# [1] "2016-01-01 00:01:00 AEDT"
## adding 3 hours, 14 minutes, 15 seconds

as.POSIXct("2016-01-01") + ( (3 * 60 * 60) + (14 * 60) + 15)
# [1] "2016-01-01 03:14:15 AEDT"
More formally, as.difftime can be used to specify time periods to add to a date or datetime object.
E.g.:
as.POSIXct("2016-01-01") +
as.difftime(3, units="hours") +
as.difftime(14, units="mins") +
as.difftime(15, units="secs")
# [1] "2016-01-01 03:14:15 AEDT"
To find the difference between dates/times use difftime() for differences in seconds, minutes,
hours, days or weeks.
# using POSIXct objects

difftime(
as.POSIXct("2016-01-01 12:00:00"),
as.POSIXct("2016-01-01 11:59:59"),
unit = "secs")
# Time difference of 1 secs
To generate sequences of date-times use seq.POSIXt() or simply seq.
Read Date-time classes (POSIXct and POSIXlt) online: https://riptutorial.com/r/topic/9027/date-

time-classes--posixct-and-posixlt-
Chapter 30: Debugging
Examples
Using browser
The browser function can be used like a breakpoint: code execution will pause at the point it is
called. Then user can then inspect variable values, execute arbitrary R code and step through the
code line by line.
Once browser() is hit in the code the interactive interpreter will start. Any R code can be run as
normal, and in addition the following commands are present,
Command Meaning
c Exit browser and continue program
f Finish current loop or function \
n Step Over (evaluate next statement, stepping over function calls)
s Step Into (evaluate next statement, stepping into function calls)
where Print stack trace
r Invoke "resume" restart
Q Exit browser and quit
For example we might have a script like,
toDebug <- function() {

a = 1
b = 2
browser()
for(i in 1:100) {
a = a * b
}
}
toDebug()
When running the above script we initially see something like,
Called from: toDebug

Browser[1]>
We could then interact with the prompt as so,
Called from: toDebug

Browser[1]> a
[1] 1
Browser[1]> b
[1] 2
Browse[1]> n
debug at #7: for (i in 1:100) {
a = a * b
}
Browse[2]> n
debug at #8: a = a * b
Browse[2]> a
[1] 1
Browse[2]> n
debug at #8: a = a * b
Browse[2]> a
[1] 2
Browse[2]> Q
browser() can also be used as part of a functional chain, like so:
mtcars %>% group_by(cyl) %>% {browser()}
Using debug
You can set any function for debugging with debug.
debug(mean)
mean(1:3)
All subsequent calls to the function will enter debugging mode. You can disable this behavior with
undebug.
undebug(mean)
mean(1:3)
If you know you only want to enter the debugging mode of a function once, consider the use of
debugonce.
debugonce(mean)
mean(1:3)
mean(1:3)
Read Debugging online: https://riptutorial.com/r/topic/1695/debugging
Chapter 31: Distribution Functions
Introduction
R has many built-in functions to work with probability distributions, with official docs starting at
?Distributions.
Remarks
There are generally four prefixes:
• d-The density function for the given distribution

• p-The cumulative distribution function
• q-Get the quantile associated with the given probability
• r-Get a random sample
For the distributions built into R's base installation, see ?Distributions.
Examples
Normal distribution
Let's use *norm as an example. From the documentation:
dnorm(x, mean = 0, sd = 1, log = FALSE)

pnorm(q, mean = 0, sd = 1, lower.tail = TRUE, log.p = FALSE)
qnorm(p, mean = 0, sd = 1, lower.tail = TRUE, log.p = FALSE)
rnorm(n, mean = 0, sd = 1)
So if I wanted to know the value of a standard normal distribution at 0, I would do
dnorm(0)
Which gives us 0.3989423, a reasonable answer.
In the same way pnorm(0) gives .5. Again, this makes sense, because half of the distribution is to
the left of 0.
qnorm will essentially do the opposite of pnorm. qnorm(.5) gives 0.
Finally, there's the rnorm function:
rnorm(10)
Will generate 10 samples from standard normal.
If you want to change the parameters of a given distribution, simply change them like so
rnorm(10, mean=4, sd= 3)
Binomial Distribution
We now illustrate the functions dbinom,pbinom,qbinom and rbinom defined for Binomial distribution.
The dbinom() function gives the probabilities for various values of the binomial variable. Minimally it
requires three arguments. The first argument for this function must be a vector of quantiles(the
possible values of the random variable X). The second and third arguments are the defining
parameters of the distribution, namely, n(the number of independent trials) and p(the probability of
success in each trial). For example, for a binomial distribution with n = 5, p = 0.5, the possible
values for X are 0,1,2,3,4,5. That is, the dbinom(x,n,p) function gives the probability values P( X =
x ) for x = 0, 1, 2, 3, 4, 5.
#Binom(n = 5, p = 0.5) probabilities

> n <- 5; p<- 0.5; x <- 0:n
> dbinom(x,n,p)
[1] 0.03125 0.15625 0.31250 0.31250 0.15625 0.03125
#To verify the total probability is 1
> sum(dbinom(x,n,p))
[1] 1
>
The binomial probability distribution plot can be displayed as in the following figure:
> x <- 0:12

> prob <- dbinom(x,12,.5)
> barplot(prob,col = "red",ylim = c(0,.2),names.arg=x,
main="Binomial Distribution\n(n=12,p=0.5)")
Note that the binomial distribution is symmetric when p = 0.5. To demonstrate that the binomial
distribution is negatively skewed when p is larger than 0.5, consider the following example:
> n=9; p=.7; x=0:n; prob=dbinom(x,n,p);

> barplot(prob,names.arg = x,main="Binomial Distribution\n(n=9, p=0.7)",col="lightblue")
When p is smaller than 0.5 the binomial distribution is positively skewed as shown below.
> n=9; p=.3; x=0:n; prob=dbinom(x,n,p);

> barplot(prob,names.arg = x,main="Binomial Distribution\n(n=9, p=0.3)",col="cyan")
We will now illustrate the usage of the cumulative distribution function pbinom(). This function can
be used to calculate probabilities such as P( X <= x ). The first argument to this function is a
vector of quantiles(values of x).
# Calculating Probabilities
# P(X <= 2) in a Bin(n=5,p=0.5) distribution
> pbinom(2,5,0.5)
[1] 0.5
The above probability can also be obtained as follows:
# P(X <= 2) = P(X=0) + P(X=1) + P(X=2)

> sum(dbinom(0:2,5,0.5))
[1] 0.5
To compute, probabilities of the type: P( a <= X <= b )
# P(3<= X <= 5) = P(X=3) + P(X=4) + P(X=5) in a Bin(n=9,p=0.6) dist

> sum(dbinom(c(3,4,5),9,0.6))
[1] 0.4923556
>
Presenting the binomial distribution in the form of a table:
> n = 10; p = 0.4; x = 0:n;

> prob = dbinom(x,n,p)
> cdf = pbinom(x,n,p)
> distTable = cbind(x,prob,cdf)
> distTable
x prob cdf
[1,] 0 0.0060466176 0.006046618
[2,] 1 0.0403107840 0.046357402
[3,] 2 0.1209323520 0.167289754
[4,] 3 0.2149908480 0.382280602
[5,] 4 0.2508226560 0.633103258
[6,] 5 0.2006581248 0.833761382
[7,] 6 0.1114767360 0.945238118
[8,] 7 0.0424673280 0.987705446
[9,] 8 0.0106168320 0.998322278
[10,] 9 0.0015728640 0.999895142
[11,] 10 0.0001048576 1.000000000
>
The rbinom() is used to generate random samples of specified sizes with a given parameter
values.
# Simulation
> xVal<-names(table(rbinom(1000,8,.5)))
> barplot(as.vector(table(rbinom(1000,8,.5))),names.arg =xVal,
main="Simulated Binomial Distribution\n (n=8,p=0.5)")
Read Distribution Functions online: https://riptutorial.com/r/topic/1885/distribution-functions
Chapter 32: dplyr
Remarks
dplyr is an iteration of plyr that provides a flexible "verb" based functions to manipulate data in R.
The latest version of dplyr can be downloaded from CRAN using
install.package("dplyr")
The key object in dplyr is a tbl, a representation of a tabular data structure. Currently dplyr (version
0.5.0) supports:
• data frames
• data tables
• SQLite
• PostgreSQL/Redshift
• MySQL/MariaDB
• Bigquery
• MonetDB
• data cubes with arrays (partial implementation)
Examples
dplyr's single table verbs
dplyr introduces a grammar of data manipulation in R. It provides a consistent interface to work

with data no matter where it is stored: data.frame, data.table, or a database. The key pieces of
dplyr are written using Rcpp, which makes it very fast for working with in-memory data.
dplyr's philosophy is to have small functions that do one thing well. The five simple functions (
filter, arrange, select, mutate, and summarise) can be used to reveal new ways to describe data.
When combined with group_by, these functions can be used to calculate group wise summary
statistics.
Syntax commonalities
All these functions have a similar syntax:
• The first argument to all these functions is always a data frame

• Columns can be referred directly using bare variable names (i.e., without using $)
• These functions do not modify the original data itself, i.e., they don't have side effects.
Hence, the results should always be saved to an object.
We will use the built-in mtcars dataset to explore dplyr's single table verbs. Before converting the
type of mtcars to tbl_df (since it makes printing cleaner), we add the rownames of the dataset as a
column using rownames_to_column function from the tibble package.
library(dplyr) # This documentation was written using version 0.5.0
mtcars_tbl <- as_data_frame(tibble::rownames_to_column(mtcars, "cars"))
# examine the structure of data

head(mtcars_tbl)
# A tibble: 6 x 12
# cars mpg cyl disp hp drat wt qsec vs am gear carb
# <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#1 Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
#2 Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
#3 Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1
#4 Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
#5 Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2
#6 Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1
filter
filter helps subset rows that match certain criteria. The first argument is the name of the
data.frame and the second (and subsequent) arguments are the criteria that filter the data (these
criteria should evaluate to either TRUE or FALSE)
Subset all cars that have 4 cylinders - cyl:
filter(mtcars_tbl, cyl == 4)
# A tibble: 11 x 12
#1 Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1
#2 Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2
#3 Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2
#4 Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1
#5 Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2
# ... with 6 more rows
We can pass multiple criteria separated by a comma. To subset the cars which have either 4 or 6
cylinders - cyl and have 5 gears - gear:
filter(mtcars_tbl, cyl == 4 | cyl == 6, gear == 5)
# A tibble: 3 x 12
#1 Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.7 0 1 5 2
#2 Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.9 1 1 5 2
#3 Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.5 0 1 5 6
selects rows based on criteria, to select rows by position, use slice. slice takes only 2
filter
arguments: the first one is a data.frame and the second is integer row values.
To select rows 6 through 9:
slice(mtcars_tbl, 6:9)
# A tibble: 4 x 12
#1 Valiant 18.1 6 225.0 105 2.76 3.46 20.22 1 0 3 1
#2 Duster 360 14.3 8 360.0 245 3.21 3.57 15.84 0 0 3 4
#3 Merc 240D 24.4 4 146.7 62 3.69 3.19 20.00 1 0 4 2
#4 Merc 230 22.8 4 140.8 95 3.92 3.15 22.90 1 0 4 2
Or:
slice(mtcars_tbl, -c(1:5, 10:n()))
This results in the same output as slice(mtcars_tbl, 6:9)
n() represents the number of observations in the current group
arrange
arrange is used to sort the data by a specified variable(s). Just like the previous verb (and all other
functions in dplyr), the first argument is a data.frame, and consequent arguments are used to sort
the data. If more than one variable is passed, the data is first sorted by the first variable, and then
by the second variable, and so on..
To order the data by horsepower - hp
arrange(mtcars_tbl, hp)
# A tibble: 32 x 12
#1 Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2
#2 Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2
#3 Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1
#4 Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1
#5 Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1
#6 Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2
To arrange the data by miles per gallon - mpg in descending order, followed by number of cylinders -
cyl:
arrange(mtcars_tbl, desc(mpg), cyl)
# A tibble: 32 x 12
#1 Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1
#2 Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1
#3 Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2
#4 Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2
#5 Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1
#6 Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2
select
select is used to select only a subset of variables. To select only mpg, disp, wt, qsec, and vs from
mtcars_tbl:
select(mtcars_tbl, mpg, disp, wt, qsec, vs)
# A tibble: 32 x 5
# mpg disp wt qsec vs
# <dbl> <dbl> <dbl> <dbl> <dbl>
#1 21.0 160.0 2.620 16.46 0
#2 21.0 160.0 2.875 17.02 0
#3 22.8 108.0 2.320 18.61 1
#4 21.4 258.0 3.215 19.44 1
#5 18.7 360.0 3.440 17.02 0
#6 18.1 225.0 3.460 20.22 1
:notation can be used to select consecutive columns. To select columns from cars through disp
and vs through carb:
select(mtcars_tbl, cars:disp, vs:carb)
# A tibble: 32 x 8
# cars mpg cyl disp vs am gear carb
# <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#1 Mazda RX4 21.0 6 160.0 0 1 4 4
#2 Mazda RX4 Wag 21.0 6 160.0 0 1 4 4
#3 Datsun 710 22.8 4 108.0 1 1 4 1
#4 Hornet 4 Drive 21.4 6 258.0 1 0 3 1
#5 Hornet Sportabout 18.7 8 360.0 0 0 3 2
#6 Valiant 18.1 6 225.0 1 0 3 1
or select(mtcars_tbl, -(hp:qsec))
For datasets that contain several columns, it can be tedious to select several columns by name.
To make life easier, there are a number of helper functions (such as starts_with(), ends_with(),
contains(), matches(), num_range(), one_of(), and everything()) that can be used in select. To learn
more about how to use them, see ?select_helpers and ?select.
Note: While referring to columns directly in select(), we use bare column names, but quotes
should be used while referring to columns in helper functions.
To rename columns while selecting:
select(mtcars_tbl, cylinders = cyl, displacement = disp)
# A tibble: 32 x 2
# cylinders displacement
# <dbl> <dbl>
#1 6 160.0
#2 6 160.0
#3 4 108.0
#4 6 258.0
#5 8 360.0
#6 6 225.0
As expected, this drops all other variables.
To rename columns without dropping other variables, use rename:
rename(mtcars_tbl, cylinders = cyl, displacement = disp)
# A tibble: 32 x 12
# cars mpg cylinders displacement hp drat wt qsec vs
# <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#1 Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0
#2 Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0
#3 Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1
#4 Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1
#5 Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0
#6 Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1
# ... with 26 more rows, and 3 more variables: am <dbl>, gear <dbl>, carb <dbl>
mutate
mutate can be used to add new columns to the data. Like all other functions in dplyr, mutate
doesn't add the newly created columns to the original data. Columns are added at the end of the
data.frame.
mutate(mtcars_tbl, weight_ton = wt/2, weight_pounds = weight_ton * 2000)
# A tibble: 32 x 14
weight_ton weight_pounds
<dbl> <dbl>
#1 Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4
1.3100 2620
#2 Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4
1.4375 2875
#3 Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1
1.1600 2320
#4 Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1
1.6075 3215
#5 Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2
1.7200 3440
#6 Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1
1.7300 3460
Note the use of weight_ton while creating weight_pounds. Unlike base R, mutate allows us to refer to
columns that we just created to be used for a subsequent operation.
To retain only the newly created columns, use transmute instead of mutate:
transmute(mtcars_tbl, weight_ton = wt/2, weight_pounds = weight_ton * 2000)
# A tibble: 32 x 2
# weight_ton weight_pounds
# <dbl> <dbl>
#1 1.3100 2620
#2 1.4375 2875
#3 1.1600 2320
#4 1.6075 3215
#5 1.7200 3440
#6 1.7300 3460
summarise
summarise calculates summary statistics of variables by collapsing multiple values to a single value.
It can calculate multiple statistics and we can name these summary columns in the same
statement.
To calculate the mean and standard deviation of mpg and disp of all cars in the dataset:
summarise(mtcars_tbl, mean_mpg = mean(mpg), sd_mpg = sd(mpg),

mean_disp = mean(disp), sd_disp = sd(disp))
# A tibble: 1 x 4
# mean_mpg sd_mpg mean_disp sd_disp
# <dbl> <dbl> <dbl> <dbl>
#1 20.09062 6.026948 230.7219 123.9387
group_by
group_by can be used to perform group wise operations on data. When the verbs defined above
are applied on this grouped data, they are automatically applied to each group separately.
To find mean and sd of mpg by cyl:
by_cyl <- group_by(mtcars_tbl, cyl)

summarise(by_cyl, mean_mpg = mean(mpg), sd_mpg = sd(mpg))
# A tibble: 3 x 3
# cyl mean_mpg sd_mpg
# <dbl> <dbl> <dbl>
#1 4 26.66364 4.509828
#2 6 19.74286 1.453567
#3 8 15.10000 2.560048
Putting it all togther

We select columns from cars through hp and gear, order the rows by cyl and from highest to lowest
mpg, group the data by gear, and finally subset only those cars have mpg > 20 and hp > 75
selected <- select(mtcars_tbl, cars:hp, gear)

ordered <- arrange(selected, cyl, desc(mpg))
by_cyl <- group_by(ordered, gear)
filter(by_cyl, mpg > 20, hp > 75)
Source: local data frame [9 x 6]

Groups: gear [3]
# cars mpg cyl disp hp gear

# <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#1 Lotus Europa 30.4 4 95.1 113 5
#2 Porsche 914-2 26.0 4 120.3 91 5
#3 Datsun 710 22.8 4 108.0 93 4
#4 Merc 230 22.8 4 140.8 95 4
#5 Toyota Corona 21.5 4 120.1 97 3
Maybe we are not interested the intermediate results, we can achieve the same result as above by
wrapping the function calls:
filter(
group_by(
arrange(
select(
mtcars_tbl, cars:hp
), cyl, desc(mpg)
), cyl
),mpg > 20, hp > 75
)
This can be a little difficult to read. So, dplyr operations can be chained using the pipe %>%
operator. The above code transalates to:
mtcars_tbl %>%
select(cars:hp) %>%
arrange(cyl, desc(mpg)) %>%
group_by(cyl) %>%
filter(mpg > 20, hp > 75)
summarise multiple columns

dplyr provides summarise_all() to apply functions to all (non-grouping) columns.
To find the number of distinct values for each column:
mtcars_tbl %>%
summarise_all(n_distinct)
# A tibble: 1 x 12
# <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int>
#1 32 25 3 27 22 22 29 30 2 2 3 6
To find the number of distinct values for each column by cyl:
mtcars_tbl %>%
group_by(cyl) %>%
summarise_all(n_distinct)
# A tibble: 3 x 12
# cyl cars mpg disp hp drat wt qsec vs am gear carb
# <dbl> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int>
#1 4 11 9 11 10 10 11 11 2 2 3 2
#2 6 7 6 5 4 5 6 7 2 2 3 3
#3 8 14 12 11 9 11 13 14 1 2 2 4
Note that we just had to add the group_by statement and the rest of the code is the same. The
output now consists of three rows - one for each unique value of cyl.
To summarise specific multiple columns, use summarise_at
mtcars_tbl %>%
group_by(cyl) %>%
summarise_at(c("mpg", "disp", "hp"), mean)
# A tibble: 3 x 4
# cyl mpg disp hp
# <dbl> <dbl> <dbl> <dbl>
#1 4 26.66364 105.1364 82.63636
#2 6 19.74286 183.3143 122.28571
#3 8 15.10000 353.1000 209.21429
helperfunctions (?select_helpers) can be used in place of column names to select specific

columns
To apply multiple functions, either pass the function names as a character vector:
mtcars_tbl %>%
group_by(cyl) %>%
summarise_at(c("mpg", "disp", "hp"),
c("mean", "sd"))
or wrap them inside funs:
mtcars_tbl %>%
group_by(cyl) %>%
funs(mean, sd))
# A tibble: 3 x 7
# cyl mpg_mean disp_mean hp_mean mpg_sd disp_sd hp_sd
# <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#1 4 26.66364 105.1364 82.63636 4.509828 26.87159 20.93453
#2 6 19.74286 183.3143 122.28571 1.453567 41.56246 24.26049
#3 8 15.10000 353.1000 209.21429 2.560048 67.77132 50.97689
Column names are now be appended with function names to keep them distinct. In order to
change this, pass the name to be appended with the function:
mtcars_tbl %>%
group_by(cyl) %>%
c(Mean = "mean", SD = "sd"))
mtcars_tbl %>%
group_by(cyl) %>%
funs(Mean = mean, SD = sd))
# A tibble: 3 x 7
# cyl mpg_Mean disp_Mean hp_Mean mpg_SD disp_SD hp_SD
#1 4 26.66364 105.1364 82.63636 4.509828 26.87159 20.93453
#2 6 19.74286 183.3143 122.28571 1.453567 41.56246 24.26049
#3 8 15.10000 353.1000 209.21429 2.560048 67.77132 50.97689
To select columns conditionally, use summarise_if:
Take the mean of all columns that are numeric grouped by cyl:
mtcars_tbl %>%
group_by(cyl) %>%
summarise_if(is.numeric, mean)
# A tibble: 3 x 11
# cyl mpg disp hp drat wt qsec
#1 4 26.66364 105.1364 82.63636 4.070909 2.285727 19.13727
#2 6 19.74286 183.3143 122.28571 3.585714 3.117143 17.97714
#3 8 15.10000 353.1000 209.21429 3.229286 3.999214 16.77214
# ... with 4 more variables: vs <dbl>, am <dbl>, gear <dbl>,
# carb <dbl>
However, some variables are discrete, and mean of these variables doesn't make sense.
To take the mean of only continuous variables by cyl:
mtcars_tbl %>%
group_by(cyl) %>%
summarise_if(function(x) is.numeric(x) & n_distinct(x) > 6, mean)
# A tibble: 3 x 7
# cyl mpg disp hp drat wt qsec
#1 4 26.66364 105.1364 82.63636 4.070909 2.285727 19.13727
#2 6 19.74286 183.3143 122.28571 3.585714 3.117143 17.97714
#3 8 15.10000 353.1000 209.21429 3.229286 3.999214 16.77214
Subset Observation (Rows)
- Select a subset of rows in a data frame that meet

dplyr::filter()
a logical criteria:
dplyr::filter(iris,Sepal.Length>7)
# Sepal.Length Sepal.Width Petal.Length Petal.Width Species
# 1 7.1 3.0 5.9 2.1 virginica
# 2 7.6 3.0 6.6 2.1 virginica
# 3 7.3 2.9 6.3 1.8 virginica
# 4 7.2 3.6 6.1 2.5 virginica
# 5 7.7 3.8 6.7 2.2 virginica
# 6 7.7 2.6 6.9 2.3 virginica
# 7 7.7 2.8 6.7 2.0 virginica
# 8 7.2 3.2 6.0 1.8 virginica
# 9 7.2 3.0 5.8 1.6 virginica
# 10 7.4 2.8 6.1 1.9 virginica
# 11 7.9 3.8 6.4 2.0 virginica
# 12 7.7 3.0 6.1 2.3 virginica
dplyr::distinct() - Remove duplicate rows:
distinct(iris, Sepal.Length, .keep_all = TRUE)

# Sepal.Length Sepal.Width Petal.Length Petal.Width Species
# 1 5.1 3.5 1.4 0.2 setosa
# 2 4.9 3.0 1.4 0.2 setosa
# 3 4.7 3.2 1.3 0.2 setosa
# 4 4.6 3.1 1.5 0.2 setosa
# 5 5.0 3.6 1.4 0.2 setosa
# 6 5.4 3.9 1.7 0.4 setosa
# 7 4.4 2.9 1.4 0.2 setosa
# 8 4.8 3.4 1.6 0.2 setosa
# 9 4.3 3.0 1.1 0.1 setosa
# 10 5.8 4.0 1.2 0.2 setosa
# 11 5.7 4.4 1.5 0.4 setosa
# 12 5.2 3.5 1.5 0.2 setosa
# 13 5.5 4.2 1.4 0.2 setosa
# 14 4.5 2.3 1.3 0.3 setosa
# 15 5.3 3.7 1.5 0.2 setosa
# 16 7.0 3.2 4.7 1.4 versicolor
# 17 6.4 3.2 4.5 1.5 versicolor
# 18 6.9 3.1 4.9 1.5 versicolor
# 19 6.5 2.8 4.6 1.5 versicolor
# 20 6.3 3.3 4.7 1.6 versicolor
# 21 6.6 2.9 4.6 1.3 versicolor
# 22 5.9 3.0 4.2 1.5 versicolor
# 23 6.0 2.2 4.0 1.0 versicolor
# 24 6.1 2.9 4.7 1.4 versicolor
# 25 5.6 2.9 3.6 1.3 versicolor
# 26 6.7 3.1 4.4 1.4 versicolor
# 27 6.2 2.2 4.5 1.5 versicolor
# 28 6.8 2.8 4.8 1.4 versicolor
# 29 7.1 3.0 5.9 2.1 virginica
# 30 7.6 3.0 6.6 2.1 virginica
# 31 7.3 2.9 6.3 1.8 virginica
# 32 7.2 3.6 6.1 2.5 virginica
# 33 7.7 3.8 6.7 2.2 virginica
# 34 7.4 2.8 6.1 1.9 virginica
# 35 7.9 3.8 6.4 2.0 virginica
Aggregating with %>% (pipe) operator
The pipe (%>%) operator could be used in combination with dplyr functions. In this example we
use the mtcars dataset (see help("mtcars") for more information) to show how to sumarize a data
frame, and to add variables to the data with the result of the application of a function.
library(dplyr)
library(magrittr)
df <- mtcars
df$cars <- rownames(df) #just add the cars names to the df
df <- df[,c(ncol(df),1:(ncol(df)-1))] # and place the names in the first column
1. Sumarize the data
To compute statistics we use summarize and the appropriate functions. In this case n() is used for
counting the number of cases.
df %>%
summarize(count=n(),mean_mpg = mean(mpg, na.rm = TRUE),
min_weight = min(wt),max_weight = max(wt))
# count mean_mpg min_weight max_weight

#1 32 20.09062 1.513 5.424
2. Compute statistics by group
It is possible to compute the statistics by groups of the data. In this case by Number of cylinders
and Number of forward gears
df %>%
group_by(cyl, gear) %>%
summarize(count=n(),mean_mpg = mean(mpg, na.rm = TRUE),
min_weight = min(wt),max_weight = max(wt))
# Source: local data frame [8 x 6]

# Groups: cyl [?]
#
# cyl gear count mean_mpg min_weight max_weight
# <dbl> <dbl> <int> <dbl> <dbl> <dbl>
#1 4 3 1 21.500 2.465 2.465
#2 4 4 8 26.925 1.615 3.190
#3 4 5 2 28.200 1.513 2.140
#4 6 3 2 19.750 3.215 3.460
#5 6 4 4 19.750 2.620 3.440
#6 6 5 1 19.700 2.770 2.770
#7 8 3 12 15.050 3.435 5.424
#8 8 5 2 15.400 3.170 3.570
Examples of NSE and string variables in dpylr
dplyr uses Non-Standard Evaluation(NSE), which is why we normally can use the variable names
without quotes. However, sometimes during the data pipeline, we need to get our variable names
from other sources such as a Shiny selection box. In case of functions like select, we can just use
select_ to use a string variable to select
variable1 <- "Sepal.Length"

variable2 <- "Sepal.Width"
iris %>%
select_(variable1, variable2) %>%
head(n=5)
# Sepal.Length Sepal.Width
# 1 5.1 3.5
# 2 4.9 3.0
# 3 4.7 3.2
# 4 4.6 3.1
# 5 5.0 3.6
But if we want to use other features such as summarize or filter we need to use interp function
from lazyeval package
variable1 <- "Sepal.Length"

variable2 <- "Sepal.Width"
variable3 <- "Species"
iris %>%
select_(variable1, variable2, variable3) %>%
group_by_(variable3) %>%
summarize_(mean1 = lazyeval::interp(~mean(var), var = as.name(variable1)), mean2 =
lazyeval::interp(~mean(var), var = as.name(variable2)))
# Species mean1 mean2
# <fctr> <dbl> <dbl>
# 1 setosa 5.006 3.428
# 2 versicolor 5.936 2.770
# 3 virginica 6.588 2.974
Read dplyr online: https://riptutorial.com/r/topic/4250/dplyr
Chapter 33: Expression: parse + eval
Remarks
The function parse convert text and files into expressions.
The function eval evaluate expressions.
Examples
Execute code in string format
In this exemple, we want to execute code which is stored in a string format.
# the string
str <- "1+1"
# A string is not an expression.

is.expression(str)
[1] FALSE
eval(str)
[1] "1+1"
# parse convert string into expressions

parsed.str <- parse(text="1+1")
is.expression(parsed.str)
[1] TRUE
eval(parsed.str)
[1] 2
Read Expression: parse + eval online: https://riptutorial.com/r/topic/5746/expression--parse-plus-

eval
Chapter 34: Extracting and Listing Files in
Compressed Archives
Examples
Extracting files from a .zip archive
Unzipping a zip archive is done with unzip function from the utils package (which is included in
base R).
unzip(zipfile = "bar.zip", exdir = "./foo")
This will extract all files in "bar.zip" to the "foo" directory, which will be created if necessary. Tilde
expansion is done automatically from your working directory. Alternatively, you can pass the whole
path name to the zipfile.
Listing files in a .zip archive
Listing files in a zip archive is done with unzip function from the utils package (which is included in
base R).
unzip(zipfile = "bar.zip", list = TRUE)
This will list all files in "bar.zip" and extract none. Tilde expansion is done automatically from your
working directory. Alternatively, you can pass the whole path name to the zipfile.
Listing files in a .tar archive
Listing files in a tar archive is done with untar function from the utils package (which is included in
base R).
untar(zipfile = "bar.tar", list = TRUE)
This will list all files in "bar.tar" and extract none. Tilde expansion is done automatically from your
working directory. Alternatively, you can pass the whole path name to the tarfile.
Extracting files from a .tar archive
Extracting files from a tar archive is done with untar function from the utils package (which is
included in base R).
untar(tarfile = "bar.tar", exdir = "./foo")
This will extract all files in "bar.tar" to the "foo" directory, which will be created if necessary. Tilde
expansion is done automatically from your working directory. Alternatively, you can pass the whole
path name to the tarfile.
Extract all .zip archives in a directory
With a simple for loop, all zip archives in a directory can be extracted.
for (i in dir(pattern=".zip$"))
unzip(i)
The dir function produces a character vector of the names of the files in a directory matching the
regex pattern specified by pattern. This vector is looped through with index i, using the unzip
function to extract each zip archive.
Read Extracting and Listing Files in Compressed Archives online:

https://riptutorial.com/r/topic/4323/extracting-and-listing-files-in-compressed-archives
Chapter 35: Factors
Syntax
1. factor(x = character(), levels, labels = levels, exclude = NA, ordered = is.ordered(x), nmax =
NA)
2. Run ?factor or see the documentation online.
Remarks
An object with class factor is a vector with a particular set of characteristics.
1. It is stored internally as an integer vector.

2. It maintains a levels attribute the shows the character representation of the values.
3. Its class is stored as factor
To illustrate, let us generate a vector of 1,000 observations from a set of colors.
set.seed(1)
Color <- sample(x = c("Red", "Blue", "Green", "Yellow"),
size = 1000,
replace = TRUE)
Color <- factor(Color)
We can observe each of the characteristics of Color listed above:
#* 1. It is stored internally as an ìnteger` vector

typeof(Color)
[1] "integer"
#* 2. It maintains a `levels` attribute the shows the character representation of the values.
#* 3. Its class is stored as `factor`
attributes(Color)
$levels
[1] "Blue" "Green" "Red" "Yellow"
$class
[1] "factor"
The primary advantage of a factor object is efficiency in data storage. An integer requires less
memory to store than a character. Such efficiency was highly desirable when many computers had
much more limited resources than current machines (for a more detailed history of the motivations
behind using factors, see stringsAsFactors: an Unauthorized Biography). The difference in memory
use can be seen even in our Color object. As you can see, storing Color as a character requires
about 1.7 times as much memory as the factor object.
#* Amount of memory required to store Color as a factor.
object.size(Color)
4624 bytes
#* Amount of memory required to store Color as a character

object.size(as.character(Color))
8232 bytes
Mapping the integer to the level

While the internal computation of factors sees the object as an integer, the desired representation
for human consumption is the character level. For example,
head(Color)
[1] Blue Blue Green Yellow Red Yellow

Levels: Blue Green Red Yellow
is a easier for human comprehension than
head(as.numeric(Color))
[1] 1 1 2 4 3 4
An approximate illustration of how R goes about matching the character representation to the
internal integer value is:
head(levels(Color)[as.numeric(Color)])
[1] "Blue" "Blue" "Green" "Yellow" "Red" "Yellow"
Compare these results to
head(Color)
[1] Blue Blue Green Yellow Red Yellow

Levels: Blue Green Red Yellow
Modern use of factors

In 2007, R introduced a hashing method for characters the reduced the memory burden of
character vectors (ref: stringsAsFactors: an Unauthorized Biography). Take note that when we
determined that characters require 1.7 times more storage space than factors, that was calculated
in a recent version of R, meaning that the memory use of character vectors was even more taxing
before 2007.
Owing to the hashing method in modern R and to far greater memory resources in modern
computers, the issue of memory efficiency in storing character values has been reduced to a very
small concern. The prevailing attitude in the R Community is a preference for character vectors
over factors in most situations. The primary causes for the shift away from factors are
1. The increase of unstructured and/or loosely controlled character data

2. The tendency of factors to not behave as desired when the user forgets she is dealing with a
factor and not a character
In the first case, it makes no sense to store free text or open response fields as factors, as there
will unlikely be any pattern that allows for more than one observation per level. Alternatively, if the
data structure is not carefully controlled, it is possible to get multiple levels that correspond to the
same category (such as "blue", "Blue", and "BLUE"). In such cases, many prefer to manage these
discrepancies as characters prior to converting to a factor (if conversion takes place at all).
In the second case, if the user thinks she is working with a character vector, certain methods may
not respond as anticipated. This basic understanding can lead to confusion and frustration while
trying to debug scripts and codes. While, strictly speaking, this may be considered the fault of the
user, most users are happy to avoid using factors and avoid these situations altogether.
Examples
Basic creation of factors
Factors are one way to represent categorical variables in R. A factor is stored internally as a
vector of integers. The unique elements of the supplied character vector are known as the levels
of the factor. By default, if the levels are not supplied by the user, then R will generate the set of
unique values in the vector, sort these values alphanumerically, and use them as the levels.
charvar <- rep(c("n", "c"), each = 3)

f <- factor(charvar)
f
levels(f)
> f
[1] n n n c c c
Levels: c n
> levels(f)
[1] "c" "n"
If you want to change the ordering of the levels, then one option to to specify the levels manually:
levels(factor(charvar, levels = c("n","c")))
> levels(factor(charvar, levels = c("n","c")))
[1] "n" "c"
Factors have a number of properties. For example, levels can be given labels:
> f <- factor(charvar, levels=c("n", "c"), labels=c("Newt", "Capybara"))

> f
[1] Newt Newt Newt Capybara Capybara Capybara
Levels: Newt Capybara
Another property that can be assigned is whether the factor is ordered:
> Weekdays <- factor(c("Monday", "Wednesday", "Thursday", "Tuesday", "Friday", "Sunday",

"Saturday"))
> Weekdays
[1] Monday Wednesday Thursday Tuesday Friday Sunday Saturday
Levels: Friday Monday Saturday Sunday Thursday Tuesday Wednesday
> Weekdays <- factor(Weekdays, levels=c("Monday", "Tuesday", "Wednesday", "Thursday",
"Friday", "Saturday", "Sunday"), ordered=TRUE)
> Weekdays
[1] Monday Wednesday Thursday Tuesday Friday Sunday Saturday
Levels: Monday < Tuesday < Wednesday < Thursday < Friday < Saturday < Sunday
When a level of the factor is no longer used, you can drop it using the droplevels() function:
> Weekend <- subset(Weekdays, Weekdays == "Saturday" | Weekdays == "Sunday")

> Weekend
[1] Sunday Saturday
Levels: Monday < Tuesday < Wednesday < Thursday < Friday < Saturday < Sunday
> Weekend <- droplevels(Weekend)
> Weekend
[1] Sunday Saturday
Levels: Saturday < Sunday
Consolidating Factor Levels with a List
There are times in which it is desirable to consolidate factor levels into fewer groups, perhaps
because of sparse data in one of the categories. It may also occur when you have varying
spellings or capitalization of the category names. Consider as an example the factor
set.seed(1)
colorful <- sample(c("red", "Red", "RED", "blue", "Blue", "BLUE", "green", "gren"),
size = 20,
replace = TRUE)
colorful <- factor(colorful)
Since R is case-sensitive, a frequency table of this vector would appear as below.
table(colorful)
colorful
blue Blue BLUE green gren red Red RED
3 1 4 2 4 1 3 2
This table, however, doesn't represent the true distribution of the data, and the categories may
effectively be reduced to three types: Blue, Green, and Red. Three examples are provided. The
first illustrates what seems like an obvious solution, but won't actually provide a solution. The
second gives a working solution, but is verbose and computationally expensive. The third is not an
obvious solution, but is relatively compact and computationally efficient.
Consolidating levels using factor (factor_approach)
factor(as.character(colorful),
levels = c("blue", "Blue", "BLUE", "green", "gren", "red", "Red", "RED"),
labels = c("Blue", "Blue", "Blue", "Green", "Green", "Red", "Red", "Red"))
[1] Green Blue Red Red Blue Red Red Red Blue Red Green Green Green
Blue Red Green
[17] Red Green Green Red
Levels: Blue Blue Blue Green Green Red Red Red
Warning message:
In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else
paste0(labels, :
duplicated levels in factors are deprecated
Notice that there are duplicated levels. We still have three categories for "Blue", which doesn't
complete our task of consolidating levels. Additionally, there is a warning that duplicated levels are
deprecated, meaning that this code may generate an error in the future.
Consolidating levels using ifelse (ifelse_approach)
factor(ifelse(colorful %in% c("blue", "Blue", "BLUE"),

"Blue",
ifelse(colorful %in% c("green", "gren"),
"Green",
"Red")))
Blue Red Green
Levels: Blue Green Red
This code generates the desired result, but requires the use of nested ifelse statements. While
there is nothing wrong with this approach, managing nested ifelse statements can be a tedious
task and must be done carefully.
Consolidating Factors Levels with a List (list_approach)

A less obvious way of consolidating levels is to use a list where the name of each element is the
desired category name, and the element is a character vector of the levels in the factor that should
map to the desired category. This has the added advantage of working directly on the levels
attribute of the factor, without having to assign new objects.
levels(colorful) <-
list("Blue" = c("blue", "Blue", "BLUE"),
"Green" = c("green", "gren"),
"Red" = c("red", "Red", "RED"))
Blue Red Green
Levels: Blue Green Red
Benchmarking each approach

The time required to execute each of these approaches is summarized below. (For the sake of
space, the code to generate this summary is not shown)
Unit: microseconds
factor 78.725 83.256 93.26023 87.5030 97.131 218.899 100 b
ifelse 104.494 107.609 123.53793 113.4145 128.281 254.580 100 c
list_approach 49.557 52.955 60.50756 54.9370 65.132 138.193 100 a
The list approach runs about twice as fast as the ifelse approach. However, except in times of
very, very large amounts of data, the differences in execution time will likely be measured in either
microseconds or milliseconds. With such small time differences, efficiency need not guide the
decision of which approach to use. Instead, use an approach that is familiar and comfortable, and
which you and your collaborators will understand on future review.
Factors
Factors are one method to represent categorical variables in R. Given a vector x whose values
can be converted to characters using as.character(), the default arguments for factor() and
as.factor() assign an integer to each distinct element of the vector as well as a level attribute and
a label attribute. Levels are the values x can possibly take and labels can either be the given
element or determined by the user.
To example how factors work we will create a factor with default attributes, then custom levels,
and then custom levels and labels.
# standard
factor(c(1,1,2,2,3,3))
[1] 1 1 2 2 3 3
Levels: 1 2 3
Instances can arise where the user knows the number of possible values a factor can take on is
greater than the current values in the vector. For this we assign the levels ourselves in factor().
factor(c(1,1,2,2,3,3),
levels = c(1,2,3,4,5))
[1] 1 1 2 2 3 3
Levels: 1 2 3 4 5
For style purposes the user may wish to assign labels to each level. By default, labels are the
character representation of the levels. Here we assign labels for each of the possible levels in the
factor.
factor(c(1,1,2,2,3,3),
levels = c(1,2,3,4,5),
labels = c("Fox","Dog","Cow","Brick","Dolphin"))
[1] Fox Fox Dog Dog Cow Cow
Levels: Fox Dog Cow Brick Dolphin
Normally, factors can only be compared using == and != and if the factors have the same levels.
The following comparison of factors fails even though they appear equal because the factors have
different factor levels.
factor(c(1,1,2,2,3,3),levels = c(1,2,3)) == factor(c(1,1,2,2,3,3),levels = c(1,2,3,4,5))

Error in Ops.factor(factor(c(1, 1, 2, 2, 3, 3), levels = c(1, 2, 3)), :
level sets of factors are different
This makes sense as the extra levels in the RHS mean that R does not have enough information
about each factor to compare them in a meaningful way.
The operators <, <=, > and >= are only usable for ordered factors. These can represent categorical
values which still have a linear order. An ordered factor can be created by providing the ordered =
TRUE argument to the factor function or just using the ordered function.
x <- factor(1:3, labels = c('low', 'medium', 'high'), ordered = TRUE)

print(x)
[1] low medium high
Levels: low < medium < high
y <- ordered(3:1, labels = c('low', 'medium', 'high'))

print(y)
[1] high medium low
Levels: low < medium < high
x < y
[1] TRUE FALSE FALSE
For more information, see the Factor documentation.
Changing and reordering factors
When factors are created with defaults, levels are formed by as.character applied to the inputs
and are ordered alphabetically.
charvar <- rep(c("W", "n", "c"), times=c(17,20,14))

f <- factor(charvar)
levels(f)
# [1] "c" "n" "W"
In some situations the treatment of the default ordering of levels (alphabetic/lexical order) will be
acceptable. For example, if one justs want to plot the frequencies, this will be the result:
plot(f,col=1:length(levels(f)))
But if we want a different ordering of levels, we need to specify this in the levels or labels
parameter (taking care that the meaning of "order" here is different from ordered factors, see
below). There are many alternatives to accomplish that task depending on the situation.
1. Redefine the factor
When it is possible, we can recreate the factor using the levels parameter with the order we want.
ff <- factor(charvar, levels = c("n", "W", "c"))

levels(ff)
# [1] "n" "W" "c"
gg <- factor(charvar, levels = c("W", "c", "n"))

levels(gg)
# [1] "W" "c" "n"
When the input levels are different than the desired output levels, we use the labels parameter
which causes the levels parameter to become a "filter" for acceptable input values, but leaves the
final values of "levels" for the factor vector as the argument to labels:
fm <- factor(as.numeric(f),levels = c(2,3,1),
labels = c("nn", "WW", "cc"))
levels(fm)
# [1] "nn" "WW" "cc"
fm <- factor(LETTERS[1:6], levels = LETTERS[1:4], # only 'A'-'D' as input

labels = letters[1:4]) # but assigned to 'a'-'d'
fm
#[1] a b c d <NA> <NA>
#Levels: a b c d
2. Use relevel function
When there is one specific level that needs to be the first we can use relevel. This happens, for
example, in the context of statistical analysis, when a base category is necessary for testing
hypothesis.
g<-relevel(f, "n") # moves n to be the first level

levels(g)
# [1] "n" "c" "W"
As can be verified f and g are the same
all.equal(f, g)
# [1] "Attributes: < Component “levels”: 2 string mismatches >"
all.equal(f, g, check.attributes = F)
# [1] TRUE
3. Reordering factors
There are cases when we need to reorder the levels based on a number, a partial result, a
computed statistic, or previous calculations. Let's reorder based on the frequencies of the levels
table(g)
# g
# n c W
# 20 14 17
The reorder function is generic (see help(reorder)), but in this context needs: x, in this case the
factor; X, a numeric value of the same length as x; and FUN, a function to be applied to X and
computed by level of the x, which determines the levels order, by default increasing. The result is
the same factor with its levels reordered.
g.ord <- reorder(g,rep(1,length(g)), FUN=sum) #increasing

levels(g.ord)
# [1] "c" "W" "n"
To get de decreasing order we consider negative values (-1)
g.ord.d <- reorder(g,rep(-1,length(g)), FUN=sum)

levels(g.ord.d)
# [1] "n" "W" "c"
Again the factor is the same as the others.
data.frame(f,g,g.ord,g.ord.d)[seq(1,length(g),by=5),] #just same lines

# f g g.ord g.ord.d
# 1 W W W W
# 6 W W W W
# 11 W W W W
# 16 W W W W
# 21 n n n n
# 26 n n n n
# 31 n n n n
# 36 n n n n
# 41 c c c c
# 46 c c c c
# 51 c c c c
When there is a quantitative variable related to the factor variable, we could use other functions
to reorder the levels. Lets take the iris data (help("iris") for more information), for reordering the
Species factor by using its mean Sepal.Width.
miris <- iris #help("iris") # copy the data

with(miris, tapply(Sepal.Width,Species,mean))
# setosa versicolor virginica
# 3.428 2.770 2.974
miris$Species.o<-with(miris,reorder(Species,-Sepal.Width))
levels(miris$Species.o)
# [1] "setosa" "virginica" "versicolor"
The usual boxplot (say: with(miris, boxplot(Petal.Width~Species)) will show the especies in this
order: setosa, versicolor, and virginica. But using the ordered factor we get the species ordered by
its mean Sepal.Width:
boxplot(Petal.Width~Species.o, data = miris,

xlab = "Species", ylab = "Petal Width",
main = "Iris Data, ordered by mean sepal width", varwidth = TRUE,
col = 2:4)
Additionally, it is also possible to change the names of levels, combine them into groups, or add
new levels. For that we use the function of the same name levels.
f1<-f
levels(f1)
# [1] "c" "n" "W"
levels(f1) <- c("upper","upper","CAP") #rename and grouping
levels(f1)
# [1] "upper" "CAP"
f2<-f1
levels(f2) <- c("upper","CAP", "Number") #add Number level, which is empty
levels(f2)
# [1] "upper" "CAP" "Number"
f2[length(f2):(length(f2)+5)]<-"Number" # add cases for the new level
table(f2)
# f2
# upper CAP Number
# 33 17 6
f3<-f1
levels(f3) <- list(G1 = "upper", G2 = "CAP", G3 = "Number") # The same using list
levels(f3)
# [1] "G1" "G2" "G3"
f3[length(f3):(length(f3)+6)]<-"G3" ## add cases for the new level
table(f3)
# f3
# G1 G2 G3
# 33 17 7
- Ordered factors
Finally, we know that ordered factors are different from factors, the first one are used to represent
ordinal data, and the second one to work with nominal data. At first, it does not make sense to
change the order of levels for ordered factors, but we can change its labels.
ordvar<-rep(c("Low", "Medium", "High"), times=c(7,2,4))
of<-ordered(ordvar,levels=c("Low", "Medium", "High"))

levels(of)
# [1] "Low" "Medium" "High"
of1<-of
levels(of1)<- c("LOW", "MEDIUM", "HIGH")
levels(of1)
# [1] "LOW" "MEDIUM" "HIGH"
is.ordered(of1)
# [1] TRUE
of1
# [1] LOW LOW LOW LOW LOW LOW LOW MEDIUM MEDIUM HIGH HIGH HIGH HIGH
# Levels: LOW < MEDIUM < HIGH
Rebuilding factors from zero
Problem
Factors are used to represent variables that take values from a set of categories, known as Levels
in R. For example, some experiment could be characterized by the energy level of a battery, with
four levels: empty, low, normal, and full. Then, for 5 different sampling sites, those levels could be
identified, in those terms, as follows:
full, full, normal, empty, low
Typically, in databases or other information sources, the handling of these data is by arbitrary
integer indices associated with the categories or levels. If we assume that, for the given example,
we would assign, the indices as follows: 1 = empty, 2 = low, 3 = normal, 4 = full, then the 5
samples could be coded as:
4, 4, 3, 1, 2
It could happen that, from your source of information, e.g. a database, you only have the encoded
list of integers, and the catalog associating each integer with each level-keyword. How can a factor
of R be reconstructed from that information?
Solution
We will simulate a vector of 20 integers that represents the samples, each of which may have one
of four different values:
set.seed(18)
ii <- sample(1:4, 20, replace=T)
ii
[1] 4 3 4 1 1 3 2 3 2 1 3 4 1 2 4 1 3 1 4 1
The first step is to make a factor, from the previous sequence, in which the levels or categories are
exactly the numbers from 1 to 4.
fii <- factor(ii, levels=1:4) # it is necessary to indicate the numeric levels

fii
[1] 4 3 4 1 1 3 2 3 2 1 3 4 1 2 4 1 3 1 4 1
Levels: 1 2 3 4
Now simply, you have to dress the factor already created with the index tags:
levels(fii) <- c("empty", "low", "normal", "full")

fii
[1] full normal full empty empty normal low normal low empty
[11] normal full empty low full empty normal empty full empty
Levels: empty low normal full
Read Factors online: https://riptutorial.com/r/topic/1104/factors
Chapter 36: Fault-tolerant/resilient code
Parameters
Parameter Details
In case the "try part" was completed successfully tryCatch will return the
last evaluated expression. Hence, the actual value being returned in
case everything went well and there is no condition (i.e. a warning or an
expr error) is the return value of readLines. Note that you don't need to explicilty
state the return value via return as code in the "try part" is not wrapped
insided a function environment (unlike that for the condition handlers for
warnings and error below)
Provide/define a handler function for all the conditions that you want to
handle explicitly. AFAIU, you can provide handlers for any type of
conditions (not just warnings and errors, but also custom conditions; see
warning/error/etc
simpleCondition and friends for that) as long as the name of the
respective handler function matches the class of the respective
condition (see the Details part of the doc for tryCatch).
Here goes everything that should be executed at the very end,

regardless if the expression in the "try part" succeeded or if there was
finally any condition. If you want more than one expression to be executed, then
you need to wrap them in curly brackets, otherwise you could just have
written finally = <expression> (i.e. the same logic as for "try part".
Remarks
tryCatch
tryCatch returns the value associated to executing expr unless there's a condition: a warning or an
error. If that's the case, specific return values (e.g. return(NA) above) can be specified by
supplying a handler function for the respective conditions (see arguments warning and error in
?tryCatch). These can be functions that already exist, but you can also define them within tryCatch
(as we did above).
Implications of choosing specific return values of the handler functions
As we've specified that NA should be returned in case of an error in the "try part", the third element
in y is NA. If we'd have chosen NULL to be the return value, the length of y would just have been 2
instead of 3 as lapply will simply "ignore/drop" return values that are NULL. Also note that if you
don't specify an explicit return value via return, the handler functions will return NULL (i.e. in case
of an error or a warning condition).
"Undesired" warning message
When the third element of our urls vector hits our function, we get the following warning in
addition to the fact that an error occurs (readLines first complains that it can't open the connection
via a warning before actually failing with an error):
Warning message:
In file(con, "r") : cannot open file 'I'm no URL': No such file or directory
An error "wins" over a warning, so we're not really interested in the warning in this particular case.
Thus we have set warn = FALSE in readLines, but that doesn't seem to have any effect. An
alternative way to suppress the warning is to use
suppressWarnings(readLines(con = url))
instead of
readLines(con = url, warn = FALSE)
Examples
Using tryCatch()
We're defining a robust version of a function that reads the HTML code from a given URL. Robust
in the sense that we want it to handle situations where something either goes wrong (error) or not
quite the way we planned it to (warning). The umbrella term for errors and warnings is condition
Function definition using tryCatch
readUrl <- function(url) {

out <- tryCatch(
########################################################
# Try part: define the expression(s) you want to "try" #
########################################################
{
# Just to highlight:
# If you want to use more than one R expression in the "try part"
# then you'll have to use curly brackets.
# Otherwise, just write the single expression you want to try and
message("This is the 'try' part")

readLines(con = url, warn = FALSE)
},
########################################################################
# Condition handler part: define how you want conditions to be handled #
########################################################################
# Handler when a warning occurs:
warning = function(cond) {
message(paste("Reading the URL caused a warning:", url))
message("Here's the original warning message:")
message(cond)
# Choose a return value when such a type of condition occurs

return(NULL)
},
# Handler when an error occurs:

error = function(cond) {
message(paste("This seems to be an invalid URL:", url))
message("Here's the original error message:")
message(cond)
# Choose a return value when such a type of condition occurs

return(NA)
},
###############################################
# Final part: define what should happen AFTER #
# everything has been tried and/or handled #
###############################################
finally = {
message(paste("Processed URL:", url))
message("Some message at the end\n")
}
)
return(out)
}
Testing things out

Let's define a vector of URLs where one element isn't a valid URL
urls <- c(
"http://stat.ethz.ch/R-manual/R-devel/library/base/html/connections.html",
"http://en.wikipedia.org/wiki/Xz",
"I'm no URL"
)
And pass this as input to the function we defined above
y <- lapply(urls, readUrl)

# Processed URL: http://stat.ethz.ch/R-manual/R-devel/library/base/html/connections.html
# Some message at the end
#
# Processed URL: http://en.wikipedia.org/wiki/Xz
#
# URL does not seem to exist: I'm no URL
# Here's the original error message:
# cannot open the connection
# Processed URL: I'm no URL
#
# Warning message:
# In file(con, "r") : cannot open file 'I'm no URL': No such file or directory
Investigating the output
length(y)
# [1] 3
head(y[[1]])
# [1] "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.01 Transitional//EN\">"
# [2] "<html><head><title>R: Functions to Manipulate Connections</title>"
# [3] "<meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\">"
# [4] "<link rel=\"stylesheet\" type=\"text/css\" href=\"R.css\">"
# [5] "</head><body>"
# [6] ""
y[[3]]
# [1] NA
Read Fault-tolerant/resilient code online: https://riptutorial.com/r/topic/4060/fault-tolerant-resilient-

code
Chapter 37: Feature Selection in R --
Removing Extraneous Features
Examples
Removing features with zero or near-zero variance
A feature that has near zero variance is a good candidate for removal.
You can manually detect numerical variance below your own threshold:
data("GermanCredit")
variances<-apply(GermanCredit, 2, var)
variances[which(variances<=0.0025)]
Or, you can use the caret package to find near zero variance. An advantage here is that is defines
near zero variance not in the numerical calculation of variance, but rather as a function of rarity:
"nearZeroVar diagnoses predictors that have one unique value (i.e. are zero variance
predictors) or predictors that are have both of the following characteristics: they have
very few unique values relative to the number of samples and the ratio of the frequency
of the most common value to the frequency of the second most common value is
large..."
library(caret)
names(GermanCredit)[nearZeroVar(GermanCredit)]
Removing features with high numbers of NA
If a feature is largely lacking data, it is a good candidate for removal:
library(VIM)
data(sleep)
colMeans(is.na(sleep))
BodyWgt BrainWgt NonD Dream Sleep Span Gest

0.00000000 0.00000000 0.22580645 0.19354839 0.06451613 0.06451613 0.06451613
Pred Exp Danger
0.00000000 0.00000000 0.00000000
In this case, we may want to remove NonD and Dream, which each have around 20% missing
values (your cutoff may vary)
Removing closely correlated features
Closely correlated features may add variance to your model, and removing one of a correlated pair
might help reduce that. There are lots of ways to detect correlation. Here's one:
library(purrr) # in order to use keep()
# select correlatable vars

toCorrelate<-mtcars %>% keep(is.numeric)
# calculate correlation matrix

correlationMatrix <- cor(toCorrelate)
# pick only one out of each highly correlated pair's mirror image
correlationMatrix[upper.tri(correlationMatrix)]<-0
# and I don't remove the highly-correlated-with-itself group

diag(correlationMatrix)<-0
# find features that are highly correlated with another feature at the +- 0.85 level
apply(correlationMatrix,2, function(x) any(abs(x)>=0.85))
mpg cyl disp hp drat wt qsec vs am gear carb

TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
I'll want to look at what MPG is correlated to so strongly, and decide what to keep and what to
toss. Same for cyl and disp. Alternatively, I might need to combine some strongly correlated
features.
Read Feature Selection in R -- Removing Extraneous Features online:

https://riptutorial.com/r/topic/7561/feature-selection-in-r----removing-extraneous-features
Chapter 38: Formula
Examples
The basics of formula
Statistical functions in R make heavy use of the so-called Wilkinson-Rogers formula notation1 .
When running model functions like lm for the Linear Regressions, they need a formula. This formula
specifies which regression coefficients shall be estimated.
my_formula1 <- formula(mpg ~ wt)

class(my_formula1)
# gives "formula"
mod1 <- lm(my_formula1, data = mtcars)

coef(mod1)
# gives (Intercept) wt
# 37.285126 -5.344472
On the left side of the ~ (LHS) the dependent variable is specified, while the right hand side (RHS)
contains the independent variables. Technically the formula call above is redundant because the
tilde-operator is an infix function that returns an object with formula class:
form <- mpg ~ wt

class(form)
#[1] "formula"
The advantage of the formula function over ~ is that it also allows an environment for evaluation to
be specified:
form_mt <- formula(mpg ~ wt, env = mtcars)
In this case, the output shows that a regression coefficient for wt is estimated, as well as (per
default) an intercept parameter. The intercept can be excluded / forced to be 0 by including 0 or -1
in the formula:
coef(lm(mpg ~ 0 + wt, data = mtcars))

coef(lm(mpg ~ wt -1, data = mtcars))
Interactions between variables a and b can added by included a:b to the formula:
coef(lm(mpg ~ wt:vs, data = mtcars))
As it is (from a statistical point of view) generally advisable not have interactions in the model
without the main effects, the naive approach would be to expand the formula to a + b + a:b. This
works but can be simplified by writing a*b, where the * operator indicates factor crossing (when
between two factor columns) or multiplication when one or both of the columns are 'numeric':
coef(lm(mpg ~ wt*vs, data = mtcars))
Using the * notation expands a term to include all lower order effects, such that:
coef(lm(mpg ~ wt*vs*hp, data = mtcars))
will give, in addition to the intercept, 7 regression coefficients. One for the three-way interaction,
three for the two-way interactions and three for the main effects.
If one wants, for example, to exclude the three-way interaction, but retain all two-way interactions
there are two shorthands. First, using - we can subtract any particular term:
coef(lm(mpg ~ wt*vs*hp - wt:vs:hp, data = mtcars))
Or, we can use the ^ notation to specify which level of interaction we require:
coef(lm(mpg ~ (wt + vs + hp) ^ 2, data = mtcars))
Those two formula specifications should create the same model matrix.
Finally, . is shorthand to use all available variables as main effects. In this case, the data argument
is used to obtain the available variables (which are not on the LHS). Therefore:
coef(lm(mpg ~ ., data = mtcars))
gives coefficients for the intercept and 10 independent variables. This notation is frequently used
in machine learning packages, where one would like to use all variables for prediction or
classification. Note that the meaning of . depends on context (see e.g. ?update.formula for a
different meaning).
1. G. N. Wilkinson and C. E. Rogers. Journal of the Royal Statistical Society. Series C (Applied
Statistics) Vol. 22, No. 3 (1973), pp. 392-399
Create Linear, Quadratic and Second Order Interaction Terms
y ~ . : Here . is interpreted as all variables except y in the data frame used in fitting the model. It
is equivalent to the linear combinations of predictor variables. For example y ~ var1 + var2 +
var3+...+var15
y ~ . ^ 2 will give all linear (main effects) and second order interaction terms of the variables in
the data frame. It is equivalent to y ~ var1 + var2 + ...+var15 + var1:var2 + var1:var3 +
var1:var4...and so on
y ~ var1 + var2 + ...+var15 + I(var1^2) + I(var2^2) + I(var3^2)...+I(var15^2) : Here I(var^2)

indicates quadratic polynomial of one variable in the data frame.
y ~ poly(var1, degree = 2) + poly(var2, degree = 2)+...poly(var15, degree = 2)
or
y ~ poly(var1, var2, var3, ....var15, degree = 2) will be equivalent to the above expression.
poly(var1, degree = 2) is equivalent to var1 + I(var1^2).
To get cubic polynomials, use degree = 3 in poly().
There is a caveat in using poly versus I(var, 2), which is after fitting the model, each of them will
produce different coefficients, but the fitted values are equivalent, because they represent different
parameterizations of the same model. It is recommended to use I(var, 2) over poly() to avoid the
summary effect seen in poly().
In summary, to get linear, quadratic and second order interaction terms, you will have an
expression like
y ~ .^2 + I(var1^2) + I(var2^2)+...I(var15^2)
Demo for four variables:
old <- reformulate( 'y ~ x1+x2+x3+x4' )

new <- reformulate( " y ~ .^2 + I(x1^2) + I(x2^2) + I(x3^2) + I(x4^2) ")
tmp <- .Call(stats:::C_updateform, old, new)
terms.formula(tmp, simplify = TRUE )
# ~y ~ x1 + x2 + x3 + x4 + I(x1^2) + I(x2^2) + I(x3^2) + I(x4^2) +

# x1:x2 + x1:x3 + x1:x4 + x2:x3 + x2:x4 + x3:x4
# attr(,"variables")
# list(~y, x1, x2, x3, x4, I(x1^2), I(x2^2), I(x3^2), I(x4^2))
# attr(,"factors")
# x1 x2 x3 x4 I(x1^2) I(x2^2) I(x3^2) I(x4^2) x1:x2 x1:x3 x1:x4 x2:x3 x2:x4 x3:x4
# ~y 0 0 0 0 0 0 0 0 0 0 0 0 0 0
# x1 1 0 0 0 0 0 0 0 1 1 1 0 0 0
# x2 0 1 0 0 0 0 0 0 1 0 0 1 1 0
# x3 0 0 1 0 0 0 0 0 0 1 0 1 0 1
# x4 0 0 0 1 0 0 0 0 0 0 1 0 1 1
# I(x1^2) 0 0 0 0 1 0 0 0 0 0 0 0 0 0
# I(x2^2) 0 0 0 0 0 1 0 0 0 0 0 0 0 0
# I(x3^2) 0 0 0 0 0 0 1 0 0 0 0 0 0 0
# I(x4^2) 0 0 0 0 0 0 0 1 0 0 0 0 0 0
# attr(,"term.labels")
# [1] "x1" "x2" "x3" "x4" "I(x1^2)" "I(x2^2)" "I(x3^2)" "I(x4^2)"
# [9] "x1:x2" "x1:x3" "x1:x4" "x2:x3" "x2:x4" "x3:x4"
# attr(,"order")
# [1] 1 1 1 1 1 1 1 1 2 2 2 2 2 2
# attr(,"intercept")
# [1] 1
# attr(,"response")
# [1] 1
# attr(,".Environment")
# <environment: R_GlobalEnv>
Read Formula online: https://riptutorial.com/r/topic/1061/formula
Chapter 39: Fourier Series and
Transformations
Remarks
The Fourier transform decomposes a function of time (a signal) into the frequencies that make it
up, similarly to how a musical chord can be expressed as the amplitude (or loudness) of its
constituent notes. The Fourier transform of a function of time itself is a complex-valued function of
frequency, whose absolute value represents the amount of that frequency present in the original
function, and whose complex argument is the phase offset of the basic sinusoid in that frequency.
The Fourier transform is called the frequency domain representation of the original signal. The
term Fourier transform refers to both the frequency domain representation and the mathematical
operation that associates the frequency domain representation to a function of time. The Fourier
transform is not limited to functions of time, but in order to have a unified language, the domain of
the original function is commonly referred to as the time domain. For many functions of practical
interest one can define an operation that reverses this: the inverse Fourier transformation, also
called Fourier synthesis, of a frequency domain representation combines the contributions of all
the different frequencies to recover the original function of time.
Linear operations performed in one domain (time or frequency) have corresponding operations in
the other domain, which are sometimes easier to perform. The operation of differentiation in the
time domain corresponds to multiplication by the frequency, so some differential equations are
easier to analyze in the frequency domain. Also, convolution in the time domain corresponds to
ordinary multiplication in the frequency domain. Concretely, this means that any linear time-
invariant system, such as an electronic filter applied to a signal, can be expressed relatively simply
as an operation on frequencies. So significant simplification is often achieved by transforming time
functions to the frequency domain, performing the desired operations, and transforming the result
back to time.
Harmonic analysis is the systematic study of the relationship between the frequency and time
domains, including the kinds of functions or operations that are "simpler" in one or the other, and
has deep connections to almost all areas of modern mathematics.
Functions that are localized in the time domain have Fourier transforms that are spread out across
the frequency domain and vice versa. The critical case is the Gaussian function, of substantial
importance in probability theory and statistics as well as in the study of physical phenomena
exhibiting normal distribution (e.g., diffusion), which with appropriate normalizations goes to itself
under the Fourier transform. Joseph Fourier introduced the transform in his study of heat transfer,
where Gaussian functions appear as solutions of the heat equation.
The Fourier transform can be formally defined as an improper Riemann integral, making it an
integral transform, although this definition is not suitable for many applications requiring a more
sophisticated integration theory.
For example, many relatively simple applications use the Dirac delta function, which can be
treated formally as if it were a function, but the justification requires a mathematically more
sophisticated viewpoint. The Fourier transform can also be generalized to functions of several
variables on Euclidean space, sending a function of 3-dimensional space to a function of 3-
dimensional momentum (or a function of space and time to a function of 4-momentum).
This idea makes the spatial Fourier transform very natural in the study of waves, as well as in
quantum mechanics, where it is important to be able to represent wave solutions either as
functions either of space or momentum and sometimes both. In general, functions to which Fourier
methods are applicable are complex-valued, and possibly vector-valued. Still further generalization
is possible to functions on groups, which, besides the original Fourier transform on ℝ or ℝn (viewed
as groups under addition), notably includes the discrete-time Fourier transform (DTFT, group = ℤ), the
discrete Fourier transform (DFT, group = ℤ mod N) and the Fourier series or circular Fourier transform
(group = S1, the unit circle ≈ closed finite interval with endpoints identified). The latter is routinely
employed to handle periodic functions. The Fast Fourier transform (FFT) is an algorithm for computing the
DFT.
Examples
Fourier Series
Joseph Fourier showed that any periodic wave can be represented by a sum of simple sine
waves. This sum is called the Fourier Series. The Fourier Series only holds while the system is
linear. If there is, eg, some overflow effect (a threshold where the output remains the same no
matter how much input is given), a non-linear effect enters the picture, breaking the sinusoidal
wave and the superposition principle.
# Sine waves
xs <- seq(-2*pi,2*pi,pi/100)
wave.1 <- sin(3*xs)
wave.2 <- sin(10*xs)
par(mfrow = c(1, 2))
plot(xs,wave.1,type="l",ylim=c(-1,1)); abline(h=0,lty=3)
plot(xs,wave.2,type="l",ylim=c(-1,1)); abline(h=0,lty=3)
# Complex Wave
wave.3 <- 0.5 * wave.1 + 0.25 * wave.2
plot(xs,wave.3,type="l"); title("Eg complex wave"); abline(h=0,lty=3)
wave.4 <- wave.3
wave.4[wave.3>0.5] <- 0.5
plot(xs,wave.4,type="l",ylim=c(-1.25,1.25))
title("overflowed, non-linear complex wave")
abline(h=0,lty=3)
Also, the Fourier Series only holds if the waves are periodic, ie, they have a repeating pattern (non
periodic waves are dealt by the Fourier Transform, see below). A periodic wave has a frequency f
and a wavelength λ (a wavelength is the distance in the medium between the beginning and end
of a cycle, λ=v/f0, where v is the wave velocity) that are defined by the repeating pattern. A non-
periodic wave does not have a frequency or wavelength.
Some concepts:
• The fundamental period, T, is the period of all the samples taken, the time between the first
sample and the last
• The sampling rate, sr, is the number of samples taken over a time period (aka acquisition
frequency). For simplicity we will make the time interval between samples equal. This time
interval is called the sample interval, si, which is the fundamental period time divided by the
number of samples N. So, si=TN
• The fundamental frequency, f0, which is 1T. The fundamental frequency is the frequency of
the repeating pattern or how long the wavelength is. In the previous waves, the fundamental
frequency was 12π. The frequencies of the wave components must be integer multiples of
the fundamental frequency. f0 is called the first harmonic, the second harmonic is 2∗f0, the
third is 3∗f0, etc.
repeat.xs <- seq(-2*pi,0,pi/100)

wave.3.repeat <- 0.5*sin(3*repeat.xs) + 0.25*sin(10*repeat.xs)
plot(xs,wave.3,type="l")
title("Repeating pattern")
points(repeat.xs,wave.3.repeat,type="l",col="red");
abline(h=0,v=c(-2*pi,0),lty=3)
Here’s a R function for plotting trajectories given a fourier series:
plot.fourier <- function(fourier.series, f.0, ts) {

w <- 2*pi*f.0 trajectory <- sapply(ts, function(t)
fourier.series(t,w))
plot(ts, trajectory, type="l", xlab="time", ylab="f(t)");
abline(h=0,lty=3)}
Read Fourier Series and Transformations online: https://riptutorial.com/r/topic/4139/fourier-series-

and-transformations
Chapter 40: Functional programming
Examples
Built-in Higher Order Functions
R has a set of built in higher order functions: Map, Reduce, Filter, Find, Position, Negate.
Map applies a given function to a list of values:
words <- list("this", "is", "an", "example")

Map(toupper, words)
Reduce successively applies a binary function to a list of values in a recursive fashion.
Reduce(`*`, 1:10)
given a predicate function and a list of values returns a filtered list containing only values for
Filter
whom predicate function is TRUE.
Filter(is.character, list(1,"a",2,"b",3,"c"))
Find given a predicate function and a list of values returns the first value for which the predicate
function is TRUE.
Find(is.character, list(1,"a",2,"b",3,"c"))
Position given a predicate function and a list of values returns the position of the first value in the
list for which the predicate function is TRUE.
Position(is.character, list(1,"a",2,"b",3,"c"))
Negate inverts a predicate function making it return FALSE for values where it returned TRUE and
vice versa.
is.noncharacter <- Negate(is.character)

is.noncharacter("a")
is.noncharacter(mean)
Read Functional programming online: https://riptutorial.com/r/topic/5050/functional-programming
Chapter 41: Generalized linear models
Examples
Logistic regression on Titanic dataset
Logistic regression is a particular case of the generalized linear model, used to model
dichotomous outcomes (probit and complementary log-log models are closely related).
The name comes from the link function used, the logit or log-odds function. The inverse function of
the logit is called the logistic function and is given by:
This function takes a value between ]-Inf;+Inf[ and returns a value between 0 and 1; i.e the logistic
function takes a linear predictor and returns a probability.
Logistic regression can be performed using the glm function with the option family = binomial
(shortcut for family = binomial(link="logit"); the logit being the default link function for the
binomial family).
In this example, we try to predict the fate of the passengers aboard the RMS Titanic.
Read the data:
url <- "http://biostat.mc.vanderbilt.edu/wiki/pub/Main/DataSets/titanic.txt"

titanic <- read.csv(file = url, stringsAsFactors = FALSE)
Clean the missing values:
In that case, we replace the missing values by an approximation, the average.
titanic$age[is.na(titanic$age)] <- mean(titanic$age, na.rm = TRUE)
Train the model:
titanic.train <- glm(survived ~ pclass + sex + age,

family = binomial, data = titanic)
Summary of the model:
summary(titanic.train)
The output:
Call:
glm(formula = survived ~ pclass + sex + age, family = binomial, data = titanic)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.6452 -0.6641 -0.3679 0.6123 2.5615
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 3.552261 0.342188 10.381 < 2e-16 ***
pclass2nd -1.170777 0.211559 -5.534 3.13e-08 ***
pclass3rd -2.430672 0.195157 -12.455 < 2e-16 ***
sexmale -2.463377 0.154587 -15.935 < 2e-16 ***
age -0.042235 0.007415 -5.696 1.23e-08 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1686.8 on 1312 degrees of freedom

Residual deviance: 1165.7 on 1308 degrees of freedom
AIC: 1175.7
Number of Fisher Scoring iterations: 5
• The first thing displayed is the call. It is a reminder of the model and the options specified.
• Next we see the deviance residuals, which are a measure of model fit. This part of output
shows the distribution of the deviance residuals for individual cases used in the model.
• The next part of the output shows the coefficients, their standard errors, the z-statistic
(sometimes called a Wald z-statistic), and the associated p-values.
○ The qualitative variables are "dummified". A modality is considered as the reference.

The reference modality can be change with I in the formula.
○ All four predictors are statistically significant at a 0.1 % level.
○ The logistic regression coefficients give the change in the log odds of the outcome for a
one unit increase in the predictor variable.
○ To see the odds ratio (multiplicative change in the odds of survival per unit increase in
a predictor variable), exponentiate the parameter.
○ To see the confidence interval (CI) of the parameter, use confint.
• Below the table of coefficients are fit indices, including the null and deviance residuals and
the Akaike Information Criterion (AIC), which can be used for comparing model performance.
○ When comparing models fitted by maximum likelihood to the same data, the smaller
the AIC, the better the fit.
○ One measure of model fit is the significance of the overall model. This test asks
whether the model with predictors fits significantly better than a model with just an
intercept (i.e., a null model).
Example of odds ratios:
exp(coef(titanic.train)[3])
pclass3rd
0.08797765
With this model, compared to the first class, the 3rd class passengers have about a tenth of the
odds of survival.
Example of confidence interval for the parameters:
confint(titanic.train)
Waiting for profiling to be done...

2.5 % 97.5 %
(Intercept) 2.89486872 4.23734280
pclass2nd -1.58986065 -0.75987230
pclass3rd -2.81987935 -2.05419500
sexmale -2.77180962 -2.16528316
age -0.05695894 -0.02786211
Exemple of calculating the significance of the overall model:
The test statistic is distributed chi-squared with degrees of freedom equal to the differences in
degrees of freedom between the current and the null model (i.e., the number of predictor variables
in the model).
with(titanic.train, pchisq(null.deviance - deviance, df.null - df.residual

, lower.tail = FALSE))
[1] 1.892539e-111
The p-value is near 0, showing a strongly significant model.
Read Generalized linear models online: https://riptutorial.com/r/topic/2892/generalized-linear-

models
Chapter 42: Get user input
Syntax
• variable <- readline(prompt = "Any message for user")
• name <- readline(prompt = "What's your name")
Examples
User input in R
Sometimes it can be interesting to have a cross-talk between the user and the program, one
example being the swirl package that had been designed to teach R in R.
One can ask for user input using the readline command:
name <- readline(prompt = "What is your name?")
The user can then give any answer, such as a number, a character, vectors, and scanning the
result is here to make sure that the user has given a proper answer. For example:
result <- readline(prompt = "What is the result of 1+1?")

while(result!=2){
readline(prompt = "Wrong answer. What is the result of 1+1?")
}
However, it is to be noted that this code be stuck in a never-ending loop, as user input is saved as
a character.
We have to coerce it to a number, using as.numeric:
result <- as.numeric(readline(prompt = "What is the result of 1+1?"))

while(result!=2){
readline(prompt = "Wrong answer. What is the result of 1+1?")
}
Read Get user input online: https://riptutorial.com/r/topic/5098/get-user-input
Chapter 43: ggplot2
Remarks
ggplot2 has its own perfect reference website http://ggplot2.tidyverse.org/.
Most of the time, it is more convenient to adapt the structure or content of the plotted data (e.g. a
data.frame) than adjusting things within the plot afterwards.
RStudio publishes a very helpful "Data Visualization with ggplot2" cheatsheet that can be found
here.
Examples
Scatter Plots
We plot a simple scatter plot using the builtin iris data set as follows:
library(ggplot2)
ggplot(iris, aes(x = Petal.Width, y = Petal.Length, color = Species)) +
geom_point()
This gives:
Displaying multiple plots
Display multiple plots in one image with the different facet functions. An advantage of this method
is that all axes share the same scale across charts, making it easy to compare them at a glance.
We'll use the mpg dataset included in ggplot2.
Wrap charts line by line (attempts to create a square layout):
ggplot(mpg, aes(x = displ, y = hwy)) +

geom_point() +
facet_wrap(~class)
Display multiple charts on one row, multiple columns:

geom_point() +
facet_grid(.~class)
Display multiple charts on one column, multiple rows:

geom_point() +
facet_grid(class~.)
Display multiple charts in a grid by 2 variables:

geom_point() +
facet_grid(trans~class) #"row" parameter, then "column" parameter
Prepare your data for plotting
ggplot2works best with a long data frame. The following sample data which represents the prices
for sweets on 20 different days, in a format described as wide, because each category has a
column.
set.seed(47)
sweetsWide <- data.frame(date = 1:20,
chocolate = runif(20, min = 2, max = 4),
iceCream = runif(20, min = 0.5, max = 1),
candy = runif(20, min = 1, max = 3))
head(sweetsWide)
## date chocolate iceCream candy
## 1 1 3.953924 0.5890727 1.117311
## 2 2 2.747832 0.7783982 1.740851
## 3 3 3.523004 0.7578975 2.196754
## 4 4 3.644983 0.5667152 2.875028
## 5 5 3.147089 0.8446417 1.733543
## 6 6 3.382825 0.6900125 1.405674
To convert sweetsWide to long format for use with ggplot2, several useful functions from base R,
and the packages reshape2, data.table and tidyr (in chronological order) can be used:
# reshape from base R

sweetsLong <- reshape(sweetsWide, idvar = 'date', direction = 'long',
varying = list(2:4), new.row.names = NULL, times = names(sweetsWide)[-
1])
# melt from 'reshape2'

library(reshape2)
sweetsLong <- melt(sweetsWide, id.vars = 'date')
# melt from 'data.table'

# which is an optimized & extended version of 'melt' from 'reshape2'
library(data.table)
sweetsLong <- melt(setDT(sweetsWide), id.vars = 'date')
# gather from 'tidyr'

library(tidyr)
sweetsLong <- gather(sweetsWide, sweet, price, chocolate:candy)
The all give a similar result:
head(sweetsLong)
## date sweet price
## 1 1 chocolate 3.953924
## 2 2 chocolate 2.747832
## 3 3 chocolate 3.523004
## 4 4 chocolate 3.644983
## 5 5 chocolate 3.147089
## 6 6 chocolate 3.382825
See also Reshaping data between long and wide forms for details on converting data between
long and wide format.
The resulting sweetsLong has one column of prices and one column describing the type of sweet.
Now plotting is much simpler:
library(ggplot2)
ggplot(sweetsLong, aes(x = date, y = price, colour = sweet)) + geom_line()
function, trying to always plot out your data without requiring too much specifications.
basic qplot
qplot(x = disp, y = mpg, data = mtcars)
adding colors
qplot(x = disp, y = mpg, colour = cyl,data = mtcars)
adding a smoother
qplot(x = disp, y = mpg, geom = c("point", "smooth"), data = mtcars)
Read ggplot2 online: https://riptutorial.com/r/topic/1334/ggplot2
Chapter 44: GPU-accelerated computing
Remarks
GPU computing requires a 'platform' which can connect to and utilize the hardware. The two
primary low-level languages that accomplish this are CUDA and OpenCL. The former requires
installation of the proprietary NVIDIA CUDA Toolkit and is only applicable on NVIDIA GPUs. The
latter is both company (e.g. NVIDIA, AMD, Intel) and hardware independent (CPU or GPU) but
requires the installation of an SDK (software development kit). In order to use a GPU via R you will
need to install one of these pieces of software first.
Once either the CUDA Toolkit or a OpenCL SDK is installed, you can install an appropriate R
package. Almost all the R GPU packages are dependent upon CUDA and limited to NVIDIA
GPUs. These include:
1. gputools
2. cudaBayesreg
3. HiPLARM
4. gmatrix
There are currently only two OpenCL enabled packages
1. OpenCL - interface from R to OpenCL

2. gpuR - general purpose library
Warning - installation can be difficult for different operating systems with different environmental
variables and GPU platforms.
Examples
gpuR gpuMatrix objects
library(gpuR)
# gpuMatrix objects
X <- gpuMatrix(rnorm(100), 10, 10)
Y <- gpuMatrix(rnorm(100), 10, 10)
# transfer data to GPU when operation called

# automatically copied back to CPU
Z <- X %*% Y
gpuR vclMatrix objects
library(gpuR)
# vclMatrix objects
X <- vclMatrix(rnorm(100), 10, 10)
Y <- vclMatrix(rnorm(100), 10, 10)
# data always on GPU

# no data transfer
Z <- X %*% Y
Read GPU-accelerated computing online: https://riptutorial.com/r/topic/4680/gpu-accelerated-

computing
Chapter 45: Hashmaps
Examples
Environments as hash maps
Note: in the subsequent passages, the terms hash map and hash table are used interchangeably
and refer to the same concept, namely, a data structure providing efficient key lookup through use
of an internal hash function.
Introduction
Although R does not provide a native hash table structure, similar functionality can be achieved by
leveraging the fact that the environment object returned from new.env (by default) provides hashed
key lookups. The following two statements are equivalent, as the hash parameter defaults to TRUE:
H <- new.env(hash = TRUE)

H <- new.env()
Additionally, one may specify that the internal hash table is pre-allocated with a particular size via
the size parameter, which has a default value of 29. Like all other R objects, environments manage
their own memory and will grow in capacity as needed, so while it is not necessary to request a
non-default value for size, there may be a slight performance advantage in doing so if the object
will (eventually) contain a very large number of elements. It is worth noting that allocating extra
space via size does not, in itself, result in an object with a larger memory footprint:
object.size(new.env())
# 56 bytes
object.size(new.env(size = 10e4))
# 56 bytes
Insertion
Insertion of elements may be done using either of the [[<- or $<- methods provided for the
environment class, but not by using "single bracket" assignment ([<-):
H <- new.env()
H[["key"]] <- rnorm(1)
key2 <- "xyz"

H[[key2]] <- data.frame(x = 1:3, y = letters[1:3])
H$another_key <- matrix(rbinom(9, 1, 0.5) > 0, nrow = 3)
H["error"] <- 42
#Error in H["error"] <- 42 :
# object of type 'environment' is not subsettable
Like other facets of R, the first method (object[[key]] <- value) is generally preferred to the
second (object$key <- value) because in the former case, a variable maybe be used instead of a
literal value (e.g key2 in the example above).
As is generally the case with hash map implementations, the environment object will not store
duplicate keys. Attempting to insert a key-value pair for an existing key will replace the previously
stored value:
H[["key3"]] <- "original value"
H[["key3"]] <- "new value"
H[["key3"]]
#[1] "new value"
Key Lookup
Likewise, elements may be accessed with [[ or $, but not with [:
H[["key"]]
#[1] 1.630631
H[[key2]] ## assuming key2 <- "xyz"

# x y
# 1 1 a
# 2 2 b
# 3 3 c
H$another_key
# [,1] [,2] [,3]
# [1,] TRUE TRUE TRUE
# [2,] FALSE FALSE FALSE
# [3,] TRUE TRUE TRUE
H[1]
#Error in H[1] : object of type 'environment' is not subsettable
Inspecting the Hash Map

Being just an ordinary environment, the hash map can be inspected by typical means:
names(H)
#[1] "another_key" "xyz" "key" "key3"
ls(H)
#[1] "another_key" "key" "key3" "xyz"
str(H)
#<environment: 0x7828228>
ls.str(H)
# another_key : logi [1:3, 1:3] TRUE FALSE TRUE TRUE FALSE TRUE ...
# key : num 1.63
# key3 : chr "new value"
# xyz : 'data.frame': 3 obs. of 2 variables:
# $ x: int 1 2 3
# $ y: chr "a" "b" "c"
Elements can be removed using rm:
rm(list = c("key", "key3"), envir = H)
ls.str(H)
# another_key : logi [1:3, 1:3] TRUE FALSE TRUE TRUE FALSE TRUE ...
# xyz : 'data.frame': 3 obs. of 2 variables:
# $ x: int 1 2 3
# $ y: chr "a" "b" "c"
Flexibility
One of the major benefits of using environment objects as hash tables is their ability to store
virtually any type of object as a value, even other environments:
H2 <- new.env()
H2[["a"]] <- LETTERS

H2[["b"]] <- as.list(x = 1:5, y = matrix(rnorm(10), 2))
H2[["c"]] <- head(mtcars, 3)
H2[["d"]] <- Sys.Date()
H2[["e"]] <- Sys.time()
H2[["f"]] <- (function() {
H3 <- new.env()
for (i in seq_along(names(H2))) {
H3[[names(H2)[i]]] <- H2[[names(H2)[i]]]
}
H3
})()
ls.str(H2)
# a : chr [1:26] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" ...
# b : List of 5
# $ : int 1
# $ : int 2
# $ : int 3
# $ : int 4
# $ : int 5
# c : 'data.frame': 3 obs. of 11 variables:
# $ mpg : num 21 21 22.8
# $ cyl : num 6 6 4
# $ disp: num 160 160 108
# $ hp : num 110 110 93
# $ drat: num 3.9 3.9 3.85
# $ wt : num 2.62 2.88 2.32
# $ qsec: num 16.5 17 18.6
# $ vs : num 0 0 1
# $ am : num 1 1 1
# $ gear: num 4 4 4
# $ carb: num 4 4 1
# d : Date[1:1], format: "2016-08-03"
# e : POSIXct[1:1], format: "2016-08-03 19:25:14"
# f : <environment: 0x91a7cb8>
ls.str(H2$f)
# a : chr [1:26] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" ...
# b : List of 5
# $ : int 1
# $ : int 2
# $ : int 3
# $ : int 4
# $ : int 5
# c : 'data.frame': 3 obs. of 11 variables:
# $ mpg : num 21 21 22.8
# $ cyl : num 6 6 4
# $ disp: num 160 160 108
# $ hp : num 110 110 93
# $ drat: num 3.9 3.9 3.85
# $ wt : num 2.62 2.88 2.32
# $ qsec: num 16.5 17 18.6
# $ vs : num 0 0 1
# $ am : num 1 1 1
# $ gear: num 4 4 4
# $ carb: num 4 4 1
# d : Date[1:1], format: "2016-08-03"
# e : POSIXct[1:1], format: "2016-08-03 19:25:14"
Limitations
One of the major limitations of using environment objects as hash maps is that, unlike many
aspects of R, vectorization is not supported for element lookup / insertion:
names(H2)
#[1] "a" "b" "c" "d" "e" "f"
H2[[c("a", "b")]]
#Error in H2[[c("a", "b")]] :
# wrong arguments for subsetting an environment
Keys <- c("a", "b")

H2[[Keys]]
#Error in H2[[Keys]] : wrong arguments for subsetting an environment
Depending on the nature of the data being stored in the object, it may be possible to use vapply or
list2env for assigning many elements at once:
E1 <- new.env()
invisible({
vapply(letters, function(x) {
E1[[x]] <- rnorm(1)
logical(0)
}, FUN.VALUE = logical(0))
})
all.equal(sort(names(E1)), letters)
#[1] TRUE
Keys <- letters

E2 <- list2env(
setNames(
as.list(rnorm(26)),
nm = Keys),
envir = NULL,
hash = TRUE
)
all.equal(sort(names(E2)), letters)
#[1] TRUE
Neither of the above are particularly concise, but may be preferable to using a for loop, etc. when
the number of key-value pairs is large.
package:hash
The hash package offers a hash structure in R. However, it terms of timing for both inserts and
reads it compares unfavorably to using environments as a hash. This documentation simply
acknowledges its existence and provides sample timing code below for the above stated reasons.
There is no identified case where hash is an appropriate solution in R code today.
Consider:
# Generic unique string generator

unique_strings <- function(n){
string_i <- 1
string_len <- 1
ans <- character(n)
chars <- c(letters,LETTERS)
new_strings <- function(len,pfx){
for(i in 1:length(chars)){
if (len == 1){
ans[string_i] <<- paste(pfx,chars[i],sep='')
string_i <<- string_i + 1
} else {
new_strings(len-1,pfx=paste(pfx,chars[i],sep=''))
}
if (string_i > n) return ()
}
}
while(string_i <= n){
new_strings(string_len,'')
string_len <- string_len + 1
}
sample(ans)
}
# Generate timings using an enviornment

timingsEnv <- plyr::adply(2^(10:15),.mar=1,.fun=function(i){
strings <- unique_strings(i)
ht1 <- new.env(hash=TRUE)
lapply(strings, function(s){ ht1[[s]] <<- 0L})
data.frame(
size=c(i,i),
seconds=c(
system.time(for (j in 1:i) ht1[[strings[j]]]==0L)[3]),
type = c('1_hashedEnv')
)
})
timingsHash <- plyr::adply(2^(10:15),.mar=1,.fun=function(i){

ht <- hash::hash()
lapply(strings, function(s) ht[[s]] <<- 0L)
data.frame(
size=c(i,i),
seconds=c(
system.time(for (j in 1:i) ht[[strings[j]]]==0L)[3]),
type = c('3_stringHash')
)
})
package:listenv
Although package:listenv implements a list-like interface to environments, its performance relative

to environments for hash-like purposes is poor on hash retrieval. However, if the indexes are
numeric, it can be quite fast on retrieval. However, they have other advantages, e.g. compatibility
with package:future. Covering this package for that purpose goes beyond the scope of the current
topic. However, the timing code provided here can be used in conjunction with the example for
package:hash for write timings.
timingsListEnv <- plyr::adply(2^(10:15),.mar=1,.fun=function(i){

le <- listenv::listenv()
lapply(strings, function(s) le[[s]] <<- 0L)
data.frame(
size=c(i,i),
seconds=c(
system.time(for (k in 1:i) le[[k]]==0L)[3]),
type = c('2_numericListEnv')
)
})
Read Hashmaps online: https://riptutorial.com/r/topic/5179/hashmaps
Chapter 46: heatmap and heatmap.2
Examples
Examples from the official documentation
stats::heatmap
Example 1 (Basic usage)
require(graphics); require(grDevices)
x <- as.matrix(mtcars)
rc <- rainbow(nrow(x), start = 0, end = .3)
cc <- rainbow(ncol(x), start = 0, end = .3)
hv <- heatmap(x, col = cm.colors(256), scale = "column",
RowSideColors = rc, ColSideColors = cc, margins = c(5,10),
xlab = "specification variables", ylab = "Car Models",
main = "heatmap(<Mtcars data>, ..., scale = \"column\")")
utils::str(hv) # the two re-ordering index vectors

# List of 4
# $ rowInd: int [1:32] 31 17 16 15 5 25 29 24 7 6 ...
# $ colInd: int [1:11] 2 9 8 11 6 5 10 7 1 4 ...
# $ Rowv : NULL
# $ Colv : NULL
Example 2 (no column dendrogram (nor reordering) at all)
heatmap(x, Colv = NA, col = cm.colors(256), scale = "column",

RowSideColors = rc, margins = c(5,10),
xlab = "specification variables", ylab = "Car Models",
main = "heatmap(<Mtcars data>, ..., scale = \"column\")")
Example 3 ("no nothing")
heatmap(x, Rowv = NA, Colv = NA, scale = "column",

main = "heatmap(*, NA, NA) ~= image(t(x))")
Example 4 (with reorder())
round(Ca <- cor(attitude), 2)

# rating complaints privileges learning raises critical advance
# rating 1.00 0.83 0.43 0.62 0.59 0.16 0.16
# complaints 0.83 1.00 0.56 0.60 0.67 0.19 0.22
# privileges 0.43 0.56 1.00 0.49 0.45 0.15 0.34
# learning 0.62 0.60 0.49 1.00 0.64 0.12 0.53
# raises 0.59 0.67 0.45 0.64 1.00 0.38 0.57
# critical 0.16 0.19 0.15 0.12 0.38 1.00 0.28
# advance 0.16 0.22 0.34 0.53 0.57 0.28 1.00
symnum(Ca) # simple graphic
# rt cm p l rs cr a
# rating 1
# complaints + 1
# privileges . . 1
# learning , . . 1
# raises . , . , 1
# critical . 1
# advance . . . 1
# attr(,"legend")
# [1] 0 ‘ ’ 0.3 ‘.’ 0.6 ‘,’ 0.8 ‘+’ 0.9 ‘*’ 0.95 ‘B’ 1
heatmap(Ca, symm = TRUE, margins = c(6,6))
Example 5 (NO reorder())
heatmap(Ca, Rowv = FALSE, symm = TRUE, margins = c(6,6))
Example 6 (slightly artificial with color bar, without ordering)
cc <- rainbow(nrow(Ca))
heatmap(Ca, Rowv = FALSE, symm = TRUE, RowSideColors = cc, ColSideColors = cc,
margins = c(6,6))
Example 7 (slightly artificial with color bar, with ordering)
heatmap(Ca, symm = TRUE, RowSideColors = cc, ColSideColors = cc,

margins = c(6,6))
Example 8 (For variable clustering, rather use distance
based on cor())
symnum( cU <- cor(USJudgeRatings) )

# CO I DM DI CF DE PR F O W PH R
# CONT 1
# INTG 1
# DMNR B 1
# DILG + + 1
# CFMG + + B 1
# DECI + + B B 1
# PREP + + B B B 1
# FAMI + + B * * B 1
# ORAL * * B B * B B 1
# WRIT * + B * * B B B 1
# PHYS , , + + + + + + + 1
# RTEN * * * * * B * B B * 1
# attr(,"legend")
# [1] 0 ‘ ’ 0.3 ‘.’ 0.6 ‘,’ 0.8 ‘+’ 0.9 ‘*’ 0.95 ‘B’ 1
hU <- heatmap(cU, Rowv = FALSE, symm = TRUE, col = topo.colors(16),

distfun = function(c) as.dist(1 - c), keep.dendro = TRUE)
## The Correlation matrix with same reordering:
round(100 * cU[hU[[1]], hU[[2]]])
# CONT INTG DMNR PHYS DILG CFMG DECI RTEN ORAL WRIT PREP FAMI
# CONT 100 -13 -15 5 1 14 9 -3 -1 -4 1 -3
# INTG -13 100 96 74 87 81 80 94 91 91 88 87
# DMNR -15 96 100 79 84 81 80 94 91 89 86 84
# PHYS 5 74 79 100 81 88 87 91 89 86 85 84
# DILG 1 87 84 81 100 96 96 93 95 96 98 96
# CFMG 14 81 81 88 96 100 98 93 95 94 96 94
# DECI 9 80 80 87 96 98 100 92 95 95 96 94
# RTEN -3 94 94 91 93 93 92 100 98 97 95 94
# ORAL -1 91 91 89 95 95 95 98 100 99 98 98
# WRIT -4 91 89 86 96 94 95 97 99 100 99 99
# PREP 1 88 86 85 98 96 96 95 98 99 100 99
# FAMI -3 87 84 84 96 94 94 94 98 99 99 100
## The column dendrogram:

utils::str(hU$Colv)
# --[dendrogram w/ 2 branches and 12 members at h = 1.15]
# |--leaf "CONT"
# `--[dendrogram w/ 2 branches and 11 members at h = 0.258]
# |--[dendrogram w/ 2 branches and 2 members at h = 0.0354]
# | |--leaf "INTG"
# | `--leaf "DMNR"
# |--leaf "PHYS"
# | |--leaf "DILG"
# | `--[dendrogram w/ 2 branches and 2 members at h = 0.0189]
# | |--leaf "CFMG"
# | `--leaf "DECI"
# |--leaf "RTEN"
# | |--leaf "ORAL"
# | `--leaf "WRIT"
# |--leaf "PREP"
# `--leaf "FAMI"
Tuning parameters in heatmap.2
Given:
x <- as.matrix(mtcars)
One can use heatmap.2 - a more recent optimized version of heatmap, by loading the following
library:
require(gplots)
heatmap.2(x)
To add a title, x- or y-label to your heatmap, you need to set the main, xlab and ylab:
heatmap.2(x, main = "My main title: Overview of car features", xlab="Car features", ylab =
"Car brands")
If you wish to define your own color palette for your heatmap, you can set the col parameter by
using the colorRampPalette function:
heatmap.2(x, trace="none", key=TRUE, Colv=FALSE,dendrogram = "row",col =

colorRampPalette(c("darkblue","white","darkred"))(100))
As you can notice, the labels on the y axis (the car names) don't fit in the figure. In order to fix this,
the user can tune the margins parameter:
heatmap.2(x, trace="none", key=TRUE,col =

colorRampPalette(c("darkblue","white","darkred"))(100), margins=c(5,8))
Further, we can change the dimensions of each section of our heatmap (the key histogram, the
dendograms and the heatmap itself), by tuning lhei and lwid :
If we only want to show a row(or column) dendogram, we need to set Colv=FALSE (or Rowv=FALSE)
and adjust the dendogram parameter:
heatmap.2(x, trace="none", key=TRUE, Colv=FALSE, dendrogram = "row", col =

colorRampPalette(c("darkblue","white","darkred"))(100), margins=c(5,8), lwid = c(5,15), lhei =
c(3,15))
For changing the font size of the legend title,labels and axis, the user needs to set cex.main,
cex.lab, cex.axis in the par list:
par(cex.main=1, cex.lab=0.7, cex.axis=0.7)

heatmap.2(x, trace="none", key=TRUE, Colv=FALSE, dendrogram = "row", col =
colorRampPalette(c("darkblue","white","darkred"))(100), margins=c(5,8), lwid = c(5,15), lhei =
c(5,15))
Read heatmap and heatmap.2 online: https://riptutorial.com/r/topic/4814/heatmap-and-heatmap-2
Chapter 47: Hierarchical clustering with
hclust
Introduction
The stats package provides the hclust function to perform hierarchical clustering.
Remarks
Besides hclust, other methods are available, see the CRAN Package View on Clustering.
Examples
Example 1 - Basic use of hclust, display of dendrogram, plot clusters
The cluster library contains the ruspini data - a standard set of data for illustrating cluster analysis.
library(cluster) ## to get the ruspini data

plot(ruspini, asp=1, pch=20) ## take a look at the data
hclust expects a distance matrix, not the original data. We compute the tree using the default
parameters and display it. The hang parameter lines up all of the leaves of the tree along the
baseline.
ruspini_hc_defaults <- hclust(dist(ruspini))

dend <- as.dendrogram(ruspini_hc_defaults)
if(!require(dendextend)) install.packages("dendextend"); library(dendextend)
dend <- color_branches(dend, k = 4)
plot(dend)
Cut the tree to give four clusters and replot the data coloring the points by cluster. k is the desired
number of clusters.
rhc_def_4 = cutree(ruspini_hc_defaults,k=4)
plot(ruspini, pch=20, asp=1, col=rhc_def_4)
This clustering is a little odd. We can get a better clustering by scaling the data first.
scaled_ruspini_hc_defaults = hclust(dist(scale(ruspini)))
srhc_def_4 = cutree(scaled_ruspini_hc_defaults,4)
plot(ruspini, pch=20, asp=1, col=srhc_def_4)
The default dissimilarity measure for comparing clusters is "complete". You can specify a different
measure with the method parameter.
ruspini_hc_single = hclust(dist(ruspini), method="single")
Example 2 - hclust and outliers
With hierarchical clustering, outliers often show up as one-point clusters.
Generate three Gaussian distributions to illustrate the effect of outliers.
set.seed(656)
x = c(rnorm(150, 0, 1), rnorm(150,9,1), rnorm(150,4.5,1))
y = c(rnorm(150, 0, 1), rnorm(150,0,1), rnorm(150,5,1))
XYdf = data.frame(x,y)
plot(XYdf, pch=20)
Build the cluster structure, split it into three cluster.
XY_sing = hclust(dist(XYdf), method="single")

XYs3 = cutree(XY_sing,k=3)
table(XYs3)
XYs3
1 2 3
448 1 1
hclust found two outliers and put everything else into one big cluster. To get the "real" clusters,
you may need to set k higher.
XYs6 = cutree(XY_sing,k=6)
table(XYs6)
XYs6
1 2 3 4 5 6
148 150 1 149 1 1
plot(XYdf, pch=20, col=XYs6)
This StackOverflow post has some guidance on how to pick the number of clusters, but be aware
of this behavior in hierarchical clustering.
Read Hierarchical clustering with hclust online: https://riptutorial.com/r/topic/8084/hierarchical-

clustering-with-hclust
Chapter 48: Hierarchical Linear Modeling
Examples
basic model fitting
apologies: since I don't know of a channel for discussing/providing feedback on requests for
improvement, I'm going to put my question here. Please feel free to point out a better place for
this! @DataTx states that this is "completely unclear, incomplete, or has severe formatting
problems". Since I don't see any big formatting problems (:-) ), a little bit more guidance about
what's expected here for improving clarity or completeness, and why what's here is
unsalvageable, would be useful.
The primary packages for fitting hierarchical (alternatively "mixed" or "multilevel") linear models in
R are nlme (older) and lme4 (newer). These packages differ in many minor ways but should
generally result in very similar fitted models.
library(nlme)
library(lme4)
m1.nlme <- lme(Reaction~Days,random=~Days|Subject,data=sleepstudy,method="REML")
m1.lme4 <- lmer(Reaction~Days+(Days|Subject),data=sleepstudy,REML=TRUE)
all.equal(fixef(m1.nlme),fixef(m1.lme4))
## [1] TRUE
Differences to consider:
• formula syntax is slightly different

• nlme is (still) somewhat better documented (e.g. Pinheiro and Bates 2000 Mixed-effects
models in S-PLUS; however, see Bates et al. 2015 Journal of Statistical Software/
vignette("lmer",package="lme4") for lme4)
• lme4 is faster and allows easier fitting of crossed random effects
• nlme provides p-values for linear mixed models out of the box, lme4 requires add-on packages
such as lmerTest or afex
• nlme allows modeling of heteroscedasticity or residual correlations (in space/time/phylogeny)
The unofficial GLMM FAQ provides more information, although it is focused on generalized linear
mixed models (GLMMs).
Read Hierarchical Linear Modeling online: https://riptutorial.com/r/topic/3460/hierarchical-linear-

modeling
Chapter 49: I/O for database tables
Remarks
• RMySQL
• RODBC
Examples
Reading Data from MySQL Databases
General
Using the package RMySQL we can easily query MySQL as well as MariaDB databases and store
the result in an R dataframe:
library(RMySQL)
mydb <- dbConnect(MySQL(), user='user', password='password', dbname='dbname',host='127.0.0.1')
queryString <- "SELECT * FROM table1 t1 JOIN table2 t2 on t1.id=t2.id"

query <- dbSendQuery(mydb, queryString)
data <- fetch(query, n=-1) # n=-1 to return all results
Using limits
It is also possible to define a limit, e.g. getting only the first 100,000 rows. In order to do so, just
change the SQL query regarding the desired limit. The mentioned package will consider these
options. Example:
queryString <- "SELECT * FROM table1 limit 100000"
Reading Data from MongoDB Databases
In order to load data from a MongoDB database into an R dataframe, use the library MongoLite:
# Use MongoLite library:

#install.packages("mongolite")
library(jsonlite)
library(mongolite)
# Connect to the database and the desired collection as root:
db <- mongo(collection = "Tweets", db = "TweetCollector", url =
"mongodb://USERNAME:PASSWORD@HOSTNAME")
# Read the desired documents i.e. Tweets inside one dataframe:

documents <- db$find(limit = 100000, skip = 0, fields = '{ "_id" : false, "Text" : true }')
The code connects to the server HOSTNAME as USERNAME with PASSWORD, tries to open the database
TweetCollector and read the collection Tweets. The query tries to read the field i.e. column Text.
The results is a dataframe with columns as the yielded data set. In case of this example, the
dataframe contains the column Text, e.g. documents$Text.
Read I/O for database tables online: https://riptutorial.com/r/topic/5537/i-o-for-database-tables
Chapter 50: I/O for foreign tables (Excel, SAS,
SPSS, Stata)
Examples
Importing data with rio
A very simple way to import data from many common file formats is with rio. This package
provides a function import() that wraps many commonly used data import functions, thereby
providing a standard interface. It works simply by passing a file name or URL to import():
import("example.csv") # comma-separated values

import("example.tsv") # tab-separated values
import("example.dta") # Stata
import("example.sav") # SPSS
import("example.sas7bdat") # SAS
import("example.xlsx") # Excel
can also read from compressed directories, URLs (HTTP or HTTPS), and the clipboard. A
import()
comprehensive list of all supported file formats is available on the rio package github repository.
It is even possible to specify some further parameters related to the specific file format you are
trying to read, passing them directly within the import() function:
import("example.csv", format = ",") #for csv file where comma is used as separator
import("example.csv", format = ";") #for csv file where semicolon is used as separator
Importing Excel files
There are several R packages to read excel files, each of which using different languages or
resources, as summarized in the following table:
R package Uses
xlsx Java
XLconnect Java
openxlsx C++
readxl C++
RODBC ODBC
gdata Perl
For the packages that use Java or ODBC it is important to know details about your system
because you may have compatibility issues depending on your R version and OS. For instance, if
you are using R 64 bits then you also must have Java 64 bits to use xlsx or XLconnect.
Some examples of reading excel files with each package are provided below. Note that many of
the packages have the same or very similar function names. Therefore, it is useful to state the
package explicitly, like package::function. The package openxlsx requires prior installation of
RTools.
Reading excel files with the xlsx package

library(xlsx)
The index or name of the sheet is required to import.
xlsx::read.xlsx("Book1.xlsx", sheetIndex=1)
xlsx::read.xlsx("Book1.xlsx", sheetName="Sheet1")
Reading Excel files with the XLconnect

package
library(XLConnect)
wb <- XLConnect::loadWorkbook("Book1.xlsx")
# Either, if Book1.xlsx has a sheet called "Sheet1":

sheet1 <- XLConnect::readWorksheet(wb, "Sheet1")
# Or, more generally, just get the first sheet in Book1.xlsx:
sheet1 <- XLConnect::readWorksheet(wb, getSheets(wb)[1])
XLConnectautomatically imports the pre-defined Excel cell-styles embedded in Book1.xlsx. This is

useful when you wish to format your workbook object and export a perfectly formatted Excel
document. Firstly, you will need to create the desired cell formats in Book1.xlsx and save them, for
example, as myHeader, myBody and myPcts. Then, after loading the workbook in R (see above):
Headerstyle <- XLConnect::getCellStyle(wb, "myHeader")

Bodystyle <- XLConnect::getCellStyle(wb, "myBody")
Pctsstyle <- XLConnect::getCellStyle(wb, "myPcts")
The cell styles are now saved in your R environment. In order to assign the cell styles to certain
ranges of your data, you need to define the range and then assign the style:
Headerrange <- expand.grid(row = 1, col = 1:8)

Bodyrange <- expand.grid(row = 2:6, col = c(1:5, 8))
Pctrange <- expand.grid(row = 2:6, col = c(6, 7))
XLConnect::setCellStyle(wb, sheet = "sheet1", row = Headerrange$row,
col = Headerrange$col, cellstyle = Headerstyle)
XLConnect::setCellStyle(wb, sheet = "sheet1", row = Bodyrange$row,
col = Bodyrange$col, cellstyle = Bodystyle)
XLConnect::setCellStyle(wb, sheet = "sheet1", row = Pctrange$row,
col = Pctrange$col, cellstyle = Pctsstyle)
Note that XLConnect is easy, but can become extremely slow in formatting. A much faster, but more
cumbersome formatting option is offered by openxlsx.
Reading excel files with the openxlsx

package
Excel files can be imported with package openxlsx
library(openxlsx)
openxlsx::read.xlsx("spreadsheet1.xlsx", colNames=TRUE, rowNames=TRUE)
#colNames: If TRUE, the first row of data will be used as column names.
#rowNames: If TRUE, first column of data will be used as row names.
The sheet, which should be read into R can be selected either by providing its position in the sheet
argument:
openxlsx::read.xlsx("spreadsheet1.xlsx", sheet = 1)
or by declaring its name:
openxlsx::read.xlsx("spreadsheet1.xlsx", sheet = "Sheet1")
Additionally, openxlsx can detect date columns in a read sheet. In order to allow automatic
detection of dates, an argument detectDates should be set to TRUE:
openxlsx::read.xlsx("spreadsheet1.xlsx", sheet = "Sheet1", detectDates= TRUE)
Reading excel files with the readxl package

Excel files can be imported as a data frame into R using the readxl package.
library(readxl)
It can read both .xls and .xlsx files.
readxl::read_excel("spreadsheet1.xls")
readxl::read_excel("spreadsheet2.xlsx")
The sheet to be imported can be specified by number or name.
readxl::read_excel("spreadsheet.xls", sheet = 1)
readxl::read_excel("spreadsheet.xls", sheet = "summary")
The argument col_names = TRUE sets the first row as the column names.
readxl::read_excel("spreadsheet.xls", sheet = 1, col_names = TRUE)
The argument col_types can be used to specify the column types in the data as a vector.
readxl::read_excel("spreadsheet.xls", sheet = 1, col_names = TRUE,

col_types = c("text", "date", "numeric", "numeric"))
Reading excel files with the RODBC package

Excel files can be read using the ODBC Excel Driver that interfaces with Windows' Access
Database Engine (ACE), formerly JET. With the RODBC package, R can connect to this driver
and directly query workbooks. Worksheets are assumed to maintain column headers in first row
with data in organized columns of similar types. NOTE: This approach is limited to only
Windows/PC machines as JET/ACE are installed .dll files and not available on other operating
systems.
library(RODBC)
xlconn <- odbcDriverConnect('Driver={Microsoft Excel Driver (*.xls, *.xlsx, *.xlsm, *.xlsb)};

DBQ=C:\\Path\\To\\Workbook.xlsx')
df <- sqlQuery(xlconn, "SELECT * FROM [SheetName$]")

close(xlconn)
Connecting with an SQL engine in this approach, Excel worksheets can be queried similar to
database tables including JOIN and UNION operations. Syntax follows the JET/ACE SQL dialect.
NOTE: Only data access DML statements, specifically SELECT can be run on workbooks,
considered not updateable queries.
joindf <- sqlQuery(xlconn, "SELECT t1.*, t2.* FROM [Sheet1$] t1

INNER JOIN [Sheet2$] t2
ON t1.[ID] = t2.[ID]")
uniondf <- sqlQuery(xlconn, "SELECT * FROM [Sheet1$]

UNION
SELECT * FROM [Sheet2$]")
Even other workbooks can be queried from the same ODBC channel pointing to a current
workbook:
otherwkbkdf <- sqlQuery(xlconn, "SELECT * FROM
[Excel 12.0 Xml;HDR=Yes;
Database=C:\\Path\\To\\Other\\Workbook.xlsx].[Sheet1$];")
Reading excel files with the gdata package

example here
Read and write Stata, SPSS and SAS files
The packages foreign and haven can be used to import and export files from a variety of other
statistical packages like Stata, SPSS and SAS and related software. There is a read function for
each of the supported data types to import the files.
# loading the packages

library(foreign)
library(haven)
library(readstata13)
library(Hmisc)
Some examples for the most common data types:
# reading Stata files with `foreign`

read.dta("path\to\your\data")
# reading Stata files with `haven`
read_dta("path\to\your\data")
The foreign package can read in stata (.dta) files for versions of Stata 7-12. According to the
development page, the read.dta is more or less frozen and will not be updated for reading in
versions 13+. For more recent versions of Stata, you can use either the readstata13 package or
haven. For readstata13, the files are
# reading recent Stata (13+) files with `readstata13`

read.dta13("path\to\your\data")
For reading in SPSS and SAS files
# reading SPSS files with `foreign`

read.spss("path\to\your\data.sav", to.data.frame = TRUE)
# reading SPSS files with `haven`
read_spss("path\to\your\data.sav")
read_sav("path\to\your\data.sav")
read_por("path\to\your\data.por")
# reading SAS files with `foreign`

read.ssd("path\to\your\data")
# reading SAS files with `haven`
read_sas("path\to\your\data")
# reading native SAS files with `Hmisc`
sas.get("path\to\your\data") #requires access to saslib
# Reading SA XPORT format ( *.XPT ) files
sasxport.get("path\to\your\data.xpt") # does not require access to SAS executable
The SAScii package provides functions that will accept SAS SET import code and construct a text
file that can be processed with read.fwf. It has proved very robust for import of large public-
released datasets. Support is at https://github.com/ajdamico/SAScii
To export data frames to other statistical packages you can use the write functions write.foreign()
. This will write 2 files, one containing the data and one containing instructions the other package
needs to read the data.
# writing to Stata, SPSS or SAS files with `foreign`

write.foreign(dataframe, datafile, codefile,
package = c("SPSS", "Stata", "SAS"), ...)
write.foreign(dataframe, "path\to\data\file", "path\to\instruction\file", package = "Stata")
# writing to Stata files with `foreign`

write.dta(dataframe, "file", version = 7L,
convert.dates = TRUE, tz = "GMT",
convert.factors = c("labels", "string", "numeric", "codes"))
# writing to Stata files with `haven`

write_dta(dataframe, "path\to\your\data")
# writing to Stata files with `readstata13`

save.dta13(dataframe, file, data.label = NULL, time.stamp = TRUE,
convert.factors = TRUE, convert.dates = TRUE, tz = "GMT",
add.rownames = FALSE, compress = FALSE, version = 117,
convert.underscore = FALSE)
# writing to SPSS files with `haven`

write_sav(dataframe, "path\to\your\data")
File stored by the SPSS can also be read with read.spss in this way:
foreign::read.spss('data.sav', to.data.frame=TRUE, use.value.labels=FALSE,

use.missings=TRUE, reencode='UTF-8')
# to.data.frame if TRUE: return a data frame
# use.value.labels if TRUE: convert variables with value labels into R factors with those
levels
# use.missings if TRUE: information on user-defined missing values will used to set the
corresponding values to NA.
# reencode character strings will be re-encoded to the current locale. The default, NA, means
to do so in a UTF-8 locale, only.
Import or Export of Feather file
Feather is an implementation of Apache Arrow designed to store data frames in a language

agnostic manner while maintaining metadata (e.g. date classes), increasing interoperability
between Python and R. Reading a feather file will produce a tibble, not a standard data.frame.
library(feather)
path <- "filename.feather"

df <- mtcars
write_feather(df, path)
df2 <- read_feather(path)
head(df2)
## A tibble: 6 x 11
## mpg cyl disp hp drat wt qsec vs am gear carb
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
## 2 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
## 3 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1
## 4 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
## 5 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2
## 6 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1
head(df)
## mpg cyl disp hp drat wt qsec vs am gear carb
## Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4
## Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
## Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1
## Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
## Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2
## Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1
The current documentation contains this warning:
Note to users: Feather should be treated as alpha software. In particular, the file format
is likely to evolve over the coming year. Do not use Feather for long-term data storage.
Read I/O for foreign tables (Excel, SAS, SPSS, Stata) online: https://riptutorial.com/r/topic/5536/i-
o-for-foreign-tables--excel--sas--spss--stata-
Chapter 51: I/O for geographic data
(shapefiles, etc.)
Introduction
See also Introduction to Geographical Maps and Input and Output
Examples
Import and Export Shapefiles
With the rgdal package it is possible to import and export shapfiles with R. The function readOGR
can be used to imports shapfiles. If you want to import a file from e.g. ArcGIS the first argument
dsn is the path to the folder which contains the shapefile. layer is the name of the shapefile without
the file ending (just map and not map.shp).
library(rgdal)
readOGR(dsn = "path\to\the\folder\containing\the\shapefile", layer = "map")
To export a shapefile use thewriteOGR function. The first argument is the spatial object produced in
R. dsn and layer are the same as above. The obligatory 4. argument is the driver used to generate
the shapefile. The function ogrDrivers() lists all available drivers. If you want to export a shapfile to
ArcGis or QGis you could use driver = "ESRI Shapefile".
writeOGR(Rmap, dsn = "path\to\the\folder\containing\the\shapefile", layer = "map",

driver = "ESRI Shapefile" )
tmap package has a very convenient function read_shape(), which is a wrapper for rgdal::reagOGR().
The read_shape() function simplifies the process of importing a shapefile a lot. On the downside,
tmap is quite heavy.
Read I/O for geographic data (shapefiles, etc.) online: https://riptutorial.com/r/topic/5538/i-o-for-

geographic-data--shapefiles--etc--
Chapter 52: I/O for raster images
Introduction
See also Raster and Image Analysis and Input and Output
Examples
Load a multilayer raster
The R-Logo is a multilayer raster file (red, green, blue)
library(raster)
r <- stack("C:/Program Files/R/R-3.2.3/doc/html/logo.jpg")
plot(r)
The individual layers of the RasterStack object can be adressed by [[.
plot(r[[1]])
Read I/O for raster images online: https://riptutorial.com/r/topic/5539/i-o-for-raster-images
Chapter 53: I/O for R's binary format
Examples
Rds and RData (Rda) files
.rdsand .Rdata (also known as .rda) files can be used to store R objects in a format native to R.
There are multiple advantages of saving this way when contrasted with non-native storage
approaches, e.g. write.table:
• It is faster to restore the data to R

• It keeps R specific information encoded in the data (e.g., attributes, variable types, etc).
saveRDS/readRDS
only handle a single R object. However, they are more flexible than the multi-object
storage approach in that the object name of the restored object need not be the same as the
object name when the object was stored.
Using an .rds file, for example, saving the iris dataset we would use:
saveRDS(object = iris, file = "my_data_frame.rds")
To load it data back in:
iris2 <- readRDS(file = "my_data_frame.rds")
To save a multiple objects we can use save() and output as .Rdata.
Example, to save 2 dataframes: iris and cars
save(iris, cars, file = "myIrisAndCarsData.Rdata")
To load:
load("myIrisAndCarsData.Rdata")
Enviromments
The functions save and load allow us to specify the environment where the object will be hosted:
save(iris, cars, file = "myIrisAndCarsData.Rdata", envir = foo <- new.env())

load("myIrisAndCarsData.Rdata", envir = foo)
foo$cars
save(iris, cars, file = "myIrisAndCarsData.Rdata", envir = foo <- new.env())

load("myIrisAndCarsData.Rdata", envir = foo)
foo$cars
Read I/O for R's binary format online: https://riptutorial.com/r/topic/5540/i-o-for-r-s-binary-format
Chapter 54: Implement State Machine Pattern
using S4 Class
Introduction
Finite States Machine concepts are usually implemented under Object Oriented Programming
(OOP) languages, for example using Java language, based on the State pattern defined in GOF
(refers to the book: "Design Patterns").
R provides several mechanisms to simulate the OO paradigm, let's apply S4 Object System for
implementing this pattern.
Examples
Parsing Lines using State Machine
Let's apply the State Machine pattern for parsing lines with the specific pattern using S4 Class
feature from R.
PROBLEM ENUNCIATION
We need to parse a file where each line provides information about a person, using a delimiter (
";"), but some information provided is optional, and instead of providing an empty field, it is
missing. On each line we can have the following information: Name;[Address;]Phone. Where the
address information is optional, sometimes we have it and sometimes don’t, for example:
GREGORY BROWN; 25 NE 25TH; +1-786-987-6543

DAVID SMITH;786-123-4567
ALAN PEREZ; 25 SE 50TH; +1-786-987-5553
The second line does not provide address information. Therefore the number of delimiters may be
deferent like in this case with one delimiter and for the other lines two delimiters. Because the
number of delimiters may vary, one way to atack this problem is to recognize the presence or not
of a given field based on its pattern. In such case we can use a regular expression for identifying
such patterns. For example:
• Name: "^([A-Z]'?\\s+)* *[A-Z]+(\\s+[A-Z]{1,2}\\.?,? +)*[A-Z]+((-|\\s+)[A-Z]+)*$". For

example: RAFAEL REAL, DAVID R. SMITH, ERNESTO PEREZ GONZALEZ, 0' CONNOR BROWN, LUIS PEREZ-
MENA, etc.
• Address: "^\\s[0-9]{1,4}(\\s+[A-Z]{1,2}[0-9]{1,2}[A-Z]{1,2}|[A-Z\\s0-9]+)$". For example:
11020 LE JEUNE ROAD, 87 SW 27TH. For the sake of simplicity we don't include here the zipcode,
city, state, but I can be included in this field or adding additional fields.
• Phone: "^\\s*(\\+1(-|\\s+))*[0-9]{3}(-|\\s+)[0-9]{3}(-|\\s+)[0-9]{4}$". For example: 305-
123-4567, 305 123 4567, +1-786-123-4567.
Notes:
• I am considering the most common pattern of US addresses and phones, it can be easy
extended to consider more general situations.
• In R the sign "\" has special meaning for character variables, therefore we need to escape
it.
• In order to simplify the process of defining regular expressions a good recommendation is to
use the following web page: regex101.com, so you can play with it, with a given example,
until you get the expected result for all possible combinations.
The idea is to identify each line field based on previously defined patterns. The State pattern
define the following entities (classes) that collaborate to control the specific behavior (The State
Pattern is a behavior pattern):
Let's describe each element considering the context of our problem:
• Context:Stores the context information of the parsing process, i.e. the current state and
handles the entire State Machine Process. For each state, an action is executed (handle()),
but the context delegates it, based on the state, on the action method defined for a particular
state (handle() from State class). It defines the interface of interest to clients. Our Context
class can be defined like this:
○ Attributes: state
○ Methods: handle(), ...
• State: The abstract class that represents any state of the State Machine. It defines an
interface for encapsulating the behavior associated with a particular state of the context. It
can be defined like this:
○ Attributes: name, pattern
○ Methods: doAction(), isState (using pattern attribute verify whether the input argument
belong to this state pattern or not), …
• Concrete States (state sub-classes): Each subclass of the class State that implements a
behavior associated with a state of the Context. Our sub-classes are: InitState, NameState,
AddressState, PhoneState. Such classes just implements the generic method using the specific
logic for such states. No additional attributes are required.
Note: It is a matter of preference how to name the method that carries out the action, handle(),
doAction() or goNext(). The method name doAction() can be the same for both classes (Stateor
Context) we preferred to name as handle() in the Context class for avoiding a confusion when
defining two generic methods with the same input arguments, but different class.
PERSON CLASS
Using the S4 syntax we can define a Person class like this:
setClass(Class = "Person",
slots = c(name = "character", address = "character", phone = "character")
)
It is a good recommendation to initialize the class attributes. The setClass documentation suggests
using a generic method labeled as "initialize", instead of using deprecated attributes such as:
prototype, representation.
setMethod("initialize", "Person",
definition = function(.Object, name = NA_character_,
address = NA_character_, phone = NA_character_) {
.Object@name <- name
.Object@address <- address
.Object@phone <- phone
.Object
}
)
Because the initialize method is already a standard generic method of package methods, we need
to respect the original argument definition. We can verify it typing on R prompt:
> initialize
It returns the entire function definition, you can see at the top who the function is defined like:
function (.Object, ...) {...}
Therefore when we use setMethod we need to follow exaclty the same syntax (.Object).
Another existing generic method is show, it is equivalent toString() method from Java and it is a
good idea to have a specific implementation for class domain:
setMethod("show", signature = "Person",

definition = function(object) {
info <- sprintf("%s@[name='%s', address='%s', phone='%s']",
class(object), object@name, object@address, object@phone)
cat(info)
invisible(NULL)
}
)
Note: We use the same convention as in the default toString() Java implementation.
Let's say we want to save the parsed information (a list of Person objects) into a dataset, then we
should be able first to convert a list of objects to into something the R can transform (for example
coerce the object as a list). We can define the following additional method (for more detail about
this see the post)
setGeneric(name = "as.list", signature = c('x'),
def = function(x) standardGeneric("as.list"))
# Suggestion taken from here:

# http://stackoverflow.com/questions/30386009/how-to-extend-as-list-in-a-canonical-way-to-s4-
objects
setMethod("as.list", signature = "Person",
definition = function(x) {
mapply(function(y) {
#apply as.list if the slot is again an user-defined object
#therefore, as.list gets applied recursively
if (inherits(slot(x,y),"Person")) {
as.list(slot(x,y))
} else {
#otherwise just return the slot
slot(x,y)
}
},
slotNames(class(x)),
SIMPLIFY=FALSE)
}
)
R does not provide a sugar syntax for OO because the language was initially conceived to provide
valuable functions for Statisticians. Therefore each user method requires two parts: 1) the
Definition part (via setGeneric) and 2) the implementation part (via setMethod). Like in the above
example.
STATE CLASS
Following S4 syntax, let's define the abstract State class.
setClass(Class = "State", slots = c(name = "character", pattern = "character"))
setMethod("initialize", "State",
definition = function(.Object, name = NA_character_, pattern = NA_character_) {
.Object@pattern <- pattern
.Object
}
)
setMethod("show", signature = "State",

info <- sprintf("%s@[name='%s', pattern='%s']", class(object),
object@name, object@pattern)
cat(info)
invisible(NULL)
}
)
setGeneric(name = "isState", signature = c('obj', 'input'),

def = function(obj, input) standardGeneric("isState"))
setGeneric(name = "doAction", signature = c('obj', 'input', 'context'),

def = function(obj, input, context) standardGeneric("doAction"))
Every sub-class from State will have associated a name and pattern, but also a way to identify
whether a given input belongs to this state or not (isState() method), and also implement the
corresponding actions for this state (doAction() method).
In order to understand the process, let's define the transition matrix for each state based on the
input received:
Input/Current State Init Name Address Phone
Name Name
Address Address
Phone Phone Phone
End End
Note: The cell [row, col]=[i,j] represents the destination state for the current state j, when it
receives the input i.
It means that under the state Name it can receive two inputs: an address or a phone number.
Another way to represents the transaction table is using the following UML State Machine
diagram:
Let's implement each particular state as a sub-state of the class State
STATE SUB-CLASSES
Init State:
The initial state will be implemented via the following class:
setClass("InitState", contains = "State")
setMethod("initialize", "InitState",
definition = function(.Object, name = "init", pattern = NA_character_) {
.Object
}
)
setMethod("show", signature = "InitState",

callNextMethod()
}
)
In R to indicate a class is a sub-class of other class is using the attribute contains and indicating
the class name of the parent class.
Because the sub-classes just implement the generic methods, without adding additional attributes,
then the show method, just call the equivalent method from the upper class (via method:
callNextMethod())
The initial state does not have associated a pattern, it just represents the beginning of the process,
then we initialize the class with an NA value.
Now lets to implement the generic methods from the State class:
setMethod(f = "isState", signature = "InitState",

definition = function(obj, input) {
nameState <- new("NameState")
result <- isState(nameState, input)
return(result)
}
)
For this particular state (without pattern), the idea it just initializes the parsing process expecting
the first field will be a name, otherwise it will be an error.
setMethod(f = "doAction", signature = "InitState",

definition = function(obj, input, context) {
nameState <- new("NameState")
if (isState(nameState, input)) {
person <- context@person
person@name <- trimws(input)
context@person <- person
context@state <- nameState
} else {
msg <- sprintf("The input argument: '%s' cannot be identified", input)
stop(msg)
}
return(context)
}
)
The doAction method provides the transition and updates the context with the information
extracted. Here we are accessing to context information via the @-operator. Instead, we can define
get/set methods, to encapsulate this process (as it is mandated in OO best practices:
encapsulation), but that would add four more methods per get-set without adding value for the
purpose of this example.
It is a good recommendation in all doAction implementation, to add a safeguard when the input
argument is not properly identified.
Name State
Here is the definition of this class definition:
setClass ("NameState", contains = "State")
setMethod("initialize","NameState",
definition=function(.Object, name="name",
pattern = "^([A-Z]'?\\s+)* *[A-Z]+(\\s+[A-Z]{1,2}\\.?,? +)*[A-Z]+((-|\\s+)[A-Z]+)*$")
{
.Object
}
)
setMethod("show", signature = "NameState",

callNextMethod()
}
)
We use the function grepl for verifying the input belongs to a given pattern.
setMethod(f="isState", signature="NameState",
definition=function(obj, input) {
result <- grepl(obj@pattern, input, perl=TRUE)
return(result)
}
)
Now we define the action to carry out for a given state:
setMethod(f = "doAction", signature = "NameState",

definition=function(obj, input, context) {
addressState <- new("AddressState")
phoneState <- new("PhoneState")
if (isState(addressState, input)) {
person@address <- trimws(input)
context@state <- addressState
} else if (isState(phoneState, input)) {
person@phone <- trimws(input)
context@state <- phoneState
} else {
stop(msg)
}
return(context)
}
)
Here we consider to possible transitions: one for Address state and the other one for Phone state.
In all cases we update the context information:
• The person information: address or phone with the input argument.

• The state of the process
The way to identify the state is to invoke the method: isState() for a particular state. We create a
default specific states (addressState, phoneState) and then ask for a particular validation.
The logic for the other sub-classes (one per state) implementation is very similar.
Address State
setClass("AddressState", contains = "State")
setMethod("initialize", "AddressState",
definition = function(.Object, name="address",
pattern = "^\\s[0-9]{1,4}(\\s+[A-Z]{1,2}[0-9]{1,2}[A-Z]{1,2}|[A-Z\\s0-9]+)$") {
.Object
}
)
setMethod("show", signature = "AddressState",

callNextMethod()
}
)
setMethod(f="isState", signature="AddressState",
definition=function(obj, input) {
result <- grepl(obj@pattern, input, perl=TRUE)
return(result)
}
)
setMethod(f = "doAction", "AddressState",

definition=function(obj, input, context) {
phoneState <- new("PhoneState")
if (isState(phoneState, input)) {
person@phone <- trimws(input)
context@state <- phoneState
} else {
stop(msg)
}
return(context)
}
)
Phone State
setClass("PhoneState", contains = "State")
setMethod("initialize", "PhoneState",
definition = function(.Object, name = "phone",
pattern = "^\\s*(\\+1(-|\\s+))*[0-9]{3}(-|\\s+)[0-9]{3}(-|\\s+)[0-9]{4}$") {
.Object
}
)
setMethod("show", signature = "PhoneState",
callNextMethod()
}
)
setMethod(f = "isState", signature = "PhoneState",

result <- grepl(obj@pattern, input, perl = TRUE)
return(result)
}
)
Here is where we add the person information into the list of persons of the context.
setMethod(f = "doAction", "PhoneState",

definition = function(obj, input, context) {
context <- addPerson(context, context@person)
context@state <- new("InitState")
return(context)
}
)
CONTEXT CLASS
Now the lets to explain the Context class implementation. We can define it considering the
following attributes:
setClass(Class = "Context",
slots = c(state = "State", persons = "list", person = "Person")
)
Where
• state:
The current state of the process
• person: The current person, it represents the information we have already parsed from the
current line.
• persons: The list of parsed persons processed.
Note: Optionally, we can add a name to identify the context by name in case we are working with
more than one parser type.
setMethod(f="initialize", signature="Context",
definition = function(.Object) {
.Object@state <- new("InitState")
.Object@persons <- list()
.Object@person <- new("Person")
return(.Object)
}
)
setMethod("show", signature = "Context",

cat("An object of class ", class(object), "\n", sep = "")
info <- sprintf("[state='%s', persons='%s', person='%s']", object@state,
toString(object@persons), object@person)
cat(info)
invisible(NULL)
}
)
setGeneric(name = "handle", signature = c('obj', 'input', 'context'),

def = function(obj, input, context) standardGeneric("handle"))
setGeneric(name = "addPerson", signature = c('obj', 'person'),

def = function(obj, person) standardGeneric("addPerson"))
setGeneric(name = "parseLine", signature = c('obj', 's'),

def = function(obj, s) standardGeneric("parseLine"))
setGeneric(name = "parseLines", signature = c('obj', 's'),

def = function(obj, s) standardGeneric("parseLines"))
setGeneric(name = "as.df", signature = c('obj'),

def = function(obj) standardGeneric("as.df"))
With such generic methods, we control the entire behavior of the parsing process:
• handle():
Will invoke the particular doAction() method of the current state.
• addPerson: Once we reach the end state, we need to add a person to the list of persons we
have parsed.
• parseLine(): Parse a single line
• parseLines(): Parse multiple lines (an array of lines)
• as.df(): Extract the information from persons list into a data frame object.
Let's go on now with the corresponding implementations:
handle() method, delegates on doAction() method from the current state of the context:
setMethod(f = "handle", signature = "Context",

obj <- doAction(obj@state, input, obj)
return(obj)
}
)
setMethod(f = "addPerson", signature = "Context",

definition = function(obj, person) {
obj@persons <- c(obj@persons, person)
return(obj)
}
)
First, we split the original line in an array using the delimiter to identify each element via the R-
function strsplit(), then iterate for each element as an input value for a given state. The handle()
method returns again the context with the updated information (state, person, persons attribute).
setMethod(f = "parseLine", signature = "Context",

definition = function(obj, s) {
elements <- strsplit(s, ";")[[1]]
# Adding an empty field for considering the end state.
elements <- c(elements, "")
n <- length(elements)
input <- NULL
for (i in (1:n)) {
input <- elements[i]
obj <- handle(obj, input)
}
return(obj@person)
}
)
Becuase R makes a copy of the input argument, we need to return the context (obj):
setMethod(f = "parseLines", signature = "Context",

definition = function(obj, s) {
n <- length(s)
listOfPersons <- list()
for (i in (1:n)) {
ipersons <- parseLine(obj, s[i])
listOfPersons[[i]] <- ipersons
}
obj@persons <- listOfPersons
return(obj)
}
)
The attribute persons is a list of instance of S4 Person class. This something cannot be coerced to
any standard type because R does not know of to treat an instance of a user defined class. The
solution is to convert a Person into a list, using the as.list method previously defined. Then we can
apply this function to each element of the list persons, via the lapply() function. Then in the next
invocation to lappy() function, now applies the data.frame function for converting each element of
the persons.list into a data frame. Finally, the rbind() function is called for adding each element
converted as a new row of the data frame generated (for more detail about this see this post)
# Sugestion taken from this post:

# http://stackoverflow.com/questions/4227223/r-list-to-data-frame
setMethod(f = "as.df", signature = "Context",
definition = function(obj) {
persons <- obj@persons
persons.list <- lapply(persons, as.list)
persons.ds <- do.call(rbind, lapply(persons.list, data.frame, stringsAsFactors = FALSE))
return(persons.ds)
}
)
PUTTING ALL TOGETHER
Finally, lets to test the entire solution. Define the lines to parse where for the second line the
address information is missing.
s <- c(
"GREGORY BROWN; 25 NE 25TH; +1-786-987-6543",
"DAVID SMITH;786-123-4567",
"ALAN PEREZ; 25 SE 50TH; +1-786-987-5553"
)
Now we initialize the context, and parse the lines:
context <- new("Context")

context <- parseLines(context, s)
Finally obtain the corresponding dataset and print it:
df <- as.df(context)
> df
name address phone
1 GREGORY BROWN 25 NE 25TH +1-786-987-6543
2 DAVID SMITH <NA> 786-123-4567
3 ALAN PEREZ 25 SE 50TH +1-786-987-5553
Let's test now the show methods:
> show(context@persons[[1]])
Person@[name='GREGORY BROWN', address='25 NE 25TH', phone='+1-786-987-6543']
And for some sub-state:
>show(new("PhoneState"))
PhoneState@[name='phone', pattern='^\s*(\+1(-|\s+))*[0-9]{3}(-|\s+)[0-9]{3}(-|\s+)[0-9]{4}$']
Finally, test the as.list() method:
> as.list(context@persons[[1]])
$name
[1] "GREGORY BROWN"
$address
[1] "25 NE 25TH"
$phone
[1] "+1-786-987-6543"
>
CONCLUSION
This example shows how to implement the State pattern, using one of the available mechanisms
from R for using the OO paradigm. Nevertheless, the R OO solution is not user-friendly and differs
so much from other OOP languages. You need to switch your mindset because the syntax is
completely different, it reminds more the functional programming paradigm. For example instead
of: object.setID("A1") as in Java/C#, for R you have to invoke the method in this way:
setID(object, "A1"). Therefore you always have to include the object as an input argument to
provide the context of the function. On the same way, there is no special this class attribute and
either a "." notation for accessing methods or attributes of the given class. It is more error prompt
because to refer a class or methods is done via attribute value ("Person", "isState", etc.).
Said the above, S4 class solution, requires much more lines of codes than a traditional Java/C#
languages for doing simple tasks. Anyway, the State Pattern is a good and generic solution for
such kind of problems. It simplifies the process delegating the logic into a particular state. Instead
of having a big if-else block for controlling all situations, we have smaller if-else blocks inside on
each State sub-class implementation for implementing the action to carry out in each state.
Attachment: Here you can download the entire script.
Any suggestion is welcome.
Read Implement State Machine Pattern using S4 Class online:

https://riptutorial.com/r/topic/9126/implement-state-machine-pattern-using-s4-class
Chapter 55: Input and output
Remarks
To construct file paths, for reading or writing, use file.path.
Use dir to see what files are in a directory.
Examples
Reading and writing data frames
Data frames are R's tabular data structure. They can be written to or read from in a variety of
ways.
This example illustrates a couple common situations. See the links at the end for other resources.
Writing
Before making the example data below, make sure you're in a folder you want to write to. Run
getwd() to verify the folder you're in and read ?setwd if you need to change folders.
set.seed(1)
for (i in 1:3)
write.table(
data.frame(id = 1:2, v = sample(letters, 2)),
file = sprintf("file201%s.csv", i)
)
Now, we have three similarly-formatted CSV files on disk.
Reading
We have three similarly-formatted files (from the last section) to read in. Since these files are
related, we should store them together after reading in, in a list:
file_names = c("file2011.csv", "file2012.csv", "file2013.csv")

file_contents = lapply(setNames(file_names, file_names), read.table)
# $file2011.csv
# id v
# 1 1 g
# 2 2 j
#
# $file2012.csv
# id v
# 1 1 o
# 2 2 w
#
# $file2013.csv
# id v
# 1 1 f
# 2 2 w
To work with this list of files, first examine the structure with str(file_contents), then read about
stacking the list with ?rbind or iterating over the list with ?lapply.
Further resources
Check out ?read.table and ?write.table to extend this example. Also:
• R binary formats (for tables and other objects)

• Plain-text table formats
○ comma-delimited CSVs
○ tab-delimited TSVs
○ Fixed-width formats
• Language-agnostic binary table formats
○ Feather
• Foreign table and spreadsheet formats
○ SAS
○ SPSS
○ Stata
○ Excel
• Relational database table formats
○ MySQL
○ SQLite
○ PostgreSQL
Read Input and output online: https://riptutorial.com/r/topic/5543/input-and-output
Chapter 56: Inspecting packages
Introduction
Packages build on base R. This document explains how to inspect installed packages and their
functionality. Related Docs: Installing packages
Remarks
The Comprehensive R Archive Network (CRAN) is the primary package repository.
Examples
View package information
To retrieve information about dplyr package and its functions' descriptions:
help(package = "dplyr")
No need to load the package first.
View package's built-in data sets
To see built-in data sets from package dplyr
data(package = "dplyr")
No need to load the package first.
List a package's exported functions
To get the list of functions within package dplyr, we first must load the package:
library(dplyr)
ls("package:dplyr")
View Package Version
Conditions: package should be at least installed. If not loaded in the current session, not a
problem.
## Checking package version which was installed at past or

## installed currently but not loaded in the current session
packageVersion("seqinr")
# [1] ‘3.3.3’
packageVersion("RWeka")
# [1] ‘0.4.29’
View Loaded packages in Current Session
To check the list of loaded packages
search()
OR
(.packages())
Read Inspecting packages online: https://riptutorial.com/r/topic/7408/inspecting-packages
Chapter 57: Installing packages
Syntax
• install.packages(pkgs, lib, repos, method, destdir, dependencies, ...)
Parameters
Parameter Details
character vector of the names of packages. If repos = NULL, a character

pkgs
vector of file paths.
lib character vector giving the library directories where to install the packages.
character vector, the base URL(s) of the repositories to use, can be NULL to
repos
install from local files
method download method
destdir directory where downloaded packages are stored
logical indicating whether to also install uninstalled packages which these

dependencies packages depend on/link to/import/suggest (and so on recursively). Not used
if repos = NULL.
Arguments to be passed to ‘download.file’ or to the functions for binary

...
installs on OS X and Windows.
Remarks
Related Docs
• Inspecting packages
Examples
Download and install packages from repositories
Packages are collections of R functions, data, and compiled code in a well-defined format. Public
(and private) repositories are used to host collections of R packages. The largest collection of R
packages is available from CRAN.
Using CRAN
A package can be installed from CRAN using following code:
install.packages("dplyr")
Where "dplyr" is referred to as a character vector.
More than one packages can be installed in one go by using the combine function c() and passing
a series of character vector of package names:
install.packages(c("dplyr", "tidyr", "ggplot2"))
In some cases, install.packages may prompt for a CRAN mirror or fail, depending on the value of
getOption("repos"). To prevent this, specify a CRAN mirror as repos argument:
install.packages("dplyr", repos = "https://cloud.r-project.org/")
Using the repos argument it is also possible to install from other repositories. For complete
information about all the available options, run ?install.packages.
Most packages require functions, which were implemented in other packages (e.g. the package
data.table). In order to install a package (or multiple packages) with all the packages, which are
used by this given package, the argument dependencies should be set to TRUE):
install.packages("data.table", dependencies = TRUE)
Using Bioconductor
Bioconductor hosts a substantial collection of packages related to Bioinformatics. They provide
their own package management centred around the biocLite function:
## Try http:// if https:// URLs are not supported

source("https://bioconductor.org/biocLite.R")
biocLite()
By default this installs a subset of packages that provide the most commonly used functionality.
Specific packages can be installed by passing a vector of package names. For example, to install
RImmPort from Bioconductor:
biocLite("RImmPort")
Install package from local source
To install package from local source file:
install.packages(path_to_source, repos = NULL, type="source")
install.packages("~/Downloads/dplyr-master.zip", repos=NULL, type="source")
Here, path_to_source is absolute path of local source file.
Another command that opens a window to choose downloaded zip or tar.gz source files is:
install.packages(file.choose(), repos=NULL)
Another possible way is using the GUI based RStudio:
Step 1: Go to Tools.
Step 2: Go to Install Packages.
Step 3: In the Install From set it as Package Archive File (.zip; .tar.gz)
Step 4: Then Browse find your package file (say crayon_1.3.1.zip) and after some time (after it
shows the Package path and file name in the Package Archive tab)
Another way to install R package from local source is using install_local() function from devtools
package.
library(devtools)
install_local("~/Downloads/dplyr-master.zip")
Install packages from GitHub
To install packages directly from GitHub use the devtools package:
library(devtools)
install_github("authorName/repositoryName")
To install ggplot2 from github:
devtools::install_github("tidyverse/ggplot2")
The above command will install the version of ggplot2 that corresponds to the master branch. To
install from a different branch of a repository use the ref argument to provide the name of the
branch. For example, the following command will install the dev_general branch of the googleway
package.
devtools::install_github("SymbolixAU/googleway", ref = "dev_general")
Another option is to use the ghit package. It provides a lightweight alternative for installing
packages from github:
install.packages("ghit")
ghit::install_github("google/CausalImpact")
To install a package that is in a private repository on Github, generate a personal access token
at http://www.github.com/settings/tokens/ (See ?install_github for documentation on the same).
Follow these steps:
1. install.packages(c("curl", "httr"))
2. config = httr::config(ssl_verifypeer = FALSE)
3. install.packages("RCurl")
options(RCurlOptions = c(getOption("RCurlOptions"),ssl.verifypeer = FALSE,
ssl.verifyhost = FALSE ) )
4. getOption("RCurlOptions")
You should see the following:
ssl.verifypeer ssl.verifyhost
FALSE FALSE
5. library(httr)
set_config(config(ssl_verifypeer = 0L))
This prevents the common error: "Peer certificate cannot be authenticated with given CA
certificates"
6. Finally, use the following command to install your package seamlessly
install_github("username/package_name",auth_token="abc")
Alternatively, set an environment variable GITHUB_PAT, using
Sys.setenv(GITHUB_PAT = "access_token")
devtools::install_github("organisation/package_name")
The PAT generated in Github is only visible once, i.e., when created initially, so its prudent to save
that token in .Rprofile. This is also helpful if the organisation has many private repositories.
Using a CLI package manager -- basic pacman usage
pacman is a simple package manager for R.
pacman
allows a user to compactly load all desired packages, installing any which are missing (and their
dependencies), with a single command, p_load. pacman does not require the user to type quotation
marks around a package name. Basic usage is as follows:
p_load(data.table, dplyr, ggplot2)
The only package requiring a library, require, or install.packages statement with this approach is
pacman itself:
library(pacman)
p_load(data.table, dplyr, ggplot2)
or, equally valid:
pacman::p_load(data.table, dplyr, ggplot2)
In addition to saving time by requiring less code to manage packages, pacman also facilitates the
construction of reproducible code by installing any needed packages if and only if they are not
already installed.
Since you may not be sure if pacman is installed in the library of a user who will use your code (or
by yourself in future uses of your own code) a best practice is to include a conditional statement to
install pacman if it is not already loaded:
if(!(require(pacman)) install.packages("pacman")
pacman::p_load(data.table, dplyr, ggplot2)
Install local development version of a package
While working on the development of an R package it is often necessary to install the latest
version of the package. This can be achieved by first building a source distribution of the package
(on the command line)
R CMD build my_package
and then installing it in R. Any running R sessions with previous version of the package loaded will
need to reload it.
unloadNamespace("my_package")
library(my_package)
A more convenient approach uses the devtools package to simplify the process. In an R session
with the working directory set to the package directory
devtools::install()
will build, install and reload the package.
Read Installing packages online: https://riptutorial.com/r/topic/1719/installing-packages
Chapter 58: Introduction to Geographical
Maps
Introduction
See also I/O for geographic data
Examples
Basic map-making with map() from the package maps
The function map() from the package maps provides a simple starting point for creating maps with R.
A basic world map can be drawn as follows:
require(maps)
map()
The color of the outline can be changed by setting the color parameter, col, to either the character
name or hex value of a color:
require(maps)
map(col = "cornflowerblue")
To fill land masses with the color in col we can set fill = TRUE:
require(maps)
map(fill = TRUE, col = c("cornflowerblue"))
A vector of any length may be supplied to col when fill = TRUE is also set:
require(maps)
map(fill = TRUE, col = c("cornflowerblue", "limegreen", "hotpink"))
In the example above colors from col are assigned arbitrarily to polygons in the map representing
regions and colors are recycled if there are fewer colors than polygons.
We can also use color coding to represent a statistical variable, which may optionally be described
in a legend. A map created as such is known as a "choropleth".
The following choropleth example sets the first argument of map(), which is database to "county"
and "state" to color code unemployment using data from the built-in datasets unemp and
county.fips while overlaying state lines in white:
require(maps)
if(require(mapproj)) { # mapproj is used for projection="polyconic"
# color US county map by 2009 unemployment rate
# match counties to map using FIPS county codes
# Based on J's solution to the "Choropleth Challenge"
# Code improvements by Hack-R (hack-r.github.io)
# load data
# unemp includes data for some counties not on the "lower 48 states" county
# map, such as those in Alaska, Hawaii, Puerto Rico, and some tiny Virginia
# cities
data(unemp)
data(county.fips)
# define color buckets

colors = c("paleturquoise", "skyblue", "cornflowerblue", "blueviolet", "hotpink",
"darkgrey")
unemp$colorBuckets <- as.numeric(cut(unemp$unemp, c(0, 2, 4, 6, 8, 10, 100)))
leg.txt <- c("<2%", "2-4%", "4-6%", "6-8%", "8-10%", ">10%")
# align data with map definitions by (partial) matching state,county

# names, which include multiple polygons for some counties
cnty.fips <- county.fips$fips[match(map("county", plot=FALSE)$names,
county.fips$polyname)]
colorsmatched <- unemp$colorBuckets[match(cnty.fips, unemp$fips)]
# draw map
par(mar=c(1, 1, 2, 1) + 0.1)
map("county", col = colors[colorsmatched], fill = TRUE, resolution = 0,
lty = 0, projection = "polyconic")
map("state", col = "white", fill = FALSE, add = TRUE, lty = 1, lwd = 0.1,
projection="polyconic")
title("unemployment by county, 2009")
legend("topright", leg.txt, horiz = TRUE, fill = colors, cex=0.6)
}
50 State Maps and Advanced Choropleths with Google Viz
A common question is how to juxtapose (combine) physically separate geographical regions on

the same map, such as in the case of a choropleth describing all 50 American states (The
mainland with Alaska and Hawaii juxtaposed).
Creating an attractive 50 state map is simple when leveraging Google Maps. Interfaces to
Google's API include the packages googleVis, ggmap, and RgoogleMaps.
require(googleVis)
G4 <- gvisGeoChart(CityPopularity, locationvar='City', colorvar='Popularity',

options=list(region='US', height=350,
displayMode='markers',
colorAxis="{values:[200,400,600,800],
colors:[\'red', \'pink\', \'orange',\'green']}")
)
plot(G4)
The function gvisGeoChart() requires far less coding to create a choropleth compared to older
mapping methods, such as map() from the package maps. The colorvar parameter allows easy
coloring of a statistical variable, at a level specified by the locationvar parameter. The various
options passed to options as a list allow customization of the map's details such as size (height),
shape (markers), and color coding (colorAxis and colors).
Interactive plotly maps
The plotly package allows many kind of interactive plots, including maps. There are a few ways to
create a map in plotly. Either supply the map data yourself (via plot_ly() or ggplotly()), use
plotly's "native" mapping capabilities (via plot_geo() or plot_mapbox()), or even a combination of
both. An example of supplying the map yourself would be:
library(plotly)
map_data("county") %>%
group_by(group) %>%
plot_ly(x = ~long, y = ~lat) %>%
add_polygons() %>%
layout(
xaxis = list(title = "", showgrid = FALSE, showticklabels = FALSE),
yaxis = list(title = "", showgrid = FALSE, showticklabels = FALSE)
)
For a combination of both approaches, swap plot_ly() for plot_geo() or plot_mapbox() in the above
example. See the plotly book for more examples.
The next example is a "strictly native" approach that leverages the layout.geo attribute to set the
aesthetics and zoom level of the map. It also uses the database world.cities from maps to filter the
Brazilian cities and plot them on top of the "native" map.
The main variables: pophis a text with the city and its population (which is shown upon mouse
hover); qis a ordered factor from the population's quantile. ge has information for the layout of the
maps. See the package documentation for more information.
library(maps)
dfb <- world.cities[world.cities$country.etc=="Brazil",]
library(plotly)
dfb$poph <- paste(dfb$name, "Pop", round(dfb$pop/1e6,2), " millions")
dfb$q <- with(dfb, cut(pop, quantile(pop), include.lowest = T))
levels(dfb$q) <- paste(c("1st", "2nd", "3rd", "4th"), "Quantile")
dfb$q <- as.ordered(dfb$q)
ge <- list(
scope = 'south america',
showland = TRUE,
landcolor = toRGB("gray85"),
subunitwidth = 1,
countrywidth = 1,
subunitcolor = toRGB("white"),
countrycolor = toRGB("white")
)
plot_geo(dfb, lon = ~long, lat = ~lat, text = ~poph,

marker = ~list(size = sqrt(pop/10000) + 1, line = list(width = 0)),
color = ~q, locationmode = 'country names') %>%
layout(geo = ge, title = 'Populations<br>(Click legend to toggle)')
Making Dynamic HTML Maps with Leaflet
Leaflet is an open-source JavaScript library for making dynamic maps for the web. RStudio wrote
R bindings for Leaflet, available through its leaflet package, built with htmlwidgets. Leaflet maps
integrate well with the RMarkdown and Shiny ecosystems.
The interface is piped, using a leaflet() function to initialize a map and subsequent functions
adding (or removing) map layers. Many kinds of layers are available, from markers with popups to
polygons for creating choropleth maps. Variables in the data.frame passed to leaflet() are
accessed via function-style ~ quotation.
To map the state.name and state.center datasets:
library(leaflet)
data.frame(state.name, state.center) %>%

leaflet() %>%
addProviderTiles('Stamen.Watercolor') %>%
addMarkers(lng = ~x, lat = ~y,
popup = ~state.name,
clusterOptions = markerClusterOptions())
(Screenshot; click for dynamic version.)
Dynamic Leaflet maps in Shiny applications
The Leaflet package is designed to integerate with Shiny
In the ui you call leafletOutput() and in the server you call renderLeaflet()
library(shiny)
library(leaflet)
ui <- fluidPage(
leafletOutput("my_leaf")
)
server <- function(input, output, session){
output$my_leaf <- renderLeaflet({
leaflet() %>%
addProviderTiles('Hydda.Full') %>%
setView(lat = -37.8, lng = 144.8, zoom = 10)
})
shinyApp(ui, server)
However, reactive inputs that affect the renderLeaflet expression will cause the entire map to be
redrawn each time the reactive element is updated.
Therefore, to modify a map that's already running you should use the leafletProxy() function.
Normally you use leaflet to create the static aspects of the map, and leafletProxy to manage the
dynamic elements, for example:
library(shiny)
library(leaflet)
ui <- fluidPage(
sliderInput(inputId = "slider",
label = "values",
min = 0,
max = 100,
value = 0,
step = 1),
leafletOutput("my_leaf")
)
server <- function(input, output, session){

set.seed(123456)
df <- data.frame(latitude = sample(seq(-38.5, -37.5, by = 0.01), 100),
longitude = sample(seq(144.0, 145.0, by = 0.01), 100),
value = seq(1,100))
## create static element

output$my_leaf <- renderLeaflet({
leaflet() %>%
addProviderTiles('Hydda.Full') %>%
setView(lat = -37.8, lng = 144.8, zoom = 8)
})
## filter data
df_filtered <- reactive({
df[df$value >= input$slider, ]
})
## respond to the filtered data

observe({
leafletProxy(mapId = "my_leaf", data = df_filtered()) %>%

clearMarkers() %>% ## clear previous markers
addMarkers()
})
shinyApp(ui, server)
Read Introduction to Geographical Maps online: https://riptutorial.com/r/topic/1372/introduction-to-

geographical-maps
Chapter 59: Introspection
Examples
Functions for Learning about Variables
Often in R you'll want to know things about an object or variable you're working with. This can be
useful when reading someone else's code or even your own, especially when using packages that
are new to you.
Suppose we create a variable a:
a <- matrix(1:9, 3, 3)
What data type is this? You can find out with
> class(a)
[1] "matrix"
It's a matrix, so matrix operations will work on it:
> a %*% t(a)

[,1] [,2] [,3]
[1,] 66 78 90
[2,] 78 93 108
[3,] 90 108 126
What are the dimensions of a?
> dim(a)
[1] 3 3
> nrow(a)
[1] 3
> ncol(a)
[2] 3
Other useful functions that work for different data types are head, tail, and str:
> head(a, 1)
[,1] [,2] [,3]
[1,] 1 4 7
> tail(a, 1)
[,1] [,2] [,3]
[3,] 3 6 9
> str(a)
int [1:3, 1:3] 1 2 3 4 5 6 7 8 9
These are much more useful for large objects (such as big datasets). str is also great for learning
about the nesting of lists. Now reshape a like so:
a <- c(a)
Does the class remain the same?
> class(a)
[1] "integer"
No, a is not a matrix anymore. I won't get a good answer if I ask for dimensions now:
> dim(a)
NULL
Instead, I can ask for the length:
> length(a)
[1] 9
What about now:
> class(a * 1.0)

[1] "numeric"
Often you may work with data.frames:
a <- as.data.frame(a)
names(a) <- c("var1", "var2", "var3")
See the variable names:
> names(a)
[1] "var1" "var2" "var3"
These functions can help many ways when using R.
Read Introspection online: https://riptutorial.com/r/topic/3565/introspection
Chapter 60: JSON
Examples
JSON to / from R objects
The jsonlite package is a fast JSON parser and generator optimized for statistical data and the
web. The two main functions used to read and write JSON are fromJSON() and toJSON()
respecitively, and are designed to work with vectors, matrices and data.frames, and streams of
JSON from the web.
Create a JSON array from a vector, and vice versa
library(jsonlite)
## vector to JSON
toJSON(c(1,2,3))
# [1,2,3]
fromJSON('[1,2,3]')
# [1] 1 2 3
Create a named JSON array from a list, and vice versa
toJSON(list(myVec = c(1,2,3)))
# {"myVec":[1,2,3]}
fromJSON('{"myVec":[1,2,3]}')
# $myVec
# [1] 1 2 3
More complex list structures
## list structures
lst <- list(a = c(1,2,3),
b = list(letters[1:6]))
toJSON(lst)
# {"a":[1,2,3],"b":[["a","b","c","d","e","f"]]}
fromJSON('{"a":[1,2,3],"b":[["a","b","c","d","e","f"]]} ')
# $a
# [1] 1 2 3
#
# $b
# [,1] [,2] [,3] [,4] [,5] [,6]
# [1,] "a" "b" "c" "d" "e" "f"
Create JSON from a data.frame, and vice versa
## converting a data.frame to JSON
df <- data.frame(id = seq_along(1:10),
val = letters[1:10])
toJSON(df)
#
[{"id":1,"val":"a"},{"id":2,"val":"b"},{"id":3,"val":"c"},{"id":4,"val":"d"},{"id":5,"val":"e"},{"id":6
## reading a JSON string

fromJSON('[{"id":1,"val":"a"},{"id":2,"val":"b"},{"id":3,"val":"c"},{"id":4,"val":"d"},{"id":5,"val":"e
# id val
# 1 1 a
# 2 2 b
# 3 3 c
# 4 4 d
# 5 5 e
# 6 6 f
# 7 7 g
# 8 8 h
# 9 9 i
# 10 10 j
Read JSON direct from the internet
## Reading JSON from URL

googleway_issues <- fromJSON("https://api.github.com/repos/SymbolixAU/googleway/issues")
googleway_issues$url
# [1] "https://api.github.com/repos/SymbolixAU/googleway/issues/20"
"https://api.github.com/repos/SymbolixAU/googleway/issues/19"
Read JSON online: https://riptutorial.com/r/topic/2460/json
Chapter 61: Linear Models (Regression)
Syntax
• lm(formula, data, subset, weights, na.action, method = "qr", model = TRUE, x = FALSE, y =
FALSE, qr = TRUE, singular.ok = TRUE, contrasts = NULL, offset, ...)
Parameters
Parameter Meaning
a formula in Wilkinson-Rogers notation; response ~ ... where ... contains terms

formula corresponding to variables in the environment or in the data frame specified by
the data argument
data data frame containing the response and predictor variables
a vector specifying a subset of observations to be used: may be expressed as a

subset
logical statement in terms of the variables in data
weights analytical weights (see Weights section above)
na.action how to handle missing (NA) values: see ?na.action
how to perform the fitting. Only choices are "qr" or "model.frame" (the latter
method returns the model frame without fitting the model, identical to specifying
model=TRUE)
model whether to store the model frame in the fitted object
x whether to store the model matrix in the fitted object
y whether to store the model response in the fitted object
qr whether to store the QR decomposition in the fitted object
whether to allow singular fits, models with collinear predictors (a subset of the
singular.ok
coefficients will automatically be set to NA in this case
a list of contrasts to be used for particular factors in the model; see the
contrasts.arg argument of ?model.matrix.default. Contrasts can also be set with
contrasts
options() (see the contrasts argument) or by assigning the contrast attributes of
a factor (see ?contrasts)
used to specify an a priori known component in the model. May also be

offset
specified as part of the formula. See ?model.offset
Parameter Meaning
additional arguments to be passed to lower-level fitting functions (lm.fit() or

...
lm.wfit())
Examples
Linear regression on the mtcars dataset
The built-in mtcars data frame contains information about 32 cars, including their weight, fuel
efficiency (in miles-per-gallon), speed, etc. (To find out more about the dataset, use help(mtcars)).
If we are interested in the relationship between fuel efficiency (mpg) and weight (wt) we may start
plotting those variables with:
plot(mpg ~ wt, data = mtcars, col=2)
The plots shows a (linear) relationship!. Then if we want to perform linear regression to determine
the coefficients of a linear model, we would use the lm function:
fit <- lm(mpg ~ wt, data = mtcars)
The ~ here means "explained by", so the formula mpg ~ wt means we are predicting mpg as
explained by wt. The most helpful way to view the output is with:
summary(fit)
Which gives the output:
Call:
lm(formula = mpg ~ wt, data = mtcars)
Residuals:
Min 1Q Median 3Q Max
-4.5432 -2.3647 -0.1252 1.4096 6.8727
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 37.2851 1.8776 19.858 < 2e-16 ***
wt -5.3445 0.5591 -9.559 1.29e-10 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 3.046 on 30 degrees of freedom

Multiple R-squared: 0.7528, Adjusted R-squared: 0.7446
F-statistic: 91.38 on 1 and 30 DF, p-value: 1.294e-10
This provides information about:
• the estimated slope of each coefficient (wt and the y-intercept), which suggests the best-fit
prediction of mpg is 37.2851 + (-5.3445) * wt
• The p-value of each coefficient, which suggests that the intercept and weight are probably
not due to chance
• Overall estimates of fit such as R^2 and adjusted R^2, which show how much of the variation
in mpg is explained by the model
We could add a line to our first plot to show the predicted mpg:
abline(fit,col=3,lwd=2)
It is also possible to add the equation to that plot. First, get the coefficients with coef. Then using
paste0 we collapse the coefficients with appropriate variables and +/-, to built the equation. Finally,
we add it to the plot using mtext:
bs <- round(coef(fit), 3)
lmlab <- paste0("mpg = ", bs[1],
ifelse(sign(bs[2])==1, " + ", " - "), abs(bs[2]), " wt ")
mtext(lmlab, 3, line=-2)
The result is:
Plotting The Regression (base)
Continuing on the mtcars example, here is a simple way to produce a plot of your linear regression
that is potentially suitable for publication.
First fit the linear model and
Then plot the two variables of interest and add the regression line within the definition domain:
plot(mtcars$wt,mtcars$mpg,pch=18, xlab = 'wt',ylab = 'mpg')

lines(c(min(mtcars$wt),max(mtcars$wt)),
as.numeric(predict(fit, data.frame(wt=c(min(mtcars$wt),max(mtcars$wt))))))
Almost there! The last step is to add to the plot, the regression equation, the rsquare as well as the
correlation coefficient. This is done using the vector function:
rp = vector('expression',3)
rp[1] = substitute(expression(italic(y) == MYOTHERVALUE3 + MYOTHERVALUE4 %*% x),
list(MYOTHERVALUE3 = format(fit$coefficients[1], digits = 2),
MYOTHERVALUE4 = format(fit$coefficients[2], digits = 2)))[2]
rp[2] = substitute(expression(italic(R)^2 == MYVALUE),
list(MYVALUE = format(summary(fit)$adj.r.squared,dig=3)))[2]
rp[3] = substitute(expression(Pearson-R == MYOTHERVALUE2),
list(MYOTHERVALUE2 = format(cor(mtcars$wt,mtcars$mpg), digits = 2)))[2]
legend("topright", legend = rp, bty = 'n')
Note that you can add any other parameter such as the RMSE by adapting the vector function.
Imagine you want a legend with 10 elements. The vector definition would be the following:
rp = vector('expression',10)
and you will need to defined r[1].... to r[10]
Here is the output:
Weighting
Sometimes we want the model to give more weight to some data points or examples than others.
This is possible by specifying the weight for the input data while learning the model. There are
generally two kinds of scenarios where we might use non-uniform weights over the examples:
• Analytic Weights: Reflect the different levels of precision of different observations. For
example, if analyzing data where each observation is the average results from a geographic
area, the analytic weight is proportional to the inverse of the estimated variance. Useful
when dealing with averages in data by providing a proportional weight given the number of
observations. Source
• Sampling Weights (Inverse Probability Weights - IPW): a statistical technique for calculating
statistics standardized to a population different from that in which the data was collected.
Study designs with a disparate sampling population and population of target inference (target
population) are common in application. Useful when dealing with data that have missing
values. Source
The lm() function does analytic weighting. For sampling weights the survey package is used to
build a survey design object and run svyglm(). By default, the survey package uses sampling
weights. (NOTE: lm(), and svyglm() with family gaussian() will all produce the same point
estimates, because they both solve for the coefficients by minimizing the weighted least squares.
They differ in how standard errors are calculated.)
Test Data
data <- structure(list(lexptot = c(9.1595012302023, 9.86330744180814,
8.92372556833205, 8.58202430280175, 10.1133857229336), progvillm = c(1L,
1L, 1L, 1L, 0L), sexhead = c(1L, 1L, 0L, 1L, 1L), agehead = c(79L,
43L, 52L, 48L, 35L), weight = c(1.04273509979248, 1.01139605045319,
1.01139605045319, 1.01139605045319, 0.76305216550827)), .Names = c("lexptot",
"progvillm", "sexhead", "agehead", "weight"), class = c("tbl_df",
"tbl", "data.frame"), row.names = c(NA, -5L))
Analytic Weights
lm.analytic <- lm(lexptot ~ progvillm + sexhead + agehead,

data = data, weight = weight)
summary(lm.analytic)
Output
Call:
lm(formula = lexptot ~ progvillm + sexhead + agehead, data = data,
weights = weight)
Weighted Residuals:
1 2 3 4 5
9.249e-02 5.823e-01 0.000e+00 -6.762e-01 -1.527e-16
Coefficients:
(Intercept) 10.016054 1.744293 5.742 0.110
progvillm -0.781204 1.344974 -0.581 0.665
sexhead 0.306742 1.040625 0.295 0.818
agehead -0.005983 0.032024 -0.187 0.882
Residual standard error: 0.8971 on 1 degrees of freedom

Multiple R-squared: 0.467, Adjusted R-squared: -1.132
F-statistic: 0.2921 on 3 and 1 DF, p-value: 0.8386
Sampling Weights (IPW)
library(survey)
data$X <- 1:nrow(data) # Create unique id
# Build survey design object with unique id, ipw, and data.frame
des1 <- svydesign(id = ~X, weights = ~weight, data = data)
# Run glm with survey design object

prog.lm <- svyglm(lexptot ~ progvillm + sexhead + agehead, design=des1)
Output
Call:
svyglm(formula = lexptot ~ progvillm + sexhead + agehead, design = des1)
Survey design:
svydesign(id = ~X, weights = ~weight, data = data)
Coefficients:
(Intercept) 10.016054 0.183942 54.452 0.0117 *
progvillm -0.781204 0.640372 -1.220 0.4371
sexhead 0.306742 0.397089 0.772 0.5813
agehead -0.005983 0.014747 -0.406 0.7546
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for gaussian family taken to be 0.2078647)
Number of Fisher Scoring iterations: 2
Checking for nonlinearity with polynomial regression
Sometimes when working with linear regression we need to check for non-linearity in the data.
One way to do this is to fit a polynomial model and check whether it fits the data better than a
linear model. There are other reasons, such as theoretical, that indicate to fit a quadratic or higher
order model because it is believed that the variables relationship is inherently polynomial in nature.
Let's fit a quadratic model for the mtcars dataset. For a linear model see Linear regression on the
mtcars dataset.
First we make a scatter plot of the variables mpg (Miles/gallon), disp (Displacement (cu.in.)), and wt
(Weight (1000 lbs)). The relationship among mpg and disp appears non-linear.
plot(mtcars[,c("mpg","disp","wt")])
A linear fit will show that disp is not significant.
fit0 = lm(mpg ~ wt+disp, mtcars)

summary(fit0)
# Coefficients:
# Estimate Std. Error t value Pr(>|t|)
#(Intercept) 34.96055 2.16454 16.151 4.91e-16 ***
#wt -3.35082 1.16413 -2.878 0.00743 **
#disp -0.01773 0.00919 -1.929 0.06362 .
#---
#Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#Residual standard error: 2.917 on 29 degrees of freedom
#Multiple R-squared: 0.7809, Adjusted R-squared: 0.7658
Then, to get the result of a quadratic model, we added I(disp^2). The new model appears better
when looking at R^2 and all variables are significant.
fit1 = lm(mpg ~ wt+disp+I(disp^2), mtcars)

summary(fit1)
# Coefficients:
# Estimate Std. Error t value Pr(>|t|)
#(Intercept) 41.4019837 2.4266906 17.061 2.5e-16 ***
#wt -3.4179165 0.9545642 -3.581 0.001278 **
#disp -0.0823950 0.0182460 -4.516 0.000104 ***
#I(disp^2) 0.0001277 0.0000328 3.892 0.000561 ***
#---
#Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#Residual standard error: 2.391 on 28 degrees of freedom
#Multiple R-squared: 0.8578, Adjusted R-squared: 0.8426
As we have three variables, the fitted model is a surface represented by:
mpg = 41.4020-3.4179*wt-0.0824*disp+0.0001277*disp^2
Another way to specify polynomial regression is using poly with parameter raw=TRUE, otherwise
orthogonal polynomials will be considered (see the help(ploy) for more information). We get the
same result using:
summary(lm(mpg ~ wt+poly(disp, 2, raw=TRUE),mtcars))
Finally, what if we need to show a plot of the estimated surface? Well there are many options to
make 3D plots in R. Here we use Fit3d from p3dpackage.
library(p3d)
Init3d(family="serif", cex = 1)
Plot3d(mpg ~ disp+wt, mtcars)
Axes3d()
Fit3d(fit1)
Quality assessment
After building a regression model it is important to check the result and decide if the model is
appropriate and works well with the data at hand. This can be done by examining the residuals
plot as well as other diagnostic plots.
# fit the model

#
par(mfrow=c(2,1))
# plot model object
plot(fit, which =1:2)
These plots check for two assumptions that were made while building the model:
1. That the expected value of the predicted variable (in this case mpg) is given by a linear
combination of the predictors (in this case wt). We expect this estimate to be unbiased. So
the residuals should be centered around the mean for all values of the predictors. In this
case we see that the residuals tend to be positive at the ends and negative in the middle,
suggesting a non-linear relationship between the variables.
2. That the actual predicted variable is normally distributed around its estimate. Thus, the
residuals should be normally distributed. For normally distributed data, the points in a normal
Q-Q plot should lie on or close to the diagonal. There is some amount of skew at the ends
here.
Using the 'predict' function
Once a model is built predict is the main function to test with new data. Our example will use the
mtcars built-in dataset to regress miles per gallon against displacement:
my_mdl <- lm(mpg ~ disp, data=mtcars)

my_mdl
Call:
lm(formula = mpg ~ disp, data = mtcars)
Coefficients:
(Intercept) disp
29.59985 -0.04122
If I had a new data source with displacement I could see the estimated miles per gallon.
set.seed(1234)
newdata <- sample(mtcars$disp, 5)
newdata
[1] 258.0 71.1 75.7 145.0 400.0
newdf <- data.frame(disp=newdata)

predict(my_mdl, newdf)
1 2 3 4 5
18.96635 26.66946 26.47987 23.62366 13.11381
The most important part of the process is to create a new data frame with the same column names
as the original data. In this case, the original data had a column labeled disp, I was sure to call the
new data that same name.
Caution
Let's look at a few common pitfalls:
1. not using a data.frame in the new object:
predict(my_mdl, newdata)
Error in eval(predvars, data, env) :
numeric 'envir' arg not of length one
2. not using same names in new data frame:
newdf2 <- data.frame(newdata)
predict(my_mdl, newdf2)
Error in eval(expr, envir, enclos) : object 'disp' not found
Accuracy
To check the accuracy of the prediction you will need the actual y values of the new data. In this
example, newdf will need a column for 'mpg' and 'disp'.
newdf <- data.frame(mpg=mtcars$mpg[1:10], disp=mtcars$disp[1:10])

# mpg disp
# 1 21.0 160.0
# 2 21.0 160.0
# 3 22.8 108.0
# 4 21.4 258.0
# 5 18.7 360.0
# 6 18.1 225.0
# 7 14.3 360.0
# 8 24.4 146.7
# 9 22.8 140.8
# 10 19.2 167.6
p <- predict(my_mdl, newdf)
#root mean square error

sqrt(mean((p - newdf$mpg)^2, na.rm=TRUE))
[1] 2.325148
Read Linear Models (Regression) online: https://riptutorial.com/r/topic/801/linear-models--

regression-
Chapter 62: Lists
Examples
Quick Introduction to Lists
In general, most of the objects you would interact with as a user would tend to be a vector; e.g
numeric vector, logical vector. These objects can only take in a single type of variable (a numeric
vector can only have numbers inside it).
A list would be able to store any type variable in it, making it to the generic object that can store
any type of variables we would need.
Example of initializing a list
exampleList1 <- list('a', 'b')

exampleList2 <- list(1, 2)
exampleList3 <- list('a', 1, 2)
In order to understand the data that was defined in the list, we can use the str function.
str(exampleList1)
str(exampleList2)
str(exampleList3)
Subsetting of lists distinguishes between extracting a slice of the list, i.e. obtaining a list containing
a subset of the elements in the original list, and extracting a single element. Using the [ operator
commonly used for vectors produces a new list.
# Returns List
exampleList3[1]
exampleList3[1:2]
To obtain a single element use [[ instead.
# Returns Character
exampleList3[[1]]
List entries may be named:
exampleList4 <- list(

num = 1:3,
numeric = 0.5,
char = c('a', 'b')
)
The entries in named lists can be accessed by their name instead of their index.
exampleList4[['char']]
Alternatively the $ operator can be used to access named elements.
exampleList4$num
This has the advantage that it is faster to type and may be easier to read but it is important to be
aware of a potential pitfall. The $ operator uses partial matching to identify matching list elements
and may produce unexpected results.
exampleList5 <- exampleList4[2:3]
exampleList4$num
# c(1, 2, 3)
exampleList5$num
# 0.5
exampleList5[['num']]
# NULL
Lists can be particularly useful because they can store objects of different lengths and of various
classes.
## Numeric vector
exampleVector1 <- c(12, 13, 14)
## Character vector
exampleVector2 <- c("a", "b", "c", "d", "e", "f")
## Matrix
exampleMatrix1 <- matrix(rnorm(4), ncol = 2, nrow = 2)
## List
exampleList3 <- list('a', 1, 2)
exampleList6 <- list(

num = exampleVector1,
char = exampleVector2,
mat = exampleMatrix1,
list = exampleList3
)
exampleList6
#$num
#[1] 12 13 14
#
#$char
#[1] "a" "b" "c" "d" "e" "f"
#
#$mat
# [,1] [,2]
#[1,] 0.5013050 -1.88801542
#[2,] 0.4295266 0.09751379
#
#$list
#$list[[1]]
#[1] "a"
#
#$list[[2]]
#[1] 1
#
#$list[[3]]
#[1] 2
Introduction to lists
Lists allow users to store multiple elements (like vectors and matrices) under a single object. You
can use the list function to create a list:
l1 <- list(c(1, 2, 3), c("a", "b", "c"))

l1
## [[1]]
## [1] 1 2 3
##
## [[2]]
## [1] "a" "b" "c"
Notice the vectors that make up the above list are different classes. Lists allow users to group
elements of different classes. Each element in a list can also have a name. List names are
accessed by the names function, and are assigned in the same manner row and column names are
assigned in a matrix.
names(l1)
## NULL
names(l1) <- c("vector1", "vector2")
l1
## $vector1
## [1] 1 2 3
##
## $vector2
## [1] "a" "b" "c"
It is often easier and safer to declare the list names when creating the list object.
l2 <- list(vec = c(1, 3, 5, 7, 9),

mat = matrix(data = c(1, 2, 3), nrow = 3))
l2
## $vec
## [1] 1 3 5 7 9
##
## $mat
## [,1]
## [1,] 1
## [2,] 2
## [3,] 3
names(l2)
## [1] "vec" "mat"
Above the list has two elements, named "vec" and "mat," a vector and matrix, resepcively.
Reasons for using lists
To the average R user, the list structure may appear to be the one of the more complicated data
structures to manipulate. There are no guarantees that all the elements within it are of the same
type; There is no guaranteed structure of how complicated/non-complicated that the list would be
(An element in a list could be a list)
However, one of the main reasons when to use lists to use it to pass parameters between
functions.
# Function example which returns a single element numeric vector

exampleFunction1 <- function(num1, num2){
result <- num1 + num2
return(result)
}
# Using example function 1

exampleFunction1(1, 2)
# Function example which returns a simple numeric vector

exampleFunction2 <- function(num1, num2, multiplier){
tempResult1 <- num1 + num2
tempResult2 <- tempResult1 * multiplier
result <- c(tempResult1, tempResult2)
return(result)
}

exampleFunction2(1, 2, 4)
In the above example, the returned results are just simple numeric vectors. There is no issues to
pass over such simple vectors.
It is important to note at this point that generally, R functions only return 1 result at a time (You can
use if conditions to return different results). However, if you intend to create a function which takes
a set of parameters and returns several type of results such a numeric vector(settings value) and a
data frame (from the calculation), you would need to dump all these results in a list before
returning it.
# We will be using mtcars dataset here

# Function which returns a result that is supposed to contain multiple type of results
# This can be solved by putting the results into a list
exampleFunction3 <- function(dataframe, removeColumn, sumColumn){
resultDataFrame <- dataframe[, -removeColumn]
resultSum <- sum(dataframe[, sumColumn])
resultList <- list(resultDataFrame, resultSum)
return(resultList)
}

exampleResult <- exampleFunction3(mtcars, 2, 4)
exampleResult[[1]]
exampleResult[[2]]
Convert a list to a vector while keeping empty list elements
When one wishes to convert a list to a vector or data.frame object empty elements are typically
dropped.
This can be problematic which a list is created of a desired length are created with some empty
values (e.g. a list with n elements is created to be added to an m x n matrix, data.frame, or
data.table). It is possible to losslessly convert a list to a vector however, retaining empty elements:
res <- list(character(0), c("Luzhuang", "Laisu", "Peihui"), character(0),

c("Anjiangping", "Xinzhai", "Yongfeng"), character(0), character(0),
c("Puji", "Gaotun", "Banjingcun"), character(0), character(0),
character(0))
res
[[1]]
character(0)
[[2]]
[1] "Luzhuang" "Laisu" "Peihui"
[[3]]
character(0)
[[4]]
[1] "Anjiangping" "Xinzhai" "Yongfeng"
[[5]]
character(0)
[[6]]
character(0)
[[7]]
[1] "Puji" "Gaotun" "Banjingcun"
[[8]]
character(0)
[[9]]
character(0)
[[10]]
character(0)
res <- sapply(res, function(s) if (length(s) == 0) NA_character_ else paste(s, collapse = "
"))
res
[1] NA "Luzhuang Laisu Peihui" NA

"Anjiangping Xinzhai Yongfeng" NA
[6] NA "Puji Gaotun Banjingcun" NA

NA NA
Serialization: using lists to pass informations
There exist cases in which it is necessary to put data of different types together. In Azure ML for
example, it is necessary to pass informations from a R script module to another one exclusively
throught dataframes. Suppose we have a dataframe and a number:
> df
name height team fun_index title age desc Y
1 Andrea 195 Lazio 97 6 33 eccellente 1
2 Paja 165 Fiorentina 87 6 31 deciso 1
3 Roro 190 Lazio 65 6 28 strano 0
4 Gioele 70 Lazio 100 0 2 simpatico 1
5 Cacio 170 Juventus 81 3 33 duro 0
6 Edola 171 Lazio 72 5 32 svampito 1
7 Salami 175 Inter 75 3 30 doppiopasso 1
8 Braugo 180 Inter 79 5 32 gjn 0
9 Benna 158 Juventus 80 6 28 esaurito 0
10 Riggio 182 Lazio 92 5 31 certezza 1
11 Giordano 185 Roma 79 5 29 buono 1
> number <- "42"
We can access to this information:
> paste(df$name[4],"is a",df3$team[4], "supporter." )

[1] "Gioele is a Lazio supporter."
> paste("The answer to THE question is", number )
[1] "The answer to THE question is 42"
In order to put different types of data in a dataframe we have to use the list object and the
serialization. In particular we have to put the data in a generic list and then put the list in a
particular dataframe:
l <- list(df,number)
dataframe_container <- data.frame(out2 = as.integer(serialize(l, connection=NULL)))
Once we have stored the information in the dataframe, we need to deserialize it in order to use it:
#----- unserialize ----------------------------------------+

unser_obj <- unserialize(as.raw(dataframe_container$out2))
#----- taking back the elements----------------------------+
df_mod <- unser_obj[1][[1]]
number_mod <- unser_obj[2][[1]]
Then, we can verify that the data are transfered correctly:
> paste(df_mod$name[4],"is a",df_mod$team[4], "supporter." )

[1] "Gioele is a Lazio supporter."
> paste("The answer to THE question is", number_mod )
[1] "The answer to THE question is 42"
Read Lists online: https://riptutorial.com/r/topic/1365/lists
Chapter 63: lubridate
Syntax
• ymd_hms(..., quiet = FALSE, tz = "UTC", locale = Sys.getlocale("LC_TIME"))
• now(tzone = "")
• interval(start, end, tzone = attr(start, "tzone"))
• duration(num = NULL, units = "seconds", ...)
• period(num = NULL, units = "second", ...)
Remarks
To install package from CRAN:
install.packages("lubridate")
To install development version from Github:
library(devtools)
# dev mode allows testing of development packages in a sandbox, without interfering
# with the other packages you have installed.
dev_mode(on=T)
install_github("hadley/lubridate")
dev_mode(on=F)
To get vignettes on lubridate package:
vignette("lubridate")
To get help about some function foo:
help(foo) # help about function foo

?foo # same thing
# Example
# help("is.period")
# ?is.period
To get examples for a function foo:
example("foo")
# Example
# example("interval")
Examples
Parsing dates and datetimes from strings with lubridate
The lubridate package provides convenient functions to format date and datetime objects from
character strings. The functions are permutations of
Letter Element to parse Base R equivalent
y year %y, %Y
m (with y and d) month %m, %b, %h, %B
d day %d, %e
h hour %H, %I%p
m (with h and s) minute %M
s seconds %S
e.g. ymd() for parsing a date with the year followed by the month followed by the day, e.g. "2016-
07-22", or ymd_hms() for parsing a datetime in the order year, month, day, hours, minutes, seconds,
e.g. "2016-07-22 13:04:47".
The functions are able to recognize most separators (such as /, -, and whitespace) without
additional arguments. They also work with inconsistent separators.
Dates
The date functions return an object of class Date.
library(lubridate)
mdy(c(' 07/02/2016 ', '7 / 03 / 2016', ' 7 / 4 / 16 '))

## [1] "2016-07-02" "2016-07-03" "2016-07-04"
ymd(c("20160724","2016/07/23","2016-07-25")) # inconsistent separators

## [1] "2016-07-24" "2016-07-23" "2016-07-25"
Datetimes
Utility functions
Datetimes can be parsed using ymd_hms variants including ymd_hm and ymd_h. All datetime functions
can accept a tz timezone argument akin to that of as.POSIXct or strptime, but which defaults to
"UTC"
instead of the local timezone.
The datetime functions return an object of class POSIXct.
x <- c("20160724 130102","2016/07/23 14:02:01","2016-07-25 15:03:00")

ymd_hms(x, tz="EST")
## [1] "2016-07-24 13:01:02 EST" "2016-07-23 14:02:01 EST"
## [3] "2016-07-25 15:03:00 EST"
ymd_hms(x)
## [1] "2016-07-24 13:01:02 UTC" "2016-07-23 14:02:01 UTC"
## [3] "2016-07-25 15:03:00 UTC"
Parser functions
lubridate also includes three functions for parsing datetimes with a formatting string like as.POSIXct
or strptime:
Function Output Class Formatting strings accepted
Flexible. Will accept strptime-style with % or lubridate

datetime function name style, e.g "ymd hms". Will accept
parse_date_time POSIXct
a vector of orders for heterogeneous data and guess
which is appropriate.
Default
Strict. Accepts only strptime tokens (with or without %)
parse_date_time2 POSIXct; if lt =
from a limited set.
TRUE, POSIXlt
Default POSIXlt;
Strict. Accepts only %-delimited strptime tokens with
fast_strptime if lt = FALSE,
delimiters (-, /, :, etc.) from a limited set.
POSIXct
x <- c('2016-07-22 13:04:47', '07/22/2016 1:04:47 pm')
parse_date_time(x, orders = c('mdy Imsp', 'ymd hms'))

## [1] "2016-07-22 13:04:47 UTC" "2016-07-22 13:04:47 UTC"
x <- c('2016-07-22 13:04:47', '2016-07-22 14:47:58')
parse_date_time2(x, orders = 'Ymd HMS')

## [1] "2016-07-22 13:04:47 UTC" "2016-07-22 14:47:58 UTC"
fast_strptime(x, format = '%Y-%m-%d %H:%M:%S')

## [1] "2016-07-22 13:04:47 UTC" "2016-07-22 14:47:58 UTC"
parse_date_time2 and fast_strptime use a fast C parser for efficiency.
See ?parse_date_time for formatting tokens.
Parsing date and time in lubridate
Lubridate provides ymd() series of functions for parsing character strings into dates. The letters y,
m, and d correspond to the year, month, and day elements of a date-time.
mdy("07-21-2016") # Returns Date
## [1] "2016-07-21"
mdy("07-21-2016", tz = "UTC") # Returns a vector of class POSIXt
## "2016-07-21 UTC"
dmy("21-07-2016") # Returns Date
## [1] "2016-07-21"
dmy(c("21.07.2016", "22.07.2016")) # Returns vector of class Date
## [1] "2016-07-21" "2016-07-22"
Manipulating date and time in lubridate
date <- now()

date
## "2016-07-22 03:42:35 IST"
year(date)
## 2016
minute(date)
## 42
wday(date, label = T, abbr = T)

# [1] Fri
# Levels: Sun < Mon < Tues < Wed < Thurs < Fri < Sat
day(date) <- 31
## "2016-07-31 03:42:35 IST"
# If an element is set to a larger value than it supports, the difference

# will roll over into the next higher element
day(date) <- 32
## "2016-08-01 03:42:35 IST"
Instants
An instant is a specific moment in time. Any date-time object that refers to a moment of time is
recognized as an instant. To test if an object is an instant, use is.instant.
library(lubridate)
today_start <- dmy_hms("22.07.2016 12:00:00", tz = "IST") # default tz="UTC"

today_start
## [1] "2016-07-22 12:00:00 IST"
is.instant(today_start)
## [1] TRUE
now_dt <- ymd_hms(now(), tz="IST")
now_dt
## [1] "2016-07-22 13:53:09 IST"
is.instant(now_dt)
## [1] TRUE
is.instant("helloworld")
## [1] FALSE
is.instant(60)
## [1] FALSE
Intervals, Durations and Periods
Intervals are simplest way of recording timespans in lubridate. An interval is a span of time that
occurs between two specific instants.
# create interval by substracting two instants

today_start <- ymd_hms("2016-07-22 12-00-00", tz="IST")
today_start
## [1] "2016-07-22 12:00:00 IST"
today_end <- ymd_hms("2016-07-22 23-59-59", tz="IST")
today_end
## [1] "2016-07-22 23:59:59 IST"
span <- today_end - today_start
span
## Time difference of 11.99972 hours
as.interval(span, today_start)
## [1] 2016-07-22 12:00:00 IST--2016-07-22 23:59:59 IST
# create interval using interval() function

span <- interval(today_start, today_end)
[1] 2016-07-22 12:00:00 IST--2016-07-22 23:59:59 IST
Durations measure the exact amount of time that occurs between two instants.
duration(60, "seconds")
## [1] "60s"
duration(2, "minutes")
## [1] "120s (~2 minutes)"
Note: Units larger than weeks are not used due to their variability.
Durations can be created using dseconds, dminutes and other duration helper functions.
Run ?quick_durations for complete list.
dseconds(60)
## [1] "60s"
dhours(2)
## [1] "7200s (~2 hours)"
dyears(1)
## [1] "31536000s (~365 days)"
Durations can be subtracted and added to instants to get new instants.
today_start + dhours(5)
## [1] "2016-07-22 17:00:00 IST"
today_start + dhours(5) + dminutes(30) + dseconds(15)

## [1] "2016-07-22 17:30:15 IST"
Durations can be created from intervals.
as.duration(span)
[1] "43199s (~12 hours)"
Periods measure the change in clock time that occurs between two instants.
Periods can be created using period function as well other helper functions like seconds, hours, etc.
To get a complete list of period helper functions, Run ?quick_periods.
period(1, "hour")
## [1] "1H 0M 0S"
hours(1)
## [1] "1H 0M 0S"
period(6, "months")
## [1] "6m 0d 0H 0M 0S"
months(6)
## [1] "6m 0d 0H 0M 0S"
years(1)
## [1] "1y 0m 0d 0H 0M 0S"
is.period function can be used to check if an object is a period.
is.period(years(1))
## [1] TRUE
is.period(dyears(1))
## [1] FALSE
Rounding dates
now_dt <- ymd_hms(now(), tz="IST")

now_dt
## [1] "2016-07-22 13:53:09 IST"
round_date() takes a date-time object and rounds it to the nearest integer value of the specified
time unit.
round_date(now_dt, "minute")
## [1] "2016-07-22 13:53:00 IST"
round_date(now_dt, "hour")
## [1] "2016-07-22 14:00:00 IST"
round_date(now_dt, "year")
## [1] "2017-01-01 IST"
floor_date() takes a date-time object and rounds it down to the nearest integer value of the
specified time unit.
floor_date(now_dt, "minute")
## [1] "2016-07-22 13:53:00 IST"
floor_date(now_dt, "hour")
## [1] "2016-07-22 13:00:00 IST"
floor_date(now_dt, "year")
## [1] "2016-01-01 IST"
ceiling_date() takes a date-time object and rounds it up to the nearest integer value of the
specified time unit.
ceiling_date(now_dt, "minute")
## [1] "2016-07-22 13:54:00 IST"
ceiling_date(now_dt, "hour")
## [1] "2016-07-22 14:00:00 IST"
ceiling_date(now_dt, "year")
## [1] "2017-01-01 IST"
Difference between period and duration
Unlike durations, periods can be used to accurately model clock times without knowing when
events such as leap seconds, leap days, and DST changes occur.
start_2012 <- ymd_hms("2012-01-01 12:00:00")

## [1] "2012-01-01 12:00:00 UTC"
# period() considers leap year calculations.

start_2012 + period(1, "years")
## [1] "2013-01-01 12:00:00 UTC"
# Here duration() doesn't consider leap year calculations.

start_2012 + duration(1)
## [1] "2012-12-31 12:00:00 UTC"
Time Zones
with_tz returns a date-time as it would appear in a different time zone.
nyc_time <- now("America/New_York")

nyc_time
## [1] "2016-07-22 05:49:08 EDT"
# corresponding Europe/Moscow time

with_tz(nyc_time, tzone = "Europe/Moscow")
## [1] "2016-07-22 12:49:08 MSK"
force_tz returns a the date-time that has the same clock time as x in the new time zone.
nyc_time <- now("America/New_York")

nyc_time
## [1] "2016-07-22 05:49:08 EDT"
force_tz(nyc_time, tzone = "Europe/Moscow") # only timezone changes

## [1] "2016-07-22 05:49:08 MSK"
Read lubridate online: https://riptutorial.com/r/topic/2496/lubridate
Chapter 64: Machine learning
Examples
Creating a Random Forest model
One example of machine learning algorithms is the Random Forest alogrithm (Breiman, L. (2001).
Random Forests. Machine Learning 45(5), p. 5-32). This algorithm is implemented in R according
to Breiman's original Fortran implementation in the randomForest package.
Random Forest classifier objects can be created in R by preparing the class variable as factor,
which is already apparent in the iris data set. Therefore we can easily create a Random Forest
by:
library(randomForest)
rf <- randomForest(x = iris[, 1:4],

y = iris$Species,
ntree = 500,
do.trace = 100)
rf
# Call:
# randomForest(x = iris[, 1:4], y = iris$Species, ntree = 500, do.trace = 100)
# Type of random forest: classification
# Number of trees: 500
# No. of variables tried at each split: 2
#
# OOB estimate of error rate: 4%
# Confusion matrix:
# setosa versicolor virginica class.error
# setosa 50 0 0 0.00
# versicolor 0 47 3 0.06
# virginica 0 3 47 0.06
parameters Description
x a data frame holding the describing variables of the classes
the classes of the individual obserbations. If this vector is factor, a

y
classification model is created, if not a regression model is created.
ntree The number of individual CART trees built
do.trace every ith step, the out-of-the-box errors overall and for each class are returned
Read Machine learning online: https://riptutorial.com/r/topic/8326/machine-learning
Chapter 65: Matrices
Introduction
Matrices store data
Examples
Creating matrices
Under the hood, a matrix is a special kind of vector with two dimensions. Like a vector, a matrix
can only have one data class. You can create matrices using the matrix function as shown below.
matrix(data = 1:6, nrow = 2, ncol = 3)

## [,1] [,2] [,3]
## [1,] 1 3 5
## [2,] 2 4 6
As you can see this gives us a matrix of all numbers from 1 to 6 with two rows and three columns.
The data parameter takes a vector of values, nrow specifies the number of rows in the matrix, and
ncol specifies the number of columns. By convention the matrix is filled by column. The default
behavior can be changed with the byrow parameter as shown below:
matrix(data = 1:6, nrow = 2, ncol = 3, byrow = TRUE)

## [,1] [,2] [,3]
## [1,] 1 2 3
## [2,] 4 5 6
Matrices do not have to be numeric – any vector can be transformed into a matrix. For example:
matrix(data = c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE), nrow = 3, ncol = 2)

## [,1] [,2]
## [1,] TRUE FALSE
## [2,] TRUE FALSE
## [3,] TRUE FALSE
matrix(data = c("a", "b", "c", "d", "e", "f"), nrow = 3, ncol = 2)
## [,1] [,2]
## [1,] "a" "d"
## [2,] "b" "e"
## [3,] "c" "f"
Like vectors matrices can be stored as variables and then called later. The rows and columns of a
matrix can have names. You can look at these using the functions rownames and colnames. As
shown below, the rows and columns don't initially have names, which is denoted by NULL.
However, you can assign values to them.
mat1 <- matrix(data = 1:6, nrow = 2, ncol = 3, byrow = TRUE)

rownames(mat1)
## NULL
colnames(mat1)
## NULL
rownames(mat1) <- c("Row 1", "Row 2")
colnames(mat1) <- c("Col 1", "Col 2", "Col 3")
mat1
## Col 1 Col 2 Col 3
## Row 1 1 2 3
## Row 2 4 5 6
It is important to note that similarly to vectors, matrices can only have one data type. If you try to
specify a matrix with multiple data types the data will be coerced to the higher order data class.
The class, is, and as functions can be used to check and coerce data structures in the same way
they were used on the vectors in class 1.
class(mat1)
## [1] "matrix"
is.matrix(mat1)
## [1] TRUE
as.vector(mat1)
## [1] 1 4 2 5 3 6
Read Matrices online: https://riptutorial.com/r/topic/9019/matrices
Chapter 66: Meta: Documentation Guidelines
Remarks
To discuss editing the R tag Docs, visit the R chat.
Examples
Making good examples
Most of the guidance for creating good examples for Q&A carries over into the documentation.
• Make it minimal and get to the point. Complications and digressions are counterproductive.
• Include both working code and prose explaining it. Neither one is sufficient on its own.
• Don't rely on external sources for data. Generate data or use the datasets library if possible:
library(help = "datasets")
There are some additional considerations in the context of Docs:
• Refer to built-in docs like ?data.frame whenever relevant. The SO Docs are not an attempt to
replace the built-in docs. It is important to make sure new R users know that the built-in docs
exist as well as how to find them.
• Move content that applies to multiple examples to the Remarks section.
Style
Prompts
If you want your code to be copy-pastable, remove prompts such as R>, >, or + at the beginning of
each new line. Some Docs authors prefer to not make copy-pasting easy, and that is okay.
Console output
Console output should be clearly distinguished from code. Common approaches include:
• Include prompts on input (as seen when using the console).

• Comment out all output, with # or ## starting each line.
• Print as-is, trusting the leading [1] to make the output stand out from the input.
• Add a blank line between code and console output.
Assignment
= and <- are fine for assigning R objects. Use white space appropriately to avoid writing code that
is difficult to parse, such as x<-1 (ambiguous between x <- 1 and x < -1)
Code comments
Be sure to explain the purpose and function of the code itself. There isn't any hard-and-fast rule on
whether this explanation should be in prose or in code comments. Prose may be more readable
and allows for longer explanations, but code comments make for easier copy-pasting. Keep both
options in mind.
Sections
Many examples are short enough to not need sections, but if you use them, start with H1.
Read Meta: Documentation Guidelines online: https://riptutorial.com/r/topic/5410/meta--

documentation-guidelines
Chapter 67: Missing values
Introduction
When we don't know the value a variable takes, we say its value is missing, indicated by NA.
Remarks
Missing values are represented by the symbol NA (not available). Impossible values (e.g., as a
result of sqrt(-1)) are represented by the symbol NaN (not a number).
Examples
Examining missing data
anyNAreports whether any missing values are present; while is.na reports missing values
elementwise:
vec <- c(1, 2, 3, NA, 5)
anyNA(vec)
# [1] TRUE
is.na(vec)
# [1] FALSE FALSE FALSE TRUE FALSE
returns a logical vector that is coerced to integer values under arithmetic operations (with
ìs.na
FALSE=0, TRUE=1). We can use this to find out how many missing values there are:
sum(is.na(vec))
# [1] 1
Extending this approach, we can use colSums and is.na on a data frame to count NAs per column:
colSums(is.na(airquality))
# Ozone Solar.R Wind Temp Month Day
# 37 7 0 0 0 0
The naniar package (currently on github but not CRAN) offers further tools for exploring missing
values.
Reading and writing data with NA values
When reading tabular datasets with the read.* functions, R automatically looks for missing values
that look like "NA". However, missing values are not always represented by NA. Sometimes a dot (.
), a hyphen(-) or a character-value (e.g.: empty) indicates that a value is NA. The na.strings
parameter of the read.* function can be used to tell R which symbols/characters need to be
treated as NA values:
read.csv("name_of_csv_file.csv", na.strings = "-")
It is also possible to indicate that more than one symbol needs to be read as NA:
read.csv('missing.csv', na.strings = c('.','-'))
Similarly, NAs can be written with customized strings using the na argument to write.csv. Other
tools for reading and writing tables have similar options.
Using NAs of different classes
The symbol NA is for a logical missing value:
class(NA)
#[1] "logical"
This is convenient, since it can easily be coerced to other atomic vector types, and is therefore
usually the only NA you will need:
x <- c(1, NA, 1)

class(x[2])
#[1] "numeric"
If you do need a single NA value of another type, use NA_character_, NA_integer_, NA_real_ or
NA_complex_. For missing values of fancy classes, subsetting with NA_integer_ usually works; for
example, to get a missing-value Date:
class(Sys.Date()[NA_integer_])
# [1] "Date"
TRUE/FALSE and/or NA
NA is a logical type and a logical operator with an NA will return NA if the outcome is ambiguous.
Below, NA OR TRUE evaluates to TRUE because at least one side evaluates to TRUE, however NA OR
FALSE returns NA because we do not know whether NA would have been TRUE or FALSE
NA | TRUE
# [1] TRUE
# TRUE | TRUE is TRUE and FALSE | TRUE is also TRUE.
NA | FALSE
# [1] NA
# TRUE | FALSE is TRUE but FALSE | FALSE is FALSE.
NA & TRUE
# [1] NA
# TRUE & TRUE is TRUE but FALSE & TRUE is FALSE.
NA & FALSE
# [1] FALSE
# TRUE & FALSE is FALSE and FALSE & FALSE is also FALSE.
These properties are helpful if you want to subset a data set based on some columns that contain
NA.
df <- data.frame(v1=0:9,
v2=c(rep(1:2, each=4), NA, NA),
v3=c(NA, letters[2:10]))
df[df$v2 == 1 & !is.na(df$v2), ]

# v1 v2 v3
#1 0 1 <NA>
#2 1 1 b
#3 2 1 c
#4 3 1 d
df[df$v2 == 1, ]
v1 v2 v3
#1 0 1 <NA>
#2 1 1 b
#3 2 1 c
#4 3 1 d
#NA NA NA <NA>
#NA.1 NA NA <NA>
Omitting or replacing missing values
Recoding missing values

Regularly, missing data isn't coded as NA in datasets. In SPSS for example, missing values are
often represented by the value 99.
num.vec <- c(1, 2, 3, 99, 5)

num.vec
## [1] 1 2 3 99 5
It is possible to directly assign NA using subsetting
num.vec[num.vec == 99] <- NA
However, the preferred method is to use is.na<- as below. The help file (?is.na) states:
is.na<-may provide a safer way to set missingness. It behaves differently for factors,
for example.
is.na(num.vec) <- num.vec == 99
Both methods return
num.vec
## [1] 1 2 3 NA 5
Removing missing values

Missing values can be removed in several ways from a vector:
num.vec[!is.na(num.vec)]
num.vec[complete.cases(num.vec)]
na.omit(num.vec)
## [1] 1 2 3 5
Excluding missing values from calculations

When using arithmetic functions on vectors with missing values, a missing value will be returned:
mean(num.vec) # returns: [1] NA
The na.rm parameter tells the function to exclude the NA values from the calculation:
mean(num.vec, na.rm = TRUE) # returns: [1] 2.75
# an alternative to using 'na.rm = TRUE':

mean(num.vec[!is.na(num.vec)]) # returns: [1] 2.75
Some R functions, like lm, have a na.action parameter. The default-value for this is na.omit, but
with options(na.action = 'na.exclude') the default behavior of R can be changed.
If it is not necessary to change the default behavior, but for a specific situation another na.action is
needed, the na.action parameter needs to be included in the function call, e.g.:
lm(y2 ~ y1, data = anscombe, na.action = 'na.exclude')
Read Missing values online: https://riptutorial.com/r/topic/3388/missing-values
Chapter 68: Modifying strings by substitution
Introduction
suband gsub are used to edit strings using patterns. See Pattern Matching and Replacement for
more on related functions and Regular Expressions for how to build a pattern.
Examples
Rearrange character strings using capture groups
If you want to change the order of a character strings you can use parentheses in the pattern to
group parts of the string together. These groups can in the replacement argument be addresed
using consecutive numbers.
The following example shows how you can reorder a vector of names of the form "surname,
forename" into a vector of the form "forename surname".
library(randomNames)
set.seed(1)
strings <- randomNames(5)

strings
# [1] "Sigg, Zachary" "Holt, Jake" "Ortega, Sandra" "De La Torre,
Nichole"
# [5] "Perkins, Donovon"
sub("^(.+),\\s(.+)$", "\\2 \\1", strings)

# [1] "Zachary Sigg" "Jake Holt" "Sandra Ortega" "Nichole De La Torre"
# [5] "Donovon Perkins"
If you only need the surname you could just address the first pairs of parentheses.
sub("^(.+),\\s(.+)", "\\1", strings)

# [1] "Sigg" "Holt" "Ortega" "De La Torre" "Perkins"
Eliminate duplicated consecutive elements
Let's say we want to eliminate duplicated subsequence element from a string (it can be more than
one). For example:
2,14,14,14,19
and convert it into:
2,14,19
Using gsub, we can achieve it:
gsub("(\\d+)(,\\1)+","\\1", "2,14,14,14,19")
[1] "2,14,19"
It works also for more than one different repetition, for example:
> gsub("(\\d+)(,\\1)+", "\\1", "2,14,14,14,19,19,20,21")

[1] "2,14,19,20,21"
Let's explain the regular expression:
1. (\\d+): A group 1 delimited by () and finds any digit (at least one). Remember we need to
use the double backslash (\\) here because for a character variable a backslash represents
special escape character for literal string delimiters (\" or \'). \d\ is equivalent to: [0-9].
2. ,: A punctuation sign: , (we can include spaces or any other delimiter)
3. \\1: An identical string to the group 1, i.e.: the repeated number. If that doesn't happen, then
the pattern doesn't match.
Let's try a similar situation: eliminate consecutive repeated words:
one,two,two,three,four,four,five,six
Then, just replace \d by \w, where \w matches any word character, including: any letter, digit or
underscore. It is equivalent to [a-zA-Z0-9_]:
> gsub("(\\w+)(,\\1)+", "\\1", "one,two,two,three,four,four,five,six")

[1] "one,two,three,four,five,six"
>
Then, the above pattern includes as a particular case duplicated digits case.
Read Modifying strings by substitution online: https://riptutorial.com/r/topic/9219/modifying-strings-

by-substitution
Chapter 69: Natural language processing
Introduction
Natural language processing (NLP) is the field of computer sciences focused on retrieving
information from textual input generated by human beings.
Examples
Create a term frequency matrix
The simplest approach to the problem (and the most commonly used so far) is to split sentences
into tokens. Simplifying, words have abstract and subjective meanings to the people using and
receiving them, tokens have an objective interpretation: an ordered sequence of characters (or
bytes). Once sentences are split, the order of the token is disregarded. This approach to the
problem in known as bag of words model.
A term frequency is a dictionary, in which to each token is assigned a weight. In the first example,
we construct a term frequency matrix from a corpus corpus (a collection of documents) with the
R package tm.
require(tm)
doc1 <- "drugs hospitals doctors"
doc2 <- "smog pollution environment"
doc3 <- "doctors hospitals healthcare"
doc4 <- "pollution environment water"
corpus <- c(doc1, doc2, doc3, doc4)
tm_corpus <- Corpus(VectorSource(corpus))
In this example, we created a corpus of class Corpus defined by the package tm with two functions
Corpus and VectorSource, which returns a VectorSource object from a character vector. The object
tm_corpus is a list our documents with additional (and optional) metadata to describe each
document.
str(tm_corpus)
List of 4
$ 1:List of 2
..$ content: chr "drugs hospitals doctors"
..$ meta :List of 7
.. ..$ author : chr(0)
.. ..$ datetimestamp: POSIXlt[1:1], format: "2017-06-03 00:31:34"
.. ..$ description : chr(0)
.. ..$ heading : chr(0)
.. ..$ id : chr "1"
.. ..$ language : chr "en"
.. ..$ origin : chr(0)
.. ..- attr(*, "class")= chr "TextDocumentMeta"
..- attr(*, "class")= chr [1:2] "PlainTextDocument" "TextDocument"
[truncated]
Once we have a Corpus, we can proceed to preprocess the tokens contained in the Corpus to
improve the quality of the final output (the term frequency matrix). To do this we use the tm
function tm_map, which similarly to the apply family of functions, transform the documents in the
corpus by applying a function to each document.
tm_corpus <- tm_map(tm_corpus, tolower)

tm_corpus <- tm_map(tm_corpus, removeWords, stopwords("english"))
tm_corpus <- tm_map(tm_corpus, removeNumbers)
tm_corpus <- tm_map(tm_corpus, PlainTextDocument)
tm_corpus <- tm_map(tm_corpus, stemDocument, language="english")
tm_corpus <- tm_map(tm_corpus, stripWhitespace)
tm_corpus <- tm_map(tm_corpus, PlainTextDocument)
Following these transformations, we finally create the term frequency matrix with
tdm <- TermDocumentMatrix(tm_corpus)
which gives a
<<TermDocumentMatrix (terms: 8, documents: 4)>>

Non-/sparse entries: 12/20
Sparsity : 62%
Maximal term length: 9
Weighting : term frequency (tf)
that we can view by transforming it to a matrix
as.matrix(tdm)
Docs
Terms character(0) character(0) character(0) character(0)
doctor 1 0 1 0
drug 1 0 0 0
environ 0 1 0 1
healthcar 0 0 1 0
hospit 1 0 1 0
pollut 0 1 0 1
smog 0 1 0 0
water 0 0 0 1
Each row represents the frequency of each token - that as you noticed have been stemmed (e.g.
environment to environ) - in each document (4 documents, 4 columns).
In the previous lines, we have weighted each pair token/document with the absolute frequency
(i.e. the number of instances of the token that appear in the document).
Read Natural language processing online: https://riptutorial.com/r/topic/10119/natural-language-

processing
Chapter 70: Network analysis with the igraph
package
Examples
Simple Directed and Non-directed Network Graphing
The igraph package for R is a wonderful tool that can be used to model networks, both real and
virtual, with simplicity. This example is meant to demonstrate how to create two simple network
graphs using the igraph package within R v.3.2.3.
Non-Directed Network
The network is created with this piece of code:
g<-graph.formula(Node1-Node2, Node1-Node3, Node4-Node1)

plot(g)
Directed Network
dg<-graph.formula(Tom-+Mary, Tom-+Bill, Tom-+Sam, Sue+-Mary, Bill-+Sue)

plot(dg)
This code will then generate a network with arrows:
Code example of how to make a double sided arrow:
dg<-graph.formula(Tom-+Mary, Tom-+Bill, Tom-+Sam, Sue+-Mary, Bill++Sue)

plot(dg)
Read Network analysis with the igraph package online: https://riptutorial.com/r/topic/4851/network-

analysis-with-the-igraph-package
Chapter 71: Non-standard evaluation and
standard evaluation
Introduction
Dplyr and many modern libraries in R use non-standard evaluation (NSE) for interactive
programming and standard evaluation (SE) for programming1.
For instance, the summarise() function use non-standard evaluation but relies on the summarise_()
which uses standard evaluation.
The lazyeval library makes it easy to turn standard evaluation function into NSE functions.
Examples
Examples with standard dplyr verbs
NSE functions should be used in interactive programming. However, when developping new
functions in a new package, it's better to use SE version.
Load dplyr and lazyeval :
library(dplyr)
library(lazyeval)
Filtering
NSE version
filter(mtcars, cyl == 8)
filter(mtcars, cyl < 6)
filter(mtcars, cyl < 6 & vs == 1)
SE version (to be use when programming functions in a new package)
filter_(mtcars, .dots = list(~ cyl == 8))

filter_(mtcars, .dots = list(~ cyl < 6))
filter_(mtcars, .dots = list(~ cyl < 6, ~ vs == 1))
Summarise
NSE version
summarise(mtcars, mean(disp))
summarise(mtcars, mean_disp = mean(disp))
SE version
summarise_(mtcars, .dots = lazyeval::interp(~ mean(x), x = quote(disp)))

summarise_(mtcars, .dots = setNames(list(lazyeval::interp(~ mean(x), x = quote(disp))),
"mean_disp"))
summarise_(mtcars, .dots = list("mean_disp" = lazyeval::interp(~ mean(x), x = quote(disp))))
Mutate
NSE version
mutate(mtcars, displ_l = disp / 61.0237)
SE version
mutate_(
.data = mtcars,
.dots = list(
"displ_l" = lazyeval::interp(
~ x / 61.0237, x = quote(disp)
)
)
)
Read Non-standard evaluation and standard evaluation online:

https://riptutorial.com/r/topic/9365/non-standard-evaluation-and-standard-evaluation
Chapter 72: Numeric classes and storage
modes
Examples
Numeric
Numeric represents integers and doubles and is the default mode assigned to vectors of numbers.
The function is.numeric() will evaluate whether a vector is numeric. It is important to note that
although integers and doubles will pass is.numeric(), the function as.numeric() will always attempt
to convert to type double.
x <- 12.3
y <- 12L
#confirm types
typeof(x)
[1] "double"
typeof(y)
[1] "integer"
# confirm both numeric

is.numeric(x)
[1] TRUE
is.numeric(y)
[1] TRUE
# logical to numeric
as.numeric(TRUE)
[1] 1
# While TRUE == 1, it is a double and not an integer

is.integer(as.numeric(TRUE))
[1] FALSE
Doubles are R's default numeric value. They are double precision vectors, meaning that they take
up 8 bytes of memory for each value in the vector. R has no single precision data type and so all
real numbers are stored in the double precision format.
is.double(1)
TRUE
is.double(1.0)
TRUE
is.double(1L)
FALSE
Integers are whole numbers that can be written without a fractional component. Integers are
represented by a number with an L after it. Any number without an L after it will be considered a
double.
typeof(1)
[1] "double"
class(1)
[1] "numeric"
typeof(1L)
[1] "integer"
class(1L)
[1] "integer"
Though in most cases using an integer or double will not matter, sometimes replacing doubles
with integers will consume less memory and operational time. A double vector uses 8 bytes per
element while an integer vector uses only 4 bytes per element. As the size of vectors increases,
using proper types can dramatically speed up processes.
# test speed on lots of arithmetic

microbenchmark(
for( i in 1:100000){
2L * i
10L + i
},
for( i in 1:100000){
2.0 * i
10.0 + i
}
)
Unit: milliseconds
expr min lq mean median uq
max neval
for (i in 1:1e+05) { 2L * i 10L + i } 40.74775 42.34747 50.70543 42.99120 65.46864
94.11804 100
for (i in 1:1e+05) { 2 * i 10 + i } 41.07807 42.38358 53.52588 44.26364 65.84971
83.00456 100
Read Numeric classes and storage modes online: https://riptutorial.com/r/topic/9018/numeric-

classes-and-storage-modes
Chapter 73: Object-Oriented Programming in
R
Introduction
This documentation page describes the four object systems in R and their high-level similarities
and differences. Greater detail on each individual system can be found on its own topic page.
The four systems are: S3, S4, Reference Classes, and S6.
Examples
S3
The S3 object system is a very simple OO system in R.
Every object has an S3 class. It can be get (got?) with the function class.
> class(3)
[1] "numeric"
It can also be set with the function class:
> bicycle <- 2

> class(bicycle) <- 'vehicle'
> class(bicycle)
[1] "vehicle"
It can also be set with the function attr:
> velocipede <- 2

> attr(velocipede, 'class') <- 'vehicle'
> class(velocipede)
[1] "vehicle"
An object can have many classes:
> class(x = bicycle) <- c('human-powered vehicle', class(x = bicycle))

> class(x = bicycle)
[1] "human-powered vehicle" "vehicle"
When using a generic function, R uses the first element of the class that has an available generic.
For example:
> summary.vehicle <- function(object, ...) {
+ message('this is a vehicle')
+ }
> summary(object = my_bike)
this is a vehicle
But if we now define a summary.bicycle:
> summary.bicycle <- function(object, ...) {

+ message('this is a bicycle')
+ }
> summary(object = my_bike)
this is a bicycle
Read Object-Oriented Programming in R online: https://riptutorial.com/r/topic/9723/object-oriented-

programming-in-r
Chapter 74: Parallel processing
Remarks
Parallelization on remote machines require libraries to be downloaded on each machine. Prefer
package::function() calls. Several packages have parallelization natively built-in, including caret,
pls and plyr.
Microsoft R Open (Revolution R) also uses multi-threaded BLAS/LAPACK libraries which

intrinsically parallelizes many common functions.
Examples
Parallel processing with foreach package
The foreach package brings the power of parallel processing to R. But before you want to use multi
core CPUs you have to assign a multi core cluster. The doSNOW package is one possibility.
A simple use of the foreach loop is to calculate the sum of the square root and the square of all
numbers from 1 to 100000.
library(foreach)
library(doSNOW)
cl <- makeCluster(5, type = "SOCK")

registerDoSNOW(cl)
f <- foreach(i = 1:100000, .combine = c, .inorder = F) %dopar% {

k <- i ** 2 + sqrt(i)
k
}
The structure of the output of foreach is controlled by the .combine argument. The default output
structure is a list. In the code above, c is used to return a vector instead. Note that a calculation
function (or operator) such as "+" may also be used to perform a calculation and return a further
processed object.
It is important to mention that the result of each foreach-loop is the last call. Thus, in this example
k will be added to the result.
Parameter Details
combine Function. Determines how the results of the loop are combined.
.combine
Possible values are c, cbind, rbind, "+", "*"...
if TRUE the result is ordered according to the order of the iteration vairable (here i
.inorder ). If FALSE the result is not ordered. This can have postive effects on computation
time.
Parameter Details
for functions which are provided by any package except base, like e.g. mass,
.packages randomForest or else, you have to provide these packages with c("mass",
"randomForest")
Parallel processing with parallel package
The base package parallel allows parallel computation through forking, sockets, and random-
number generation.
Detect the number of cores present on the localhost:
parallel::detectCores(all.tests = FALSE, logical = TRUE)
Create a cluster of the cores on the localhost:
parallelCluster <- parallel::makeCluster(parallel::detectCores())
First, a function appropriate for parallelization must be created. Consider the mtcars dataset. A
regression on mpg could be improved by creating a separate regression model for each level of cyl.
data <- mtcars

yfactor <- 'cyl'
zlevels <- sort(unique(data[[yfactor]]))
datay <- data[,1]
dataz <- data[,2]
datax <- data[,3:11]
fitmodel <- function(zlevel, datax, datay, dataz) {

glm.fit(x = datax[dataz == zlevel,], y = datay[dataz == zlevel])
}
Create a function that can loop through all the possible iterations of zlevels. This is still in serial,
but is an important step as it determines the exact process that will be parallelized.

}
for (zlevel in zlevels) {

print("*****")
print(zlevel)
print(fitmodel(zlevel, datax, datay, dataz))
}
Curry this function:
worker <- function(zlevel) {

fitmodel(zlevel,datax, datay, dataz)
}
Parallel computing using parallel cannot access the global environment. Luckily, each function
creates a local environment parallel can access. Creation of a wrapper function allows for
parallelization. The function to be applied also needs to be placed within the environment.
wrapper <- function(datax, datay, dataz) {

# force evaluation of all paramters not supplied by parallelization apply
force(datax)
force(datay)
force(dataz)
# these variables are now in an enviroment accessible by parallel function
# function to be applied also in the environment

}
# calling in this environment iterating over single parameter zlevel

worker <- function(zlevel) {
fitmodel(zlevel,datax, datay, dataz)
}
return(worker)
}
Now create a cluster and run the wrapper function.
parallelcluster <- parallel::makeCluster(parallel::detectCores())

models <- parallel::parLapply(parallelcluster,zlevels,
wrapper(datax, datay, dataz))
Always stop the cluster when finished.
parallel::stopCluster(parallelcluster)
The parallel package includes the entire apply() family, prefixed with par.
Random Number Generation
A major problem with parallelization is the used of RNG as seeds. Random numbers by the
number are iterated by the number of operations from either the start of the session or the most
recent set.seed(). Since parallel processes arise from the same function, it can use the same
seed, possibly causing identical results! Calls will run in serial on the different cores, provide no
advantage.
A set of seeds must be generated and sent to each parallel process. This is automatically done in
some packages (parallel, snow, etc.), but must be explicitly addressed in others.
s <- seed
for (i in 1:numofcores) {
s <- nextRNGStream(s)
# send s to worker i as .Random.seed
}
Seeds can be also be set for reproducibility.
clusterSetRNGStream(cl = parallelcluster, iseed)
mcparallelDo
The mcparallelDo package allows for the evaluation of R code asynchronously on Unix-alike (e.g.
Linux and MacOSX) operating systems. The underlying philosophy of the package is aligned with
the needs of exploratory data analysis rather than coding. For coding asynchrony, consider the
future package.
Example
Create data
data(ToothGrowth)
Trigger mcparallelDo to perform analysis on a fork
mcparallelDo({glm(len ~ supp * dose, data=ToothGrowth)},"interactionPredictorModel")
Do other things, e.g.
binaryPredictorModel <- glm(len ~ supp, data=ToothGrowth)

gaussianPredictorModel <- glm(len ~ dose, data=ToothGrowth)
The result from mcparallelDo returns in your targetEnvironment, e.g. .GlobalEnv, when it is
complete with a message (by default)
summary(interactionPredictorModel)
Other Examples
# Example of not returning a value until we return to the top level
for (i in 1:10) {
if (i == 1) {
mcparallelDo({2+2}, targetValue = "output")
}
if (exists("output")) print(i)
}
# Example of getting a value without returning to the top level

for (i in 1:10) {
if (i == 1) {
mcparallelDo({2+2}, targetValue = "output")
}
mcparallelDoCheck()
if (exists("output")) print(i)
}
Read Parallel processing online: https://riptutorial.com/r/topic/1677/parallel-processing
Chapter 75: Pattern Matching and
Replacement
Introduction
This topic covers matching string patterns, as well as extracting or replacing them. For details on
defining complicated patterns see Regular Expressions.
Syntax
• grep("query", "subject", optional_args)
• grepl("query", "subject", optional_args)
• gsub("(group1)(group2)", "\\group#", "subject")
Remarks
Differences from other languages

Escaped regex symbols (like \1) are must be escaped a second time (like \\1), not only in the
pattern argument, but also in the replacement to sub and gsub.
By default, the pattern for all commands (grep, sub, regexpr) is not Perl Compatible Regular
Expression (PCRE) so some things like lookarounds are not supported. However, each function
accepts a perl=TRUE argument to enable them. See the R Regular Expressions topic for details.
• stringi
• stringr
Examples
Making substitutions
# example data
test_sentences <- c("The quick brown fox quickly", "jumps over the lazy dog")
Let's make the brown fox red:
sub("brown","red", test_sentences)
#[1] "The quick red fox quickly" "jumps over the lazy dog"
Now, let's make the "fast" fox act "fastly". This won't do it:
sub("quick", "fast", test_sentences)

#[1] "The fast red fox quickly" "jumps over the lazy dog"
sub only makes the first available replacement, we need gsub for global replacement:
gsub("quick", "fast", test_sentences)

#[1] "The fast red fox fastly" "jumps over the lazy dog"
See Modifying strings by substitution for more examples.
Finding Matches
# example data
test_sentences <- c("The quick brown fox", "jumps over the lazy dog")
Is there a match?
grepl() is used to check whether a word or regular expression exists in a string or character
vector. The function returns a TRUE/FALSE (or "Boolean") vector.
Notice that we can check each string for the word "fox" and receive a Boolean vector in return.
grepl("fox", test_sentences)
#[1] TRUE FALSE
Match locations
greptakes in a character string and a regular expression. It returns a numeric vector of
indexes.This will return which sentence contains the word "fox" in it.
grep("fox", test_sentences)
#[1] 1
Matched values
To select sentences that match a pattern:
# each of the following lines does the job:

test_sentences[grep("fox", test_sentences)]
test_sentences[grepl("fox", test_sentences)]
grep("fox", test_sentences, value = TRUE)
# [1] "The quick brown fox"
Details
Since the "fox" pattern is just a word, rather than a regular expression, we could improve
performance (with either grep or grepl) by specifying fixed = TRUE.
grep("fox", test_sentences, fixed = TRUE)

#[1] 1
To select sentences that don't match a pattern, one can use grep with invert = TRUE; or follow
subsetting rules with -grep(...) or !grepl(...).
In both grepl(pattern, x) and grep(pattern, x), the x parameter is vectorized, the pattern
parameter is not. As a result, you cannot use these directly to match pattern[1] against x[1],
pattern[2] against x[2], and so on.
Summary of matches
After performing the e.g. the grepl command, maybe you want to get an overview about how many
matches where TRUE or FALSE. This is useful e.g. in case of big data sets. In order to do so run the
summary command:
# example data
# find matches
matches <- grepl("fox", test_sentences)
# overview
summary(matches)
Single and Global match.
When working with regular expressions one modifier for PCRE is g for global match.
In R matching and replacement functions have two version: first match and global match:
• sub(pattern,replacement,text) will replace the first occurrence of pattern by replacement in

text
• gsub(pattern,replacement,text) will do the same as sub but for each occurrence of pattern
• regexpr(pattern,text) will return the position of match for the first instance of pattern
• gregexpr(pattern,text) will return all matches.
Some random data:
set.seed(123)
teststring <- paste0(sample(letters,20),collapse="")
# teststring
#[1] "htjuwakqxzpgrsbncvyo"
Let's see how this works if we want to replace vowels by something else:
sub("[aeiouy]"," ** HERE WAS A VOWEL** ",teststring)

#[1] "htj ** HERE WAS A VOWEL** wakqxzpgrsbncvyo"
gsub("[aeiouy]"," ** HERE WAS A VOWEL** ",teststring)

#[1] "htj ** HERE WAS A VOWEL** w ** HERE WAS A VOWEL** kqxzpgrsbncv ** HERE WAS A VOWEL** **
HERE WAS A VOWEL** "
Now let's see how we can find a consonant immediately followed by one or more vowel:
regexpr("[âeiou][aeiou]+",teststring)
#[1] 3
#attr(,"match.length")
#[1] 2
#attr(,"useBytes")
#[1] TRUE
We have a match on position 3 of the string of length 2, i.e: ju
Now if we want to get all matches:
gregexpr("[âeiou][aeiou]+",teststring)
#[[1]]
#[1] 3 5 19
#attr(,"match.length")
#[1] 2 2 2
#attr(,"useBytes")
#[1] TRUE
All this is really great, but this only give use positions of match and that's not so easy to get what is
matched, and here comes regmatches it's sole purpose is to extract the string matched from
regexpr, but it has a different syntax.
Let's save our matches in a variable and then extract them from original string:
matches <- gregexpr("[âeiou][aeiou]+",teststring)

regmatches(teststring,matches)
#[[1]]
#[1] "ju" "wa" "yo"
This may sound strange to not have a shortcut, but this allow extraction from another string by the
matches of our first one (think comparing two long vector where you know there's is a common
pattern for the first but not for the second, this allow an easy comparison):
teststring2 <- "this is another string to match against"
regmatches(teststring2,matches)
#[[1]]
#[1] "is" " i" "ri"
Attention note: by default the pattern is not Perl Compatible Regular Expression, some things like
lookarounds are not supported, but each function presented here allow for perl=TRUE argument to
enable them.
Find matches in big data sets
In case of big data sets, the call of grepl("fox", test_sentences) does not perform well. Big data
sets are e.g. crawled websites or million of Tweets, etc.
The first acceleration is the usage of the perl = TRUE option. Even faster is the option fixed = TRUE.
A complete example would be:
# example data
grepl("fox", test_sentences, perl = TRUE)

#[1] TRUE FALSE
In case of text mining, often a corpus gets used. A corpus cannot be used directly with grepl.
Therefore, consider this function:
searchCorpus <- function(corpus, pattern) {

return(tm_index(corpus, FUN = function(x) {
grepl(pattern, x, ignore.case = TRUE, perl = TRUE)
}))
}
Read Pattern Matching and Replacement online: https://riptutorial.com/r/topic/1123/pattern-

matching-and-replacement
Chapter 76: Performing a Permutation Test
Examples
A fairly general function
We will use the built in tooth growth dataset. We are interested in whether there is a statistically
significant difference in tooth growth when the guinea pigs are given vitamin C vs orange juice.
Here's the full example:
teethVC = ToothGrowth[ToothGrowth$supp == 'VC',]

teethOJ = ToothGrowth[ToothGrowth$supp == 'OJ',]
permutationTest = function(vectorA, vectorB, testStat){

N = 10^5
fullSet = c(vectorA, vectorB)
lengthA = length(vectorA)
lengthB = length(vectorB)
trials <- replicate(N,
{index <- sample(lengthB + lengthA, size = lengthA, replace = FALSE)
testStat((fullSet[index]), fullSet[-index]) } )
trials
}
vec1 =teethVC$len;
vec2 =teethOJ$len;
subtractMeans = function(a, b){ return (mean(a) - mean(b))}
result = permutationTest(vec1, vec2, subtractMeans)
observedMeanDifference = subtractMeans(vec1, vec2)
result = c(result, observedMeanDifference)
hist(result)
abline(v=observedMeanDifference, col = "blue")
pValue = 2*mean(result <= (observedMeanDifference))
pValue
After we read in the CSV, we define the function
permutationTest = function(vectorA, vectorB, testStat){

N = 10^5
fullSet = c(vectorA, vectorB)
lengthA = length(vectorA)
lengthB = length(vectorB)
trials <- replicate(N,
{index <- sample(lengthB + lengthA, size = lengthA, replace = FALSE)
testStat((fullSet[index]), fullSet[-index]) } )
trials
}
This function takes two vectors, and shuffles their contents together, then performs the function
testStat on the shuffled vectors. The result of teststat is added to trials, which is the return
value.
It does this N = 10^5 times. Note that the value N could very well have been a parameter to the
function.
This leaves us with a new set of data, trials, the set of means that might result if there truly is no
relationship between the two variables.
Now to define our test statistic:
subtractMeans = function(a, b){ return (mean(a) - mean(b))}
Perform the test:
result = permutationTest(vec1, vec2, subtractMeans)
Calculate our actual observed mean difference:
observedMeanDifference = subtractMeans(vec1, vec2)
Let's see what our observation looks like on a histogram of our test statistic.
hist(result)
abline(v=observedMeanDifference, col = "blue")
It doesn't look like our observed result is very likely to occur by random chance...
We want to calculate the p-value, the likeliehood of the original observed result if their is no
relationship between the two variables.
pValue = 2*mean(result >= (observedMeanDifference))
Let's break that down a bit:
result >= (observedMeanDifference)
Will create a boolean vector, like:
FALSE TRUE FALSE FALSE TRUE FALSE ...
With TRUE every time the value of result is greater than or equal to the observedMean.
The function mean will interpret this vector as 1 for TRUE and 0 for FALSE, and give us the percentage
of 1's in the mix, ie the number of times our shuffled vector mean difference surpassed or equalled
what we observed.
Finally, we multiply by 2 because the distribution of our test statistic is highly symmetric, and we
really want to know which results are "more extreme" than our observed result.
All that's left is to output the p-value, which turns out to be 0.06093939. Interpretation of this value is
subjective, but I would say that it looks like Vitamin C promotes tooth growth quite a lot more than
Orange Juice does.
Read Performing a Permutation Test online: https://riptutorial.com/r/topic/3216/performing-a-

permutation-test
Chapter 77: Pipe operators (%>% and others)
Introduction
Pipe operators, available in magrittr, dplyr, and other R packages, process a data-object using a
sequence of operations by passing the result of one step as input for the next step using infix-
operators rather than the more typical R method of nested function calls.
Note that the intended aim of pipe operators is to increase human readability of written code. See
Remarks section for performance considerations.
Syntax
• lhs %>% rhs # pipe syntax for rhs(lhs)
• lhs %>% rhs(a = 1) # pipe syntax for rhs(lhs, a = 1)
• lhs %>% rhs(a = 1, b = .) # pipe syntax for rhs(a = 1, b = lhs)
• lhs %<>% rhs # pipe syntax for lhs <- rhs(lhs)
• lhs %$% rhs(a) # pipe syntax for with(lhs, rhs(lhs$a))
• lhs %T>% rhs # pipe syntax for { rhs(lhs); lhs }
Parameters
lhs rhs
A value or the magrittr placeholder. A function call using the magrittr semantics
Remarks
Packages that use %>%
The pipe operator is defined in the magrittr package, but it gained huge visibility and popularity
with the dplyr package (which imports the definition from magrittr). Now it is part of tidyverse,
which is a collection of packages that "work in harmony because they share common data
representations and API design".
The magrittr package also provides several variations of the pipe operator for those who want
more flexibility in piping, such as the compound assignment pipe %<>%, the exposition pipe %$%, and
the tee operator %T>%. It also provides a suite of alias functions to replace common functions that
have special syntax (+, [, [[, etc.) so that they can be easily used within a chain of pipes.
Finding documentation
As with any infix operator (such as +, *, ^, &, %in%), you can find the official documentation if you put
it in quotes: ?'%>%' or help('%>%') (assuming you have loaded a package that attaches pkg:magrittr
).
Hotkeys
There is a special hotkey in RStudio for the pipe operator: Ctrl+Shift+M (Windows & Linux),
Cmd+Shift+M (Mac).
Performance Considerations
While the pipe operator is useful, be aware that there is a negative impact on performance due
mainly to the overhead of using it. Consider the following two things carefully when using the pipe
operator:
• Machine performance (loops)

• Evaluation (object %>% rm() does not remove object)
Examples
Basic use and chaining
The pipe operator, %>%, is used to insert an argument into a function. It is not a base feature of the
language and can only be used after attaching a package that provides it, such as magrittr. The
pipe operator takes the left-hand side (LHS) of the pipe and uses it as the first argument of the
function on the right-hand side (RHS) of the pipe. For example:
library(magrittr)
1:10 %>% mean

# [1] 5.5
# is equivalent to
mean(1:10)
# [1] 5.5
The pipe can be used to replace a sequence of function calls. Multiple pipes allow us to read and
write the sequence from left to right, rather than from inside to out. For example, suppose we have
years defined as a factor but want to convert it to a numeric. To prevent possible information loss,
we first convert to character and then to numeric:
years <- factor(2008:2012)
# nesting
as.numeric(as.character(years))
# piping
years %>% as.character %>% as.numeric
If we don't want the LHS (Left Hand Side) used as the first argument on the RHS (Right Hand
Side), there are workarounds, such as naming the arguments or using . to indicate where the
piped input goes.
# example with grepl

# its syntax:
# grepl(pattern, x, ignore.case = FALSE, perl = FALSE, fixed = FALSE, useBytes = FALSE)
# note that the `substring` result is the *2nd* argument of grepl

grepl("Wo", substring("Hello World", 7, 11))
# piping while naming other arguments

"Hello World" %>% substring(7, 11) %>% grepl(pattern = "Wo")
# piping with .
"Hello World" %>% substring(7, 11) %>% grepl("Wo", .)
# piping with . and curly braces

"Hello World" %>% substring(7, 11) %>% { c(paste('Hi', .)) }
#[1] "Hi World"
#using LHS multiple times in argument with curly braces and .

"Hello World" %>% substring(7, 11) %>% { c(paste(. ,'Hi', .)) }
#[1] "World Hi World"
Functional sequences
Given a sequence of steps we use repeatedly, it's often handy to store it in a function. Pipes allow
for saving such functions in a readable format by starting a sequence with a dot as in:
. %>% RHS
As an example, suppose we have factor dates and want to extract the year:
library(magrittr) # needed to include the pipe operators

library(lubridate)
read_year <- . %>% as.character %>% as.Date %>% year
# Creating a dataset
df <- data.frame(now = "2015-11-11", before = "2012-01-01")
# now before
# 1 2015-11-11 2012-01-01
# Example 1: applying `read_year` to a single character-vector

df$now %>% read_year
# [1] 2015
# Example 2: applying `read_year` to all columns of `df`

df %>% lapply(read_year) %>% as.data.frame # implicit `lapply(df, read_year)
# now before
# 1 2015 2012
# Example 3: same as above using `mutate_all`
library(dplyr)
df %>% mutate_all(funs(read_year))
# if an older version of dplyr use `mutate_each`
# now before
# 1 2015 2012
We can review the composition of the function by typing its name or using functions:
read_year
# Functional sequence with the following components:
#
# 1. as.character(.)
# 2. as.Date(.)
# 3. year(.)
#
# Use 'functions' to extract the individual functions.
We can also access each function by its position in the sequence:
read_year[[2]]
# function (.)
# as.Date(.)
Generally, this approach may be useful when clarity is more important than speed.
Assignment with %<>%
The magrittr package contains a compound assignment infix-operator, %<>%, that updates a value
by first piping it into one or more rhs expressions and then assigning the result. This eliminates the
need to type an object name twice (once on each side of the assignment operator <-). %<>% must
be the first infix-operator in a chain:
library(magrittr)
library(dplyr)
df <- mtcars
Instead of writing
df <- df %>% select(1:3) %>% filter(mpg > 20, cyl == 6)
or
df %>% select(1:3) %>% filter(mpg > 20, cyl == 6) -> df
The compound assignment operator will both pipe and reassign df:
df %<>% select(1:3) %>% filter(mpg > 20, cyl == 6)
Exposing contents with %$%
The exposition pipe operator, %$%, exposes the column names as R symbols within the left-hand
side object to the right-hand side expression. This operator is handy when piping into functions
that do not have a data argument (unlike, say, lm) and that don't take a data.frame and column
names as arguments (most of the main dplyr functions).
The exposition pipe operator %$% allows a user to avoid breaking a pipeline when needing to refer
to column names. For instance, say you want to filter a data.frame and then run a correlation test
on two columns with cor.test:
library(magrittr)
library(dplyr)
mtcars %>%
filter(wt > 2) %$%
cor.test(hp, mpg)
#>
#> Pearson's product-moment correlation
#>
#> data: hp and mpg
#> t = -5.9546, df = 26, p-value = 2.768e-06
#> alternative hypothesis: true correlation is not equal to 0
#> 95 percent confidence interval:
#> -0.8825498 -0.5393217
#> sample estimates:
#> cor
#> -0.7595673
Here the standard %>% pipe passes the data.frame through to filter(), while the %$% pipe exposes
the column names to cor.test().
The exposition pipe works like a pipe-able version of the base R with() functions, and the same
left-hand side objects are accepted as inputs.
Using the pipe with dplyr and ggplot2
The %>% operator can also be used to pipe the dplyr output into ggplot. This creates a unified
exploratory data analysis (EDA) pipeline that is easily customizable. This method is faster than
doing the aggregations internally in ggplot and has the added benefit of avoiding unnecessary
intermediate variables.
library(dplyr)
library(ggplot)
diamonds %>%
filter(depth > 60) %>%
group_by(cut) %>%
summarize(mean_price = mean(price)) %>%
ggplot(aes(x = cut, y = mean_price)) +
geom_bar(stat = "identity")
Creating side effects with %T>%
Some functions in R produce a side effect (i.e. saving, printing, plotting, etc) and do not always
return a meaningful or desired value.
%T>% (tee operator) allows you to forward a value into a side-effect-producing function while
keeping the original lhs value intact. In other words: the tee operator works like %>%, except the
return values is lhs itself, and not the result of the rhs function/expression.
Example: Create, pipe, write, and return an object. If %>% were used in place of %T>% in this
example, then the variable all_letters would contain NULL rather than the value of the sorted
object.
all_letters <- c(letters, LETTERS) %>%

sort %T>%
write.csv(file = "all_letters.csv")
read.csv("all_letters.csv") %>% head()

# x
# 1 a
# 2 A
# 3 b
# 4 B
# 5 c
# 6 C
Warning: Piping an unnamed object to save() will produce an object named . when loaded into the
workspace with load(). However, a workaround using a helper function is possible (which can also
be written inline as an anonymous function).

sort %T>%
save(file = "all_letters.RData")
load("all_letters.RData", e <- new.env())
get("all_letters", envir = e)
# Error in get("all_letters", envir = e) : object 'all_letters' not found
get(".", envir = e)
# [1] "a" "A" "b" "B" "c" "C" "d" "D" "e" "E" "f" "F" "g" "G" "h" "H" "i" "I" "j" "J"
# [21] "k" "K" "l" "L" "m" "M" "n" "N" "o" "O" "p" "P" "q" "Q" "r" "R" "s" "S" "t" "T"
# [41] "u" "U" "v" "V" "w" "W" "x" "X" "y" "Y" "z" "Z"
# Work-around
save2 <- function(. = ., name, file = stop("'file' must be specified")) {
assign(name, .)
call_save <- call("save", ... = name, file = file)
eval(call_save)
}

sort %T>%
save2("all_letters", "all_letters.RData")
Read Pipe operators (%>% and others) online: https://riptutorial.com/r/topic/652/pipe-operators----

--and-others-
Chapter 78: Pivot and unpivot with data.table
Syntax
• Melt with melt(DT, id.vars=c(..), variable.name="CategoryLabel", value.name="Value")
• Cast with dcast(DT, LHS ~ RHS, value.var="Value", fun.aggregate=sum)
Parameters
Parameter Details
id.vars tell melt which columns to retain
variable.name tell melt what to call the column with category labels
tell melt what to call the column that has values associated with category
value.name
labels
value.var tell dcast where to find the values to cast in columns
tell dcast which columns to retain to form a unique record identifier (LHS) and
formula
which one holds the category labels (RHS)
specify the function to use when the casting operation generates a list of
fun.aggregate
values in each cell
Remarks
Much of what goes into conditioning data to build models or visualizations can be accomplished
with data.table. As compare to other options, data.table offers advantages of speed and flexibility.
Examples
Pivot and unpivot tabular data with data.table - I
Convert from wide form to long form
Load data USArrests from datasets.
data("USArrests")
head(USArrests)
Murder Assault UrbanPop Rape

Alabama 13.2 236 58 21.2
Alaska 10.0 263 48 44.5
Arizona 8.1 294 80 31.0
Arkansas 8.8 190 50 19.5
California 9.0 276 91 40.6
Colorado 7.9 204 78 38.7
Use ?USArrests to find out more. First, convert to data.table. The names of states are row names in
the original data.frame.
library(data.table)
DT <- as.data.table(USArrests, keep.rownames=TRUE)
This is data in the wide form. It has a column for each variable. The data can also be stored in
long form without loss of information. The long form has one column that stores the variable
names. Then, it has another column for the variable values. The long form of USArrests looks like
so.
State Crime Rate

1: Alabama Murder 13.2
2: Alaska Murder 10.0
3: Arizona Murder 8.1
4: Arkansas Murder 8.8
5: California Murder 9.0
---
196: Virginia Rape 20.7
197: Washington Rape 26.2
198: West Virginia Rape 9.3
199: Wisconsin Rape 10.8
200: Wyoming Rape 15.6
We use the melt function to switch from wide form to long form.
DTm <- melt(DT)

names(DTm) <- c("State", "Crime", "Rate")
By default, melt treats all columns with numeric data as variables with values. In USArrests, the
variable UrbanPop represents the percentage urban population of a state. It is different from the
other variabes, Murder, Assault and Rape, which are violent crimes reported per 100,000 people.
Suppose we want to retain UrbanPop column. We achieve this by setting id.vars as follows.
DTmu <- melt(DT, id.vars=c("rn", "UrbanPop" ),

variable.name='Crime', value.name = "Rate")
names(DTmu)[1] <- "State"
Note that we have specified the names of the column containing category names (Murder,
Assault, etc.) with variable.name and the column containing the values with value.name. Our data
looks like so.
State UrbanPop Crime Rate

1: Alabama 58 Murder 13.2
2: Alaska 48 Murder 10.0
3: Arizona 80 Murder 8.1
4: Arkansas 50 Murder 8.8
5: California 91 Murder 9.0
Generating summaries with with split-apply-combine style approach is a breeze. For example, to
summarize violent crimes by state?
DTmu[, .(ViolentCrime = sum(Rate)), by=State]
This gives:
State ViolentCrime
1: Alabama 270.4
2: Alaska 317.5
3: Arizona 333.1
4: Arkansas 218.3
5: California 325.6
6: Colorado 250.6
Pivot and unpivot tabular data with data.table - II
Convert from long form to wide form
To recover data from the previous example, use dcast like so.
DTc <- dcast(DTmu, State + UrbanPop ~ Crime)
This gives the data in the original wide form.
State UrbanPop Murder Assault Rape

1: Alabama 58 13.2 236 21.2
2: Alaska 48 10.0 263 44.5
3: Arizona 80 8.1 294 31.0
4: Arkansas 50 8.8 190 19.5
5: California 91 9.0 276 40.6
Here, the formula notation is used to specify the columns that form a unique record identifier (LHS)
and the column containing category labels for new column names (RHS). Which column to use for
the numeric values? By default, dcast uses the first column with numerical values left over when
from the formula specification. To make explicit, use the parameter value.var with column name.
When the operation produces a list of values in each cell, dcast provides a fun.aggregate method to
handle the situation. Say I am interested in states with similar urban population when investigating
crime rates. I add a column Decile with computed information.
DTmu[, Decile := cut(UrbanPop, quantile(UrbanPop, probs = seq(0, 1, by=0.1)))]

levels(DTmu$Decile) <- paste0(1:10, "D")
Now, casting Decile ~ Crime produces multiple values per cell. I can use fun.aggregate to
determine how these are handled. Both text and numerical values can be handle this way.
dcast(DTmu, Decile ~ Crime, value.var="Rate", fun.aggregate=sum)
This gives:
dcast(DTmu, Decile ~ Crime, value.var="Rate", fun.aggregate=mean)
This gives:
State UrbanPop Crime Rate Decile

1: Alabama 58 Murder 13.2 4D
2: Alaska 48 Murder 10.0 2D
3: Arizona 80 Murder 8.1 8D
4: Arkansas 50 Murder 8.8 2D
5: California 91 Murder 9.0 10D
There are multiple states in each decile of the urban population. Use fun.aggregate to specify how
these should be handled.
dcast(DTmu, Decile ~ Crime, value.var="Rate", fun.aggregate=sum)
This sums over the data for like states, giving the following.
Decile Murder Assault Rape

1: 1D 39.4 808 62.6
2: 2D 35.3 815 94.3
3: 3D 22.6 451 67.7
4: 4D 54.9 898 106.0
5: 5D 42.4 758 107.6
Read Pivot and unpivot with data.table online: https://riptutorial.com/r/topic/6934/pivot-and-

unpivot-with-data-table
Chapter 79: Probability Distributions with R
Examples
PDF and PMF for different distributions in R
PMF FOR THE BINOMIAL DISTRIBUTION
Suppose that a fair die is rolled 10 times. What is the probability of throwing exactly two sixes?
You can answer the question using the dbinom function:
> dbinom(2, 10, 1/6)

[1] 0.29071
PMF FOR THE POISSON DISTRIBUTION
The number of sandwhich ordered in a restaurant on a given day is known to follow a Poisson
distribution with a mean of 20. What is the probability that exactly eighteen sandwhich will be
ordered tomorrow?
You can answer the question with the dpois function:
> dpois(18, 20)

[1] 0.08439355
PDF FOR THE NORMAL DISTRIBUTION
To find the value of the pdf at x=2.5 for a normal distribution with a mean of 5 and a standard
deviation of 2, use the command:
> dnorm(2.5, mean=5, sd=2)

[1] 0.09132454
Read Probability Distributions with R online: https://riptutorial.com/r/topic/4333/probability-

distributions-with-r
Chapter 80: Publishing
Introduction
There are many ways of formatting R code, tables and graphs for publishing.
Remarks
R users often want to publish analysis and results in a reproducible way. See Reproducible R for
details.
Examples
Formatting tables
Here, "table" is meant broadly (covering data.frame, table,
Printing to plain text

Printing (as seen in the console) might suffice for a plain-text document to be viewed in
monospaced font:
Note: Before making the example data below, make sure you're in an empty folder you can write
to. Run getwd() and read ?setwd if you need to change folders.
..w = options()$width
options(width = 500) # reduce text wrapping
sink(file = "mytab.txt")
summary(mtcars)
sink()
options(width = ..w)
rm(..w)
Printing delimited tables

Writing to CSV (or another common format) and then opening in a spreadsheet editor to apply
finishing touches is another option:
write.csv(mtcars, file="mytab.csv")
Further resources
• knitr::kable
• stargazer
• tables::tabular
• texreg
• xtable
Formatting entire documents
from the utils package allows for formatting code, prose, graphs and tables together in a
Sweave
LaTeX document.
Further Resources
• Knitr and RMarkdown
Read Publishing online: https://riptutorial.com/r/topic/9039/publishing
Chapter 81: R code vectorization best
practices
Examples
By row operations
The key in vectorizing R code, is to reduce or eliminate "by row operations" or method dispatching
of R functions.
That means that when approaching a problem that at first glance requires "by row operations",
such as calculating the means of each row, one needs to ask themselves:
• What are the classes of the data sets I'm dealing with?
• Is there an existing compiled code that can achieve this without the need of repetitive
evaluation of R functions?
• If not, can I do these operation by columns instead by row?
• Finally, is it worth spending a lot of time on developing complicated vectorized code instead
of just running a simple apply loop? In other words, is the data big/sophisticated enough that
R can't handle it efficiently using a simple loop?
Putting aside the memory pre-allocation issue and growing object in loops, we will focus in this
example on how to possibly avoid apply loops, method dispatching or re-evaluating R functions
within loops.
A standard/easy way of calculating mean by row would be:
apply(mtcars, 1, mean)
Mazda RX4 Mazda RX4 Wag Datsun 710 Hornet 4 Drive Hornet
Sportabout Valiant Duster 360
29.90727 29.98136 23.59818 38.73955
53.66455 35.04909 59.72000
Merc 240D Merc 230 Merc 280 Merc 280C Merc
450SE Merc 450SL Merc 450SLC
24.63455 27.23364 31.86000 31.78727
46.43091 46.50000 46.35000
Cadillac Fleetwood Lincoln Continental Chrysler Imperial Fiat 128 Honda
Civic Toyota Corolla Toyota Corona
66.23273 66.05855 65.97227 19.44091
17.74227 18.81409 24.88864
Dodge Challenger AMC Javelin Camaro Z28 Pontiac Firebird Fiat
X1-9 Porsche 914-2 Lotus Europa
47.24091 46.00773 58.75273 57.37955
18.92864 24.77909 24.88027
Ford Pantera L Ferrari Dino Maserati Bora Volvo 142E
60.97182 34.50818 63.15545 26.26273
But can we do better? Lets's see what happened here:
1. First, we converted a data.frame to a matrix. (Note that his happens within the apply function.)
This is both inefficient and dangerous. a matrix can't hold several column types at a time.
Hence, such conversion will probably lead to loss of information and some times to
misleading results (compare apply(iris, 2, class) with str(iris) or with sapply(iris, class)
).
2. Second of all, we performed an operation repetitively, one time for each row. Meaning, we
had to evaluate some R function nrow(mtcars) times. In this specific case, mean is not a
computationally expensive function, hence R could likely easily handle it even for a big data
set, but what would happen if we need to calculate the standard deviation by row (which
involves an expensive square root operation)? Which brings us to the next point:
3. We evaluated the R function many times, but maybe there already is a compiled version of
this operation?
Indeed we could simply do:
rowMeans(mtcars)
Mazda RX4 Mazda RX4 Wag Datsun 710 Hornet 4 Drive Hornet
Sportabout Valiant Duster 360
29.90727 29.98136 23.59818 38.73955
53.66455 35.04909 59.72000
Merc 240D Merc 230 Merc 280 Merc 280C Merc
450SE Merc 450SL Merc 450SLC
24.63455 27.23364 31.86000 31.78727
46.43091 46.50000 46.35000
Cadillac Fleetwood Lincoln Continental Chrysler Imperial Fiat 128 Honda
Civic Toyota Corolla Toyota Corona
66.23273 66.05855 65.97227 19.44091
17.74227 18.81409 24.88864
Dodge Challenger AMC Javelin Camaro Z28 Pontiac Firebird Fiat
X1-9 Porsche 914-2 Lotus Europa
47.24091 46.00773 58.75273 57.37955
18.92864 24.77909 24.88027
Ford Pantera L Ferrari Dino Maserati Bora Volvo 142E
60.97182 34.50818 63.15545 26.26273
This involves no by row operations and therefore no repetitive evaluation of R functions. However,
we still converted a data.frame to a matrix. Though rowMeans has an error handling mechanism and
it won't run on a data set that it can't handle, it's still has an efficiency cost.
rowMeans(iris)
Error in rowMeans(iris) : 'x' must be numeric
But still, can we do better? We could try instead of a matrix conversion with error handling, a
different method that will allow us to use mtcars as a vector (because a data.frame is essentially a
list and a list is a vector).
Reduce(`+`, mtcars)/ncol(mtcars)
[1] 29.90727 29.98136 23.59818 38.73955 53.66455 35.04909 59.72000 24.63455 27.23364 31.86000
31.78727 46.43091 46.50000 46.35000 66.23273 66.05855
[17] 65.97227 19.44091 17.74227 18.81409 24.88864 47.24091 46.00773 58.75273 57.37955 18.92864
24.77909 24.88027 60.97182 34.50818 63.15545 26.26273
Now for possible speed gain, we lost column names and error handling (including NA handling).
Another example would be calculating mean by group, using base R we could try
aggregate(. ~ cyl, mtcars, mean)

cyl mpg disp hp drat wt qsec vs am gear
carb
1 4 26.66364 105.1364 82.63636 4.070909 2.285727 19.13727 0.9090909 0.7272727 4.090909
1.545455
2 6 19.74286 183.3143 122.28571 3.585714 3.117143 17.97714 0.5714286 0.4285714 3.857143
3.428571
3 8 15.10000 353.1000 209.21429 3.229286 3.999214 16.77214 0.0000000 0.1428571 3.285714
3.500000
Still, we are basically evaluating an R function in a loop, but the loop is now hidden in an internal C
function (it matters little whether it is a C or an R loop).
Could we avoid it? Well there is a compiled function in R called rowsum, hence we could do:
rowsum(mtcars[-2], mtcars$cyl)/table(mtcars$cyl)
mpg disp hp drat wt qsec vs am gear carb
4 26.66364 105.1364 82.63636 4.070909 2.285727 19.13727 0.9090909 0.7272727 4.090909 1.545455
6 19.74286 183.3143 122.28571 3.585714 3.117143 17.97714 0.5714286 0.4285714 3.857143 3.428571
8 15.10000 353.1000 209.21429 3.229286 3.999214 16.77214 0.0000000 0.1428571 3.285714 3.500000
Though we had to convert to a matrix first too.
A this point we may question whether our current data structure is the most appropriate one. Is a
data.frame is the best practice? Or should one just switch to a matrix data structure in order to gain
efficiency?
By row operations will get more and more expensive (even in matrices) as we start to evaluate
expensive functions each time. Lets us consider a variance calculation by row example.
Lets say we have a matrix m:
set.seed(100)
m <- matrix(sample(1e2), 10)
m
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 8 33 39 86 71 100 81 68 89 84
[2,] 12 16 57 80 32 82 69 11 41 92
[3,] 62 91 53 13 42 31 60 70 98 79
[4,] 66 94 29 67 45 59 20 96 64 1
[5,] 36 63 76 6 10 48 85 75 99 2
[6,] 18 4 27 19 44 56 37 95 26 40
[7,] 3 24 21 25 52 51 83 28 49 17
[8,] 46 5 22 43 47 74 35 97 77 65
[9,] 55 54 78 34 50 90 30 61 14 58
[10,] 88 73 38 15 9 72 7 93 23 87
One could simply do:
apply(m, 1, var)
[1] 871.6556 957.5111 699.2111 941.4333 1237.3333 641.8222 539.7889 759.4333 500.4889
1255.6111
On the other hand, one could also completely vectorize this operation by following the formula of
variance
RowVar <- function(x) {

rowSums((x - rowMeans(x))^2)/(dim(x)[2] - 1)
}
RowVar(m)
[1] 871.6556 957.5111 699.2111 941.4333 1237.3333 641.8222 539.7889 759.4333 500.4889
1255.6111
Read R code vectorization best practices online: https://riptutorial.com/r/topic/3327/r-code-

vectorization-best-practices
Chapter 82: R in LaTeX with knitr
Syntax
1. <<internal-code-chunk-name, options...>>=
# R Code Here
@
2. \Sexpr{ #R Code Here }
3. << read-external-R-file >>=
read_chunk('r-file.R')
@
<<external-code-chunk-name, options...>>=
@
Parameters
Option Details
echo (TRUE/FALSE) - whether to include R source code in the output file
(TRUE/FALSE) - whether to include messages from the R source execution in the

message
output file
(TRUE/FALSE) - whether to include warnings from the R source execution in the

warning
output file
(TRUE/FALSE) - whether to include errors from the R source execution in the

error
output file
cache (TRUE/FALSE) - whether to cache the results of the R source execution
fig.width (numeric) - width of the plot generated by the R source execution
fig.height (numeric) - height of the plot generated by the R source execution
Remarks
Knitr is a tool that allows us to interweave natural language (in the form of LaTeX) and source
code (in the form of R). In general, the concept of interspersing natural language and source code
is called literate programming. Since knitr files contain a mixture of LaTeX (traditionally housed in
.tex files) and R (traditionally housed in .R files) a new file extension called R noweb (.Rnw) is
required. .Rnw files contain a mixture of LaTeX and R code.
Knitr allows for the generation of statistical reports in PDF format and is a key tool for achieving
reproducable research.
Compiling .Rnw files to a PDF is a two step process. First, we need to know how to execute the R
code and capture the output in a format that a LaTeX compiler can understand (a process called
'kniting'). We do this using the knitr package. The command for this is shown below, assuming you
have installed the knitr package:
Rscript -e "library(knitr); knit('r-noweb-file.Rnw')
This will generate a normal .tex file (called r-noweb.tex in this example) which can then be turned
into a PDF file using:
pdflatex r-noweb-file.tex
Examples
R in Latex with Knitr and Code Externalization
Knitr is an R package that allows us to intermingle R code with LaTeX code. One way to achieve
this is external code chunks. External code chunks allow us to develop/test R Scripts in an R
development environment and then include the results in a report. It is a powerful organizational
technique. This approach is demonstrated below.
# r-noweb-file.Rnw
\documentclass{article}
<<echo=FALSE,cache=FALSE>>=
knitr::opts_chunk$set(echo=FALSE, cache=TRUE)
knitr::read_chunk('r-file.R')
@
\begin{document}
This is an Rnw file (R noweb). It contains a combination of LateX and R.
One we have called the read\_chunk command above we can reference sections of code in the r-
file.R script.
<<Chunk1>>=
@
\end{document}
When using this approach we keep our code in a separate R file as shown below.
## r-file.R
## note the specific comment style of a single pound sign followed by four dashes
# ---- Chunk1 ----
print("This is R Code in an external file")
x <- seq(1:10)
y <- rev(seq(1:10))
plot(x,y)
R in Latex with Knitr and Inline Code Chunks
this is inline code chunks. This apporach is demonstrated below.
# r-noweb-file.Rnw
\begin{document}
<<my-label>>=
print("This is an R Code Chunk")
x <- seq(1:10)
@
Above is an internal code chunk.

We can access data created in any code chunk inline with our LaTeX code like this.
The length of array x is \Sexpr{length(x)}.
\end{document}
R in LaTex with Knitr and Internal Code Chunks
this is internal code chunks. This apporach is demonstrated below.
# r-noweb-file.Rnw
\begin{document}
<<code-chunk-label>>=
print("This is an R Code Chunk")
x <- seq(1:10)
y <- seq(1:10)
plot(x,y) # Brownian motion
@
\end{document}
Read R in LaTeX with knitr online: https://riptutorial.com/r/topic/4334/r-in-latex-with-knitr
Chapter 83: R Markdown Notebooks (from
RStudio)
Introduction
An R Notebook is an R Markdown document with chunks that can be executed independently and
interactively, with output visible immediately beneath the input. They are similar to R Markdown
documents with the exception of results being displayed in the R Notebook creation/edit mode
rather than in the rendered output. Note: R Notebooks are new feature of RStudio and are only
available in version 1.0 or higher of RStudio.
Examples
Creating a Notebook
You can create a new notebook in RStudio with the menu command File -> New File -> R
Notebook
If you don't see the option for R Notebook, then you need to update your version of RStudio. For
installation of RStudio follow this guide
Inserting Chunks
Chunks are pieces of code that can be executed interactively. In-order to insert a new chunk by
clicking on the insert button present on the notebook toolbar and select your desired code
platform (R in this case, since we want to write R code). Alternatively we can use keyboard
shortcuts to insert a new chunk Ctrl + Alt + I (OS X: Cmd + Option + I)
Executing Chunk Code
You can run the current chunk by clicking Run current Chunk (green play button) present on
the right side of the chunk. Alternatively we can use keyboard shortcut Ctrl + Shift + Enter (OS X:
Cmd + Shift + Enter)
The output from all the lines in the chunk will appear beneath the chunk.
Splitting Code into Chunks

Since a chunk produces its output beneath the chunk, when having multiple lines of code in a
single chunk that produces multiples outputs it is often helpful to split into multiple chunks such
that each chunk produces one output.
To do this, select the code to you want to split into a new chunk and press Ctrl + Alt + I (OS X:
Cmd + Option + I)
Execution Progress
When you execute code in a notebook, an indicator will appear in the gutter to show you execution
progress. Lines of code which have been sent to R are marked with dark green; lines which have
not yet been sent to R are marked with light green.
Executing Multiple Chunks
Running or Re-Running individual chunks by pressing Run for all the chunks present in a
document can be painful. We can use Run All from the Insert menu in the toolbar to Run all the
chunks present in the notebook. Keyboard shortcut is Ctrl + Alt + R (OS X: Cmd + Option + R)
There’s also a option Restart R and Run All Chunks command (available in the Run menu on
the editor toolbar), which gives you a fresh R session prior to running all the chunks.
We also have options like Run All Chunks Above and Run All Chunks Below to run chunks
Above or Below from a selected chunk.
Preview Output
Before rendering the final version of a notebook we can preview the output. Click on the Preview
button on the toolbar and select the desired output format.
You can change the type of output by using the output options as "pdf_document" or
"html_notebook"
Saving and Sharing
When a notebook .Rmd is saved, an .nb.html file is created alongside it. This file is a self-contained
HTML file which contains both a rendered copy of the notebook with all current chunk outputs
(suitable for display on a website) and a copy of the notebook .Rmd itself.
More info can be found at RStudio docs
Read R Markdown Notebooks (from RStudio) online: https://riptutorial.com/r/topic/10728/r-

markdown-notebooks--from-rstudio-
Chapter 84: R memento by examples
Introduction
This topic is meant to be a memento about the R language without any text, with self-explanatory
examples.
Each example is meant to be as succint as possible.
Examples
Data types
Vectors
a <- c(1, 2, 3)
b <- c(4, 5, 6)
mean_ab <- (a + b) / 2
d <- c(1, 0, 1)
only_1_3 <- a[d == 1]
Matrices
mat <- matrix(c(1,2,3,4), nrow = 2, ncol = 2)
dimnames(mat) <- list(c(), c("a", "b", "c"))
mat[,] == mat
Dataframes
df <- data.frame(qualifiers = c("Buy", "Sell", "Sell"),
symbols = c("AAPL", "MSFT", "GOOGL"),
values = c(326.0, 598.3, 201.5))
df$symbols == df[[2]]
df$symbols == df[["symbols"]]
df[[2, 1]] == "AAPL"
Lists
l <- list(a = 500, "aaa", 98.2)
length(l) == 3
class(l[1]) == "list"
class(l[[1]]) == "numeric"
class(l$a) == "numeric"
Environments
env <- new.env()
env[["foo"]] = "bar"
env2 <- env
env2[["foo"]] = "BAR"
env[["foo"]] == "BAR"
get("foo", envir = env) == "BAR"
rm("foo", envir = env)
env[["foo"]] == NULL
Plotting (using plot)
# Creates a 1 row - 2 columns format

par(mfrow=c(1,2))
plot(rnorm(100), main = "Graph 1", ylab = "Normal distribution")

grid()
legend(x = 40, y = -1, legend = "A legend")
plot(rnorm(100), main = "Graph 2", type = "l")

abline(v = 50)
Result:
Commonly used functions
# Create 100 standard normals in a vector
x <- rnorm(100, mean = 0, sd = 1)
# Find the lenght of a vector

length(x)
# Compute the mean

mean(x)
# Compute the standard deviation

sd(x)
# Compute the median value

median(x)
# Compute the range (min, max)

range(x)
# Sum an iterable
sum(x)
# Cumulative sum (x[1], x[1]+x[2], ...)

cumsum(x)
# Display the first 3 elements

head(3, x)
# Display min, 1st quartile, median, mean, 3rd quartile, max

summary(x)
# Compute successive difference between elements

diff(x)
# Create a range from 1 to 10 step 1

1:10
# Create a range from 1 to 10 step 0.1

seq(1, 10, 0.1)
# Print a string
print("hello world")
Read R memento by examples online: https://riptutorial.com/r/topic/10827/r-memento-by-

examples
Chapter 85: Random Forest Algorithm
Introduction
RandomForest is an ensemble method for classification or regression that reduces the chance of
overfitting the data. Details of the method can be found in the Wikipedia article on Random
Forests. The main implementation for R is in the randomForest package, but there are other
implementations. See the CRAN view on Machine Learning.
Examples
Basic examples - Classification and Regression
###### Used for both Classification and Regression examples

library(randomForest)
library(car) ## For the Soils data
data(Soils)
######################################################
## RF Classification Example
set.seed(656) ## for reproducibility
S_RF_Class = randomForest(Gp ~ ., data=Soils[,c(4,6:14)])
Gp_RF = predict(S_RF_Class, Soils[,6:14])
length(which(Gp_RF != Soils$Gp)) ## No Errors
## Naive Bayes for comparison

library(e1071)
S_NB = naiveBayes(Soils[,6:14], Soils[,4])
Gp_NB = predict(S_NB, Soils[,6:14], type="class")
length(which(Gp_NB != Soils$Gp)) ## 6 Errors
This example tested on the training data, but illustrates that RF can make very good models.
######################################################
## RF Regression Example
set.seed(656) ## for reproducibility
S_RF_Reg = randomForest(pH ~ ., data=Soils[,6:14])
pH_RF = predict(S_RF_Reg, Soils[,6:14])
## Compare Predictions with Actual values for RF and Linear Model

S_LM = lm(pH ~ ., data=Soils[,6:14])
pH_LM = predict(S_LM, Soils[,6:14])
par(mfrow=c(1,2))
plot(Soils$pH, pH_RF, pch=20, ylab="Predicted", main="Random Forest")
abline(0,1)
plot(Soils$pH, pH_LM, pch=20, ylab="Predicted", main="Linear Model")
abline(0,1)
Read Random Forest Algorithm online: https://riptutorial.com/r/topic/8088/random-forest-algorithm
Chapter 86: Random Numbers Generator
Examples
Random permutations
To generate random permutation of 5 numbers:
sample(5)
# [1] 4 5 3 1 2
To generate random permutation of any vector:
sample(10:15)
# [1] 11 15 12 10 14 13
One could also use the package pracma
randperm(a, k)
# Generates one random permutation of k of the elements a, if a is a vector,
# or of 1:a if a is a single integer.
# a: integer or numeric vector of some length n.
# k: integer, smaller as a or length(a).
# Examples
library(pracma)
randperm(1:10, 3)
[1] 3 7 9
randperm(10, 10)
[1] 4 5 10 8 2 7 6 9 3 1
randperm(seq(2, 10, by=2))

[1] 6 4 10 2 8
Random number generator's reproducibility
When expecting someone to reproduce an R code that has random elements in it, the set.seed()
function becomes very handy. For example, these two lines will always produce different output
(because that is the whole point of random number generators):
> sample(1:10,5)
[1] 6 9 2 7 10
> sample(1:10,5)
[1] 7 6 1 2 10
These two will also produce different outputs:
> rnorm(5)
[1] 0.4874291 0.7383247 0.5757814 -0.3053884 1.5117812
> rnorm(5)
[1] 0.38984324 -0.62124058 -2.21469989 1.12493092 -0.04493361
However, if we set the seed to something identical in both cases (most people use 1 for simplicity),
we get two identical samples:
> set.seed(1)
> sample(letters,2)
[1] "g" "j"
> set.seed(1)
> sample(letters,2)
[1] "g" "j"
and same with, say, rexp() draws:
> set.seed(1)
> rexp(5)
[1] 0.7551818 1.1816428 0.1457067 0.1397953 0.4360686
> set.seed(1)
> rexp(5)
[1] 0.7551818 1.1816428 0.1457067 0.1397953 0.4360686
Generating random numbers using various density functions
Below are examples of generating 5 random numbers using various probability distributions.
Uniform distribution between 0 and 10
runif(5, min=0, max=10)

[1] 2.1724399 8.9209930 6.1969249 9.3303321 2.4054102
Normal distribution with 0 mean and standard deviation of 1
rnorm(5, mean=0, sd=1)

[1] -0.97414402 -0.85722281 -0.08555494 -0.37444299 1.20032409
Binomial distribution with 10 trials and success probability

of 0.5
rbinom(5, size=10, prob=0.5)

[1] 4 3 5 2 3
Geometric distribution with 0.2 success probability
rgeom(5, prob=0.2)
[1] 14 8 11 1 3
Hypergeometric distribution with 3 white balls, 10 black balls

and 5 draws
rhyper(5, m=3, n=10, k=5)

[1] 2 0 1 1 1
Negative Binomial distribution with 10 trials and success

probability of 0.8
rnbinom(5, size=10, prob=0.8)

[1] 3 1 3 4 2
Poisson distribution with mean and variance (lambda) of 2
rpois(5, lambda=2)
[1] 2 1 2 3 4
Exponential distribution with the rate of 1.5
rexp(5, rate=1.5)
[1] 1.8993303 0.4799358 0.5578280 1.5630711 0.6228000
Logistic distribution with 0 location and scale of 1

rlogis(5, location=0, scale=1)
[1] 0.9498992 -1.0287433 -0.4192311 0.7028510 -1.2095458
Chi-squared distribution with 15 degrees of freedom
rchisq(5, df=15)
[1] 14.89209 19.36947 10.27745 19.48376 23.32898
Beta distribution with shape parameters a=1 and b=0.5
rbeta(5, shape1=1, shape2=0.5)

[1] 0.1670306 0.5321586 0.9869520 0.9548993 0.9999737
Gamma distribution with shape parameter of 3 and scale=0.5
rgamma(5, shape=3, scale=0.5)
[1] 2.2445984 0.7934152 3.2366673 2.2897537 0.8573059
Cauchy distribution with 0 location and scale of 1
rcauchy(5, location=0, scale=1)

[1] -0.01285116 -0.38918446 8.71016696 10.60293284 -0.68017185
Log-normal distribution with 0 mean and standard deviation

of 1 (on log scale)
rlnorm(5, meanlog=0, sdlog=1)

[1] 0.8725009 2.9433779 0.3329107 2.5976206 2.8171894
Weibull distribution with shape parameter of 0.5 and scale of

1
rweibull(5, shape=0.5, scale=1)

[1] 0.337599112 1.307774557 7.233985075 5.840429942 0.005751181
Wilcoxon distribution with 10 observations in the first

sample and 20 in second.
rwilcox(5, 10, 20)

[1] 111 88 93 100 124
Multinomial distribution with 5 object and 3 boxes using the

specified probabilities
rmultinom(5, size=5, prob=c(0.1,0.1,0.8))

[,1] [,2] [,3] [,4] [,5]
[1,] 0 0 1 1 0
[2,] 2 0 1 1 0
[3,] 3 5 3 3 5
Read Random Numbers Generator online: https://riptutorial.com/r/topic/1578/random-numbers-

generator
Chapter 87: Randomization
Introduction
The R language is commonly used for statistical analysis. As such, it contains a robust set of
options for randomization. For specific information on sampling from probability distributions, see
the documentation for distribution functions.
Remarks
Users who are coming from other programming languages may be confused by the lack of a rand
function equivalent to what they may have experienced before. Basic random number generation
is done using the r* family of functions for each distribution (see the link above). Random numbers
drawn uniformly from a range can be generated using runif, for "random uniform". Since this also
looks suspiciously like "run if", it is often hard to figure out for new R users.
Examples
Random draws and permutations
The sample command can be used to simulate classic probability problems like drawing from an
urn with and without replacement, or creating random permutations.
Note that throughout this example, set.seed is used to ensure that the example code is
reproducible. However, sample will work without explicitly calling set.seed.
Random permutation
In the simplest form, sample creates a random permutation of a vector of integers. This can be
accomplished with:
set.seed(1251)
sample(x = 10)
[1] 7 1 4 8 6 3 10 5 2 9
When given no other arguments, sample returns a random permutation of the vector from 1 to x.
This can be useful when trying to randomize the order of the rows in a data frame. This is a
common task when creating randomization tables for trials, or when selecting a random subset of
rows for analysis.
library(datasets)
set.seed(1171)
iris_rand <- iris[sample(x = 1:nrow(iris)),]
> head(iris)
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3.0 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
5 5.0 3.6 1.4 0.2 setosa
6 5.4 3.9 1.7 0.4 setosa
> head(iris_rand)
145 6.7 3.3 5.7 2.5 virginica
5 5.0 3.6 1.4 0.2 setosa
85 5.4 3.0 4.5 1.5 versicolor
137 6.3 3.4 5.6 2.4 virginica
128 6.1 3.0 4.9 1.8 virginica
105 6.5 3.0 5.8 2.2 virginica
Draws without Replacement

Using sample, we can also simulate drawing from a set with and without replacement. To sample
without replacement (the default), you must provide sample with a set to be drawn from and the
number of draws. The set to be drawn from is given as a vector.
set.seed(7043)
sample(x = LETTERS,size = 7)
[1] "S" "P" "J" "F" "Z" "G" "R"
Note that if the argument to size is the same as the length of the argument to x, you are creating a
random permutation. Also note that you cannot specify a size greater than the length of x when
doing sampling without replacement.
set.seed(7305)
sample(x = letters,size = 26)
[1] "x" "z" "y" "i" "k" "f" "d" "s" "g" "v" "j" "o" "e" "c" "m" "n" "h" "u" "a" "b" "l" "r"
"w" "t" "q" "p"
sample(x = letters,size = 30)

Error in sample.int(length(x), size, replace, prob) :
cannot take a sample larger than the population when 'replace = FALSE'
This brings us to drawing with replacement.
Draws with Replacement

To make random draws from a set with replacement, you use the replace argument to sample. By
default, replace is FALSE. Setting it to TRUE means that each element of the set being drawn from
may appear more than once in the final result.
set.seed(5062)
sample(x = c("A","B","C","D"),size = 8,replace = TRUE)
[1] "D" "C" "D" "B" "A" "A" "A" "A"
Changing Draw Probabilities

By default, when you use sample, it assumes that the probability of picking each element is the
same. Consider it as a basic "urn" problem. The code below is equivalent to drawing a colored
marble out of an urn 20 times, writing down the color, and then putting the marble back in the urn.
The urn contains one red, one blue, and one green marble, meaning that the probability of drawing
each color is 1/3.
set.seed(6472)
sample(x = c("Red","Blue","Green"),
size = 20,
replace = TRUE)
Suppose that, instead, we wanted to perform the same task, but our urn contains 2 red marbles, 1
blue marble, and 1 green marble. One option would be to change the argument we send to x to
add an additional Red. However, a better choice is to use the prob argument to sample.
The prob argument accepts a vector with the probability of drawing each element. In our example
above, the probability of drawing a red marble would be 1/2, while the probability of drawing a blue
or a green marble would be 1/4.
set.seed(28432)
size = 20,
replace = TRUE,
prob = c(0.50,0.25,0.25))
Counter-intuitively, the argument given to prob does not need to sum to 1. R will always transform
the given arguments into probabilities that total to 1. For instance, consider our above example of
2 Red, 1 Blue, and 1 Green. You can achieve the same results as our previous code using those
numbers:
set.seed(28432)
frac_prob_example <- sample(x = c("Red","Blue","Green"),
size = 200,
replace = TRUE,
prob = c(0.50,0.25,0.25))
set.seed(28432)
numeric_prob_example <- sample(x = c("Red","Blue","Green"),
size = 200,
replace = TRUE,
prob = c(2,1,1))
> identical(frac_prob_example,numeric_prob_example)
[1] TRUE
The major restriction is that you cannot set all the probabilities to be zero, and none of them can
be less than zero.
You can also utilize prob when replace is set to FALSE. In that situation, after each element is drawn,
the proportions of the prob values for the remaining elements give the probability for the next draw.
In this situation, you must have enough non-zero probabilities to reach the size of the sample you
are drawing. For example:
set.seed(21741)
size = 2,
replace = FALSE,
prob = c(0.8,0.19,0.01))
In this example, Red is drawn in the first draw (as the first element). There was an 80% chance of
Red being drawn, a 19% chance of Blue being drawn, and a 1% chance of Green being drawn.
For the next draw, Red is no longer in the urn. The total of the probabilities among the remaining
items is 20% (19% for Blue and 1% for Green). For that draw, there is a 95% chance the item will
be Blue (19/20) and a 5% chance it will be Green (1/20).
Setting the seed
The set.seed function is used to set the random seed for all randomization functions. If you are
using R to create a randomization that you want to be able to reproduce, you should use set.seed
first.
set.seed(1643)
samp1 <- sample(x = 1:5,size = 200,replace = TRUE)
set.seed(1643)
samp2 <- sample(x = 1:5,size = 200,replace = TRUE)
> identical(x = samp1,y = samp2)

[1] TRUE
Note that parallel processing requires special treatment of the random seed, described more
elsewhere.
Read Randomization online: https://riptutorial.com/r/topic/9574/randomization
Chapter 88: Raster and Image Analysis
Introduction
See also I/O for Raster Images
Examples
Calculating GLCM Texture
Gray Level Co-Occurrence Matrix (Haralick et al. 1973) texture is a powerful image feature for
image analysis. The glcm package provides a easy-to-use function to calculate such texutral
features for RasterLayer objects in R.
library(glcm)
library(raster)
r <- raster("C:/Program Files/R/R-3.2.3/doc/html/logo.jpg")

plot(r)
Calculating GLCM textures in one direction
rglcm <- glcm(r,

window = c(9,9),
shift = c(1,1),
statistics = c("mean", "variance", "homogeneity", "contrast",
"dissimilarity", "entropy", "second_moment")
)
plot(rglcm)
Calculation rotation-invariant texture features
The textural features can also be calculated in all 4 directions (0°, 45°, 90° and 135°) and then
combined to one rotation-invariant texture. The key for this is the shift parameter:
rglcm1 <- glcm(r,

window = c(9,9),
shift=list(c(0,1), c(1,1), c(1,0), c(1,-1)),
statistics = c("mean", "variance", "homogeneity", "contrast",
"dissimilarity", "entropy", "second_moment")
)
plot(rglcm1)
Mathematical Morphologies
The package mmand provides functions for the calculation of Mathematical Morphologies for n-
dimensional arrays. With a little workaround, these can also be calculated for raster images.
library(raster)
library(mmand)
r <- raster("C:/Program Files/R/R-3.2.3/doc/html/logo.jpg")

plot(r)
At first, a kernel (moving window) has to be set with a size (e.g. 9x9) and a shape type (e.g. disc,
box or diamond)
sk <- shapeKernel(c(9,9), type="disc")
Afterwards, the raster layer has to be converted into an array wich is used as input for the erode()
function.
rArr <- as.array(r, transpose = TRUE)

rErode <- erode(rArr, sk)
rErode <- setValues(r, as.vector(aperm(rErode)))
Besides erode(), also the morphological functions dilate(), opening() and closing() can be applied
like this.
plot(rErode)
Read Raster and Image Analysis online: https://riptutorial.com/r/topic/3726/raster-and-image-
analysis
Chapter 89: Rcpp
Examples
Inline Code Compile
Rcpp features two functions that enable code compilation inline and exportation directly into R:
cppFunction() and evalCpp(). A third function called sourceCpp() exists to read in C++ code in a
separate file though can be used akin to cppFunction().
Below is an example of compiling a C++ function within R. Note the use of "" to surround the
source.
# Note - This is R code.

# cppFunction in Rcpp allows for rapid testing.
require(Rcpp)
# Creates a function that multiples each element in a vector

# Returns the modified vector.
cppFunction("
NumericVector exfun(NumericVector x, int i){
x = x*i;
return x;
}")
# Calling function in R
exfun(1:5, 3)
To quickly understand a C++ expression use:
# Use evalCpp to evaluate C++ expressions

evalCpp("std::numeric_limits<double>::max()")
## [1] 1.797693e+308
Rcpp Attributes
Rcpp Attributes makes the process of working with R and C++ straightforward. The form of
attributes take:
// [[Rcpp::attribute]]
The use of attributes is typically associated with:
// [[Rcpp::export]]
that is placed directly above a declared function header when reading in a C++ file via sourceCpp().
Below is an example of an external C++ file that uses attributes.
// Add code below into C++ file Rcpp_example.cpp
#include <Rcpp.h>
using namespace Rcpp;
// Place the export tag right above function declaration.

// [[Rcpp::export]]
double muRcpp(NumericVector x){
int n = x.size(); // Size of vector

double sum = 0; // Sum value
// For loop, note cpp index shift to 0

for(int i = 0; i < n; i++){
// Shorthand for sum = sum + x[i]
sum += x[i];
}
return sum/n; // Obtain and return the Mean

}
// Place dependent functions above call or

// declare the function definition with:
double muRcpp(NumericVector x);
// [[Rcpp::export]]
double varRcpp(NumericVector x, bool bias = true){
// Calculate the mean using C++ function

double mean = muRcpp(x);
double sum = 0;
int n = x.size();
for(int i = 0; i < n; i++){

sum += pow(x[i] - mean, 2.0); // Square
}
return sum/(n-bias); // Return variance

}
To use this external C++ file within R, we do the following:
require(Rcpp)
# Compile File
sourceCpp("path/to/file/Rcpp_example.cpp")
# Make some sample data

x = 1:5
all.equal(muRcpp(x), mean(x))
## TRUE
all.equal(varRcpp(x), var(x))
## TRUE
Extending Rcpp with Plugins
Within C++, one can set different compilation flags using:
// [[Rcpp::plugins(name)]]
List of the built-in plugins:
// built-in C++11 plugin

// [[Rcpp::plugins(cpp11)]]
// built-in C++11 plugin for older g++ compiler

// [[Rcpp::plugins(cpp0x)]]
// built-in C++14 plugin for C++14 standard

// [[Rcpp::plugins(cpp14)]]
// built-in C++1y plugin for C++14 and C++17 standard under development
// [[Rcpp::plugins(cpp1y)]]
// built-in OpenMP++11 plugin

// [[Rcpp::plugins(openmp)]]
Specifying Additional Build Dependencies
To use additional packages within the Rcpp ecosystem, the correct header file may not be Rcpp.h
but Rcpp<PACKAGE>.h (as e.g. for RcppArmadillo). It typically needs to be imported and then the
dependency is stated within
// [[Rcpp::depends(Rcpp<PACKAGE>)]]
Examples:
// Use the RcppArmadillo package

// Requires different header file from Rcpp.h
#include <RcppArmadillo.h>
// [[Rcpp::depends(RcppArmadillo)]]
// Use the RcppEigen package

// Requires different header file from Rcpp.h
#include <RcppEigen.h>
// [[Rcpp::depends(RcppEigen)]]
Read Rcpp online: https://riptutorial.com/r/topic/1404/rcpp
Chapter 90: Reading and writing strings
Remarks
Related Docs:
• Get user input
Examples
Printing and displaying strings
R has several built-in functions that can be used to print or display information, but print and cat
are the most basic. As R is an interpreted language, you can try these out directly in the R
console:
print("Hello World")
#[1] "Hello World"
cat("Hello World\n")
#Hello World
Note the difference in both input and output for the two functions. (Note: there are no quote-
characters in the value of x created with x <- "Hello World". They are added by print at the output
stage.)
cattakes one or more character vectors as arguments and prints them to the console. If the
character vector has a length greater than 1, arguments are separated by a space (by default):
cat(c("hello", "world", "\n"))

#hello world
Without the new-line character (\n) the output would be:
cat("Hello World")
#Hello World>
The prompt for the next command appears immediately after the output. (Some consoles such as
RStudio's may automatically append a newline to strings that do not end with a newline.)
print is an example of a "generic" function, which means the class of the first argument passed is
detected and a class-specific method is used to output. For a character vector like "Hello World",
the result is similar to the output of cat. However, the character string is quoted and a number [1]
is output to indicate the first element of a character vector (In this case, the first and only element):
print("Hello World")
#[1] "Hello World"
This default print method is also what we see when we simply ask R to print a variable. Note how
the output of typing s is the same as calling print(s) or print("Hello World"):
s <- "Hello World"

s
#[1] "Hello World"
Or even without assigning it to anything:
"Hello World"
#[1] "Hello World"
If we add another character string as a second element of the vector (using the c() function to c
oncatenate the elements together), then the behavior of print() looks quite a bit different from that
of cat:
print(c("Hello World", "Here I am."))

#[1] "Hello World" "Here I am."
Observe that the c() function does not do string-concatenation. (One needs to use paste for that
purpose.) R shows that the character vector has two elements by quoting them separately. If we
have a vector long enough to span multiple lines, R will print the index of the element starting each
line, just as it prints [1] at the start of the first line.
c("Hello World", "Here I am!", "This next string is really long.")

#[1] "Hello World" "Here I am!"
#[3] "This next string is really long."
The particular behavior of print depends on the class of the object passed to the function.
If we call print an object with a different class, such as "numeric" or "logical", the quotes are
omitted from the output to indicate we are dealing with an object that is not character class:
print(1)
#[1] 1
print(TRUE)
#[1] TRUE
Factor objects get printed in the same fashion as character variables which often creates
ambiguity when console output is used to display objects in SO question bodies. It is rare to use
cat or print except in an interactive context. Explicitly calling print() is particularly rare (unless
you wanted to suppress the appearance of the quotes or view an object that is returned as
invisible by a function), as entering foo at the console is a shortcut for print(foo). The interactive
console of R is known as a REPL, a "read-eval-print-loop". The cat function is best saved for
special purposes (like writing output to an open file connection). Sometimes it is used inside
functions (where calls to print() are suppressed), however using cat() inside a function to
generate output to the console is bad practice. The preferred method is to message() or
warning() for intermediate messages; they behave similarly to cat but can be optionally
suppressed by the end user. The final result should simply returned so that the user can assign it
to store it if necessary.
message("hello world")
#hello world
suppressMessages(message("hello world"))
Reading from or writing to a file connection
Not always we have liberty to read from or write to a local system path. For example if R code
streaming map-reduce must need to read and write to file connection. There can be other
scenarios as well where one is going beyond local system and with advent of cloud and big data,
this is becoming increasingly common. One of the way to do this is in logical sequence.
Establish a file connection to read with file() command ("r" is for read mode):
conn <- file("/path/example.data", "r") #when file is in local system

conn1 <- file("stdin", "r") #when just standard input/output for files are available
As this will establish just file connection, one can read the data from these file connections as
follows:
line <- readLines(conn, n=1, warn=FALSE)
Here we are reading the data from file connection conn line by line as n=1. one can change value of
n (say 10, 20 etc.) for reading data blocks for faster reading (10 or 20 lines block read in one go).
To read complete file in one go set n=-1.
After data processing or say model execution; one can write the results back to file connection
using many different commands like writeLines(),cat() etc. which are capable of writing to a file
connection. However all of these commands will leverage file connection established for writing.
This could be done using file() command as:
conn2 <- file("/path/result.data", "w") #when file is in local system

conn3 <- file("stdout", "w") #when just standard input/output for files are available
Then write the data as follows:
writeLines("text",conn2, sep = "\n")
Capture output of operating system command
Functions which return a character vector

Base R has two functions for invoking a system command. Both require an additional parameter to
capture the output of the system command.
system("top -a -b -n 1", intern = TRUE)
system2("top", "-a -b -n 1", stdout = TRUE)
Both return a character vector.
[1] "top - 08:52:03 up 70 days, 15:09, 0 users, load average: 0.00, 0.00, 0.00"
[2] "Tasks: 125 total, 1 running, 124 sleeping, 0 stopped, 0 zombie"
[3] "Cpu(s): 0.9%us, 0.3%sy, 0.0%ni, 98.7%id, 0.1%wa, 0.0%hi, 0.0%si, 0.0%st"
[4] "Mem: 12194312k total, 3613292k used, 8581020k free, 216940k buffers"
[5] "Swap: 12582908k total, 2334156k used, 10248752k free, 1682340k cached"
[6] ""
[7] " PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND "
[8] "11300 root 20 0 1278m 375m 3696 S 0.0 3.2 124:40.92 trala "
[9] " 6093 user1 20 0 1817m 269m 1888 S 0.0 2.3 12:17.96 R "
[10] " 4949 user2 20 0 1917m 214m 1888 S 0.0 1.8 11:16.73 R "
For illustration, the UNIX command top -a -b -n 1 is used. This is OS specific and may
need to be amended to run the examples on your computer.
Package devtools has a function to run a system command and capture the output without an
additional parameter. It also returns a character vector.
devtools::system_output("top", "-a -b -n 1")
Functions which return a data frame

The fread function in package data.table allows to execute a shell command and to read the
output like read.table. It returns a data.table or a data.frame.
fread("top -a -b -n 1", check.names = TRUE)

PID USER PR NI VIRT RES SHR S X.CPU X.MEM TIME. COMMAND
1: 11300 root 20 0 1278m 375m 3696 S 0 3.2 124:40.92 trala
2: 6093 user1 20 0 1817m 269m 1888 S 0 2.3 12:18.56 R
3: 4949 user2 20 0 1917m 214m 1888 S 0 1.8 11:17.33 R
4: 7922 user3 20 0 3094m 131m 1892 S 0 1.1 21:04.95 R
Note, that fread automatically has skipped the top 6 header lines.
Here the parameter check.names = TRUE was added to convert %CPU, %MEN, and TIME+ to
syntactically valid column names.
Read Reading and writing strings online: https://riptutorial.com/r/topic/5541/reading-and-writing-

strings
Chapter 91: Reading and writing tabular data
in plain-text files (CSV, TSV, etc.)
Syntax
• read.csv(file, header = TRUE, sep = ",", quote = """, dec = ".", fill = TRUE, comment.char =
"", ...)
• read.csv2(file, header = TRUE, sep = ";", quote = """, dec = ",", fill = TRUE, comment.char =
"", ...)
• readr::read_csv(file, col_names = TRUE, col_types = NULL, locale = default_locale(), na =

c("", "NA"), comment = "", trim_ws = TRUE, skip = 0, n_max = -1, progress = interactive())
• data.table::fread(input, sep="auto", sep2="auto", nrows=-1L, header="auto",

na.strings="NA", stringsAsFactors=FALSE, verbose=getOption("datatable.verbose"),
autostart=1L, skip=0L, select=NULL, drop=NULL, colClasses=NULL,
integer64=getOption("datatable.integer64"), # default: "integer64" dec=if (sep!=".") "." else
",", col.names, check.names=FALSE, encoding="unknown", strip.white=TRUE,
showProgress=getOption("datatable.showProgress"), # default: TRUE
data.table=getOption("datatable.fread.datatable") # default: TRUE )
Parameters
Parameter Details
file name of the CSV file to read
header logical: does the .csv file contain a header row with column names?
sep character: symbol that separates the cells on each row
quote character: symbol used to quote character strings
dec character: symbol used as decimal separator
fill logical: when TRUE, rows with unequal length are filled with blank fields.
character: character used as comment in the csv file. Lines preceded by this
comment.char
character are ignored.
... extra arguments to be passed to read.table
Remarks
Note that exporting to a plain text format sacrifices much of the information encoded in the data
like variable classes for the sake of wide portability. For cases that do not require such portability,
a format like .RData or Feather may be more useful.
Input/output for other types of files is covered in several other topics, all linked from Input and
output.
Examples
Importing .csv files
Importing using base R

Comma separated value files (CSVs) can be imported using read.csv, which wraps read.table, but
uses sep = "," to set the delimiter to a comma.
# get the file path of a CSV included in R's utils package

csv_path <- system.file("misc", "exDIF.csv", package = "utils")
# path will vary based on installation location

csv_path
## [1] "/Library/Frameworks/R.framework/Resources/library/utils/misc/exDIF.csv"
df <- read.csv(csv_path)
df
## Var1 Var2
## 1 2.70 A
## 2 3.14 B
## 3 10.00 A
## 4 -7.00 A
A user friendly option, file.choose, allows to browse through the directories:
df <- read.csv(file.choose())
Notes
• Unlike read.table, read.csv defaults to header = TRUE, and uses the first row as column
names.
• All these functions will convert strings to factor class by default unless either as.is = TRUE or
stringsAsFactors = FALSE.
• The read.csv2 variant defaults to sep = ";" and dec = "," for use on data from countries
where the comma is used as a decimal point and the semicolon as a field separator.
Importing using packages

The readr package's read_csv function offers much faster performance, a progress bar for large
files, and more popular default options than standard read.csv, including stringsAsFactors = FALSE.
library(readr)
df <- read_csv(csv_path)
df
## # A tibble: 4 x 2
## Var1 Var2
## <dbl> <chr>
## 1 2.70 A
## 2 3.14 B
## 3 10.00 A
## 4 -7.00 A
Importing with data.table
The data.table package introduces the function fread. While it is similar to read.table, fread is
usually faster and more flexible, guessing the file's delimiter automatically.
# get the file path of a CSV included in R's utils package

csv_path <- system.file("misc", "exDIF.csv", package = "utils")
# path will vary based on R installation location

csv_path
## [1] "/Library/Frameworks/R.framework/Resources/library/utils/misc/exDIF.csv"
dt <- fread(csv_path)
dt
## Var1 Var2
## 1: 2.70 A
## 2: 3.14 B
## 3: 10.00 A
## 4: -7.00 A
Where argument input is a string representing:
• the filename (e.g. "filename.csv"),

• a shell command that acts on a file (e.g. "grep 'word' filename"), or
• the input itself (e.g. "input1, input2 \n A, B \n C, D").
fread returns an object of class data.table that inherits from class data.frame, suitable for use with
the data.table's usage of []. To return an ordinary data.frame, set the data.table parameter to
FALSE:
df <- fread(csv_path, data.table = FALSE)
class(df)
## [1] "data.frame"
df
## Var1 Var2
## 1 2.70 A
## 2 3.14 B
## 3 10.00 A
## 4 -7.00 A
Notes
• does not have all same options as read.table. One missing argument is na.comment,
fread
which may lead in unwanted behaviors if the source file contains #.
• fread uses only " for quote parameter.
• fread uses few (5) lines to guess variables types.
Importing .tsv files as matrices (basic R)
Many people don't make use of file.path when making path to a file. But if you are working across
Windows, Mac and Linux machines it's usually good practice to use it for making paths instead of
paste.
FilePath <- file.path(AVariableWithFullProjectPath,"SomeSubfolder","SomeFileName.txt.gz")
Data <- as.matrix(read.table(FilePath, header=FALSE, sep ="\t"))
Generally this is sufficient for most people.
Sometimes it happens the matrix dimensions are so large that procedure of memory allocation
must be taken into account while reading in the matrix, which means reading in the matrix line by
line.
Take the previous example, In this case FilePath contains a file of dimension 8970 8970 with 79%
of the cells containing non-zero values.
system.time(expr=Data<-as.matrix(read.table(file=FilePath,header=FALSE,sep=" ") ))
system.time says 267 seconds were taken to read the file.
user system elapsed

265.563 1.949 267.563
Similarly this file can be read line by line,
FilePath <- "SomeFile"

connection<- gzfile(FilePath,open="r")
TableList <- list()
Counter <- 1
system.time(expr= while ( length( Vector<-as.matrix(scan(file=connection, sep=" ", nlines=1,
quiet=TRUE)) ) > 0 ) {
TableList[[Counter]]<-Vector
Counter<-Counter+1
})
user system elapsed
165.976 0.060 165.941
close(connection)
system.time(expr=(Data <- do.call(rbind,TableList)))
user system elapsed
0.477 0.088 0.565
There's also the futile.matrix package which implements a read.matrix method, the code itself will
reveal itself to be the same thing as described in example 1.
Exporting .csv files
Exporting using base R

Data can be written to a CSV file using write.csv():
write.csv(mtcars, "mtcars.csv")
Commonly-specified parameters include row.names = FALSE and na = "".
Exporting using packages

readr::write_csv is significantly faster than write.csv and does not write row names.
library(readr)
write_csv(mtcars, "mtcars.csv")
Import multiple csv files
files = list.files(pattern="*.csv")
data_list = lapply(files, read.table, header = TRUE)
This read every file and adds it to a list. Afterwards, if all data.frame have the same structure they
can be combined into one big data.frame:
df <- do.call(rbind, data_list)
Importing fixed-width files
Fixed-width files are text files in which columns are not separated by any character delimiter, like ,
or ;, but rather have a fixed character length (width). Data is usually padded with white spaces.
An example:
Column1 Column2 Column3 Column4Column5
1647 pi 'important' 3.141596.28318
1731 euler 'quite important' 2.718285.43656
1979 answer 'The Answer.' 42 42
Let's assume this data table exists in the local file constants.txt in the working directory.
Importing with base R

df <- read.fwf('constants.txt', widths = c(8,10,18,7,8), header = FALSE, skip = 1)
df
#> V1 V2 V3 V4 V5
#> 1 1647 pi 'important' 3.14159 6.28318
#> 2 1731 euler 'quite important' 2.71828 5.43656
#> 3 1979 answer 'The Answer.' 42 42.0000
Note:
• Column titles don't need to be separated by a character (Column4Column5)

• The widths parameter defines the width of each column
• Non-separated headers are not readable with read.fwf()
Importing with readr

library(readr)
df <- read_fwf('constants.txt',
fwf_cols(Year = 8, Name = 10, Importance = 18, Value = 7, Doubled = 8),
skip = 1)
df
#> # A tibble: 3 x 5
#> Year Name Importance Value Doubled
#> <int> <chr> <chr> <dbl> <dbl>
#> 1 1647 pi 'important' 3.14159 6.28318
#> 2 1731 euler 'quite important' 2.71828 5.43656
#> 3 1979 answer 'The Answer.' 42.00000 42.00000
Note:
• readr's fwf_* helper functions offer alternative ways of specifying column lengths, including
automatic guessing (fwf_empty)
• readr is faster than base R
• Column titles cannot be automatically imported from data file
Read Reading and writing tabular data in plain-text files (CSV, TSV, etc.) online:
https://riptutorial.com/r/topic/481/reading-and-writing-tabular-data-in-plain-text-files--csv--tsv--etc--
Chapter 92: Recycling
Remarks
What is recycling in R
Recycling is when an object is automatically extended in certain operations to match the length of
another, longer object.
For example, the vectorised addition results in the following:
c(1,2,3) + c(1,2,3,4,5,6)
[1] 2 4 6 5 7 9
Because of the recycling, the operation that actually happened was:
c(1,2,3,1,2,3) + c(1,2,3,4,5,6)
In cases where the longer object is not a multiple of the shorter one, a warning message is
presented:
c(1,2,3) + c(1,2,3,4,5,6,7)
[1] 2 4 6 5 7 9 8
Warning message:
In c(1, 2, 3) + c(1, 2, 3, 4, 5, 6, 7) :
longer object length is not a multiple of shorter object length
Another example of recycling:
matrix(nrow =5, ncol = 2, 1:5 )

[,1] [,2]
[1,] 1 1
[2,] 2 2
[3,] 3 3
[4,] 4 4
[5,] 5 5
Examples
Recycling use in subsetting
Recycling can be used in a clever way to simplify code.
Subsetting
If we want to keep every third element of a vector we can do the following:
my_vec <- c(1,2,3,4,5,6,7,8,9,10)
my_vec[c(TRUE, FALSE)]
[1] 1 3 5 7 9
Here the logical expression was expanded to the length of the vector.
We can also perform comparisons using recycling:
my_vec <- c("foo", "bar", "soap", "mix")

my_vec == "bar"
[1] FALSE TRUE FALSE FALSE
Here "bar" gets recycled.
Read Recycling online: https://riptutorial.com/r/topic/5649/recycling
Chapter 93: Regular Expression Syntax in R
Introduction
This document introduces the basics of regular expressions as used in R. For more information
about R's regular expression syntax, see ?regex. For a comprehensive list of regular expression
operators, see this ICU guide on regular expressions.
Examples
Use `grep` to find a string in a character vector
# General syntax:
# grep(<pattern>, <character vector>)
mystring <- c('The number 5',

'The number 8',
'1 is the loneliest number',
'Company, 3 is',
'Git SSH tag is [email protected]',
'My personal site is www.personal.org',
'path/to/my/file')
grep('5', mystring)
# [1] 1
grep('@', mystring)
# [1] 5
grep('number', mystring)
# [1] 1 2 3
x|y means look for "x" or "y"
grep('5|8', mystring)
# [1] 1 2
grep('com|org', mystring)
# [1] 5 6
. is a special character in Regex. It means "match any character"
grep('The number .', mystring)

# [1] 1 2
Be careful when trying to match dots!
tricky <- c('www.personal.org', 'My friend is a cyborg')

grep('.org', tricky)
# [1] 1 2
To match a literal character, you have to escape the string with a backslash (\). However, R tries
to look for escape characters when creating strings, so you actually need to escape the backslash
itself (i.e. you need to double escape regular expression characters.)
grep('\.org', tricky)
# Error: '\.' is an unrecognized escape in character string starting "'\."
grep('\\.org', tricky)
# [1] 1
If you want to match one of several characters, you can wrap those characters in brackets ([])
grep('[13]', mystring)
# [1] 3 4
grep('[@/]', mystring)
# [1] 5 7
It may be useful to indicate character sequences. E.g. [0-4] will match 0, 1, 2, 3, or 4, [A-Z] will
match any uppercase letter, [A-z] will match any uppercase or lowercase letter, and [A-z0-9] will
match any letter or number (i.e. all alphanumeric characters)
grep('[0-4]', mystring)
# [1] 3 4
grep('[A-Z]', mystring)
# [1] 1 2 4 5 6
R also has several shortcut classes that can be used in brackets. For instance, [:lower:] is short
for a-z, [:upper:] is short for A-Z, [:alpha:] is A-z, [:digit:] is 0-9, and [:alnum:] is A-z0-9. Note
that these whole expressions must be used inside brackets; for instance, to match a single digit,
you can use [[:digit:]] (note the double brackets). As another example, [@[:digit:]/] will match
the characters @, / or 0-9.
grep('[[:digit:]]', mystring)
# [1] 1 2 3 4
grep('[@[:digit:]/]', mystring)
# [1] 1 2 3 4 5 7
Brackets can also be used to negate a match with a carat (^). For instance, [^5] will match any
character other than "5".
grep('The number [^5]', mystring)

# [1] 2
Read Regular Expression Syntax in R online: https://riptutorial.com/r/topic/9743/regular-

expression-syntax-in-r
Chapter 94: Regular Expressions (regex)
Introduction
Regular expressions (also called "regex" or "regexp") define patterns that can be matched against
a string. Type ?regex for the official R documentation and see the Regex Docs for more details.
The most important 'gotcha' that will not be learned in the SO regex/topics is that most R-regex
functions need the use of paired backslashes to escape in a pattern parameter.
Remarks
Character classes
• "[AB]" could be A or B
• "[[:alpha:]]" could be any letter
• "[[:lower:]]" stands for any lower-case letter. Note that "[a-z]" is close but doesn't match,
e.g., ú.
• "[[:upper:]]" stands for any upper-case letter. Note that "[A-Z]" is close but doesn't match,
e.g., Ú.
• "[[:digit:]]" stands for any digit : 0, 1, 2, ..., or 9 and is equivalent to "[0-9]".
Quantifiers
+, *
and ? apply as usual in regex. -- + matches at least once, * matches 0 or more times, and ?
matches 0 or 1 time.
Start and end of line indicators

You can specify the position of the regex in the string :
• "^..." forces the regular expression to be at the beginning of the string

• "...$" forces the regular expression to be at the end of the string
Differences from other languages

Please note that regular expressions in R often look ever-so-slightly different from regular
expressions used in other languages.
• R requires double-backslash escapes (because "\" already implies escaping in general in R

strings), so, for example, to capture whitespace in most regular expression engines, one
simply needs to type \s, vs. \\s in R.
• UTF-8 characters in R should be escaped with a capital U, e.g. [\U{1F600}] and [\U1F600]
match , whereas in, e.g., Ruby, this would be matched with a lower-case u.
Additional Resources
The following site reg101 is a good place for checking online regex before using it R-script.
The R Programmming wikibook has a page dedicated to text processing with many examples
using regular expressions.
Examples
Eliminating Whitespace
string <- ' some text on line one;

and then some text on line two '
Trimming Whitespace
"Trimming" whitespace typically refers to removing both leading and trailing whitespace from a
string. This may be done using a combination of the previous examples. gsub is used to force the
replacement over both the leading and trailing matches.
Prior to R 3.2.0
gsub(pattern = "(^ +| +$)",

replacement = "",
x = string)
[1] "some text on line one; \nand then some text on line two"
R 3.2.0 and higher
trimws(x = string)
[1] "some text on line one; \nand then some text on line two"
Removing Leading Whitespace

Prior to R 3.2.0
sub(pattern = "^ +",

replacement = "",
x = string)
[1] "some text on line one; \nand then some text on line two "
R 3.2.0 and higher
trimws(x = string,
which = "left")
[1] "some text on line one; \nand then some text on line two "
Removing Trailing Whitespace

Prior to R 3.2.0
sub(pattern = " +$",

replacement = "",
x = string)
[1] " some text on line one; \nand then some text on line two"
R 3.2.0 and higher
trimws(x = string,
which = "right")
[1] " some text on line one; \nand then some text on line two"
Removing All Whitespace
gsub(pattern = "\\s",
replacement = "",
x = string)
[1] "sometextonlineone;andthensometextonlinetwo"
Note that this will also remove white space characterse such as tabs (\t), newlines (\r and \n),
and spaces.
Validate a date in a "YYYYMMDD" format
It is a common practice to name files using the date as prefix in the following format: YYYYMMDD, for
example: 20170101_results.csv. A date in such string format can be verified using the following
regular expression:
\\d{4}(0[1-9]|1[012])(0[1-9]|[12][0-9]|3[01])
The above expression considers dates from year: 0000-9999, months between: 01-12 and days 01-
31.
For example:
> grepl("\\d{4}(0[1-9]|1[012])(0[1-9]|[12][0-9]|3[01])", "20170101")

[1] TRUE
> grepl("\\d{4}(0[1-9]|1[012])(0[1-9]|[12][0-9]|3[01])", "20171206")
[1] TRUE
> grepl("\\d{4}(0[1-9]|1[012])(0[1-9]|[12][0-9]|3[01])", "29991231")
[1] TRUE
Note: It validates the date syntax, but we can have a wrong date with a valid syntax, for example:
20170229 (2017 it is not a leap year).
> grepl("\\d{4}(0[1-9]|1[012])(0[1-9]|[12][0-9]|3[01])", "20170229")

[1] TRUE
If you want to validate a date, it can be done via this user defined function:
is.Date <- function(x) {return(!is.na(as.Date(as.character(x), format = '%Y%m%d')))}
Then
> is.Date(c("20170229", "20170101", 20170101))

[1] FALSE TRUE TRUE
Validate US States postal abbreviations
The following regex includes 50 states and also Commonwealth/Territory (see www.50states.com):
regex <-
"(A[LKSZR])|(C[AOT])|(D[EC])|(F[ML])|(G[AU])|(HI)|(I[DLNA])|(K[SY])|(LA)|(M[EHDAINSOT])|(N[EVHJMYCD])|(M
For example:
> test <- c("AL", "AZ", "AR", "AJ", "AS", "DC", "FM", "GU","PW", "FL", "AJ", "AP")
> grepl(us.states.pattern, test)
[1] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE
>
Note:
If you want to verify only the 50 States, then we recommend to use the R-dataset: state.abb from
state, for example:
> data(state)
> test %in% state.abb
[1] TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
We get TRUE only for 50-States abbreviations: AL, AZ, AR, FL.
Validate US phone numbers
The following regular expression:
us.phones.regex <- "^\\s*(\\+\\s*1(-?|\\s+))*[0-9]{3}\\s*-?\\s*[0-9]{3}\\s*-?\\s*[0-9]{4}$"
Validates a phone number in the form of: +1-xxx-xxx-xxxx, including optional leading/trailing blanks
at the beginning/end of each group of numbers, but not in the middle, for example: +1-xxx-xxx-xx
xx is not valid. The - delimiter can be replaced by blanks: xxx xxx xxx or without delimiter:
xxxxxxxxxx. The +1 prefix is optional.
Let's check it:
us.phones.regex <- "^\\s*(\\+\\s*1(-?|\\s+))*[0-9]{3}\\s*-?\\s*[0-9]{3}\\s*-?\\s*[0-9]{4}$"
phones.OK <- c("305-123-4567", "305 123 4567", "+1-786-123-4567",

"+1 786 123 4567", "7861234567", "786 - 123 4567", "+ 1 786 - 123 4567")
phones.NOK <- c("124-456-78901", "124-456-789", "124-456-78 90",

"124-45 6-7890", "12 4-456-7890")
Valid cases:
> grepl(us.phones.regex, phones.OK)

[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE
>
Invalid cases:
> grepl(us.phones.regex, phones.NOK)

[1] FALSE FALSE FALSE FALSE FALSE
>
Note:
• \\s Matches any space, tab or newline character
Escaping characters in R regex patterns
Since both R and regex share the escape character ,"\", building correct patterns for grep, sub,
gsub or any other function that accepts a pattern argument will often need pairing of backslashes. If
you build a three item character vector in which one items has a linefeed, another a tab character
and one neither, and hte desire is to turn either the linefeed or the tab into 4-spaces then a single
backslash is need for the construction, but tpaired backslashes for matching:
x <- c( "a\nb", "c\td", "e f")

x # how it's stored
# [1] "a\nb" "c\td" "e f"
cat(x) # how it will be seen with cat
#a
#b c d e f
gsub(patt="\\n|\\t", repl=" ", x)
#[1] "a b" "c d" "e f"
Note that the pattern argument (which is optional if it appears first and only needs partial spelling)
is the only argument to require this doubling or pairing. The replacement argument does not
require the doubling of characters needing to be escaped. If you wanted all the linefeeds and 4-
space occurrences replaces with tabs it would be:
gsub("\\n| ", "\t", x)

#[1] "a\tb" "c\td" "e\tf"
Differences between Perl and POSIX regex
There are two ever-so-slightly different engines of regular expressions implemented in R. The
default is called POSIX-consistent; all regex functions in R are also equipped with an option to turn
on the latter type: perl = TRUE.
Look-ahead/look-behind
perl = TRUE enables look-ahead and look-behind in regular expressions.
• "(?<=A)B"matches an appearance of the letter B only if it's preceded by A, i.e. "ABACADABRA"

would be matched, but "abacadabra" and "aBacadabra" would not.
Read Regular Expressions (regex) online: https://riptutorial.com/r/topic/5748/regular-expressions--

regex-
Chapter 95: Reproducible R
Introduction
With 'Reproducibility' we mean that someone else (perhaps you in the future) can repeat the steps
you performed and get the same result. See the Reproducible Research Task View.
Remarks
To create reproducible results, all sources of variation need to be fixed. For instance, if a
(pseudo)random number generator is used, the seed needs to be fixed if you want to recreate the
same results. Another way to reduce variation is to combine text and computation in the same
document.
References
• Peng, R. D. (2011). Reproducible Research in Computational. Science, 334(6060),
1226–1227. http://doi.org/10.1126/science.1213847
• Peng, Roger D. Report Writing for Data Science in R. Leanpub, 2015.

https://leanpub.com/reportwriting.
Examples
Data reproducibility
dput() and dget()

The easiest way to share a (preferable small) data frame is to use a basic function dput(). It will
export an R object in a plain text form.
dput(mtcars, file = 'df.txt')
Then, anyone can load the precise R object to their GlobalEnvironment using the dget() function.
df <- dget('df.txt')
For larger R objects, there are a number of ways of saving them reproducibly. See Input and
output .
Package reproducibility
Package reproducibility is a very common issue in reproducing some R code. When various
packages get updated, some interconnections between them may break. The ideal solution for the
problem is to reproduce the image of the R code writer's machine on your computer at the date
when the code was written. And here comes checkpoint package.
Starting from 2014-09-17, the authors of the package make daily copies of the whole CRAN
package repository to their own mirror repository -- Microsoft R Archived Network. So, to avoid
package reproduciblity issues when creating a reproducible R project, all you need is to:
1. Make sure that all your packages (and R version) are up-to-date.
2. Include checkpoint::checkpoint('YYYY-MM-DD') line in your code.
checkpoint will create a directory .checkpoint in your R_home directory ("~/"). To this technical
directory it will install all the packages, that are used in your project. That means, checkpoint looks
through all the .R files in your project directory to pick up all the library() or require() calls and
install all the required packages in the form they existed at CRAN on the specified date.
PRO You are freed from the package reproducibility issue.

CONTRA For each specified date you have to download and install all the packages that are used
in a certain project that you aim to reproduce. That may take quite a while.
Read Reproducible R online: https://riptutorial.com/r/topic/4087/reproducible-r
Chapter 96: Reshape using tidyr
Introduction
tidyr has two tools for reshaping data: gather (wide to long) and spread (long to wide).
See Reshaping data for other options.
Examples
Reshape from long to wide format with spread()
library(tidyr)
## example data
set.seed(123)
df <- data.frame(
name = rep(c("firstName", "secondName"), each=4),
numbers = rep(1:4, 2),
value = rnorm(8)
)
df
# name numbers value
# 1 firstName 1 -0.56047565
# 2 firstName 2 -0.23017749
# 3 firstName 3 1.55870831
# 4 firstName 4 0.07050839
# 5 secondName 1 0.12928774
# 6 secondName 2 1.71506499
# 7 secondName 3 0.46091621
# 8 secondName 4 -1.26506123
We can "spread" the 'numbers' column, into separate columns:
spread(data = df,
key = numbers,
value = value)
# name 1 2 3 4
# 1 firstName -0.5604756 -0.2301775 1.5587083 0.07050839
# 2 secondName 0.1292877 1.7150650 0.4609162 -1.26506123
Or spread the 'name' column into separate columns:
spread(data = df,
key = name,
value = value)
# numbers firstName secondName
# 1 1 -0.56047565 0.1292877
# 2 2 -0.23017749 1.7150650
# 3 3 1.55870831 0.4609162
# 4 4 0.07050839 -1.2650612
Reshape from wide to long format with gather()
library(tidyr)
## example data
df <- read.table(text =" numbers firstName secondName
1 1 1.5862639 0.4087477
2 2 0.1499581 0.9963923
3 3 0.4117353 0.3740009
4 4 -0.4926862 0.4437916", header = T)
df
# numbers firstName secondName
# 1 1 1.5862639 0.4087477
# 2 2 0.1499581 0.9963923
# 3 3 0.4117353 0.3740009
# 4 4 -0.4926862 0.4437916
We can gather the columns together using 'numbers' as the key column:
gather(data = df,
key = numbers,
value = myValue)
# numbers numbers myValue
# 1 1 firstName 1.5862639
# 2 2 firstName 0.1499581
# 3 3 firstName 0.4117353
# 4 4 firstName -0.4926862
# 5 1 secondName 0.4087477
# 6 2 secondName 0.9963923
# 7 3 secondName 0.3740009
# 8 4 secondName 0.4437916
Read Reshape using tidyr online: https://riptutorial.com/r/topic/9195/reshape-using-tidyr
Chapter 97: Reshaping data between long
and wide forms
Introduction
In R, tabular data is stored in data frames. This topic covers the various ways of transforming a
single table.
Remarks
Helpful packages
• Reshaping, stacking and splitting with data.table
• Reshape using tidyr
• splitstackshape
Examples
The reshape function
The most flexible base R function for reshaping data is reshape. See ?reshape for its syntax.
# create unbalanced longitudinal (panel) data set

set.seed(1234)
df <- data.frame(identifier=rep(1:5, each=3),
location=rep(c("up", "down", "left", "up", "center"), each=3),
period=rep(1:3, 5), counts=sample(35, 15, replace=TRUE),
values=runif(15, 5, 10))[-c(4,8,11),]
df
identifier location period counts values

1 1 up 1 4 9.186478
2 1 up 2 22 6.431116
3 1 up 3 22 6.334104
5 2 down 2 31 6.161130
6 2 down 3 23 6.583062
7 3 left 1 1 6.513467
9 3 left 3 24 5.199980
10 4 up 1 18 6.093998
12 4 up 3 20 7.628488
13 5 center 1 10 9.573291
14 5 center 2 33 9.156725
15 5 center 3 11 5.228851
Note that the data.frame is unbalanced, that is, unit 2 is missing an observation in the first period,
while units 3 and 4 are missing observations in the second period. Also, note that there are two
variables that vary over the periods: counts and values, and two that do not vary: identifier and
location.
Long to Wide
To reshape the data.frame to wide format,
# reshape wide on time variable

df.wide <- reshape(df, idvar="identifier", timevar="period",
v.names=c("values", "counts"), direction="wide")
df.wide
identifier location values.1 counts.1 values.2 counts.2 values.3 counts.3
1 1 up 9.186478 4 6.431116 22 6.334104 22
5 2 down NA NA 6.161130 31 6.583062 23
7 3 left 6.513467 1 NA NA 5.199980 24
10 4 up 6.093998 18 NA NA 7.628488 20
13 5 center 9.573291 10 9.156725 33 5.228851 11
Notice that the missing time periods are filled in with NAs.
In reshaping wide, the "v.names" argument specifies the columns that vary over time. If the
location variable is not necessary, it can be dropped prior to reshaping with the "drop" argument.
In dropping the only non-varying / non-id column from the data.frame, the v.names argument
becomes unnecessary.
reshape(df, idvar="identifier", timevar="period", direction="wide",

drop="location")
Wide to Long
To reshape long with the current df.wide, a minimal syntax is
reshape(df.wide, direction="long")
However, this is typically trickier:
# remove "." separator in df.wide names for counts and values

names(df.wide)[grep("\\.", names(df.wide))] <-
gsub("\\.", "", names(df.wide)[grep("\\.", names(df.wide))])
Now the simple syntax will produce an error about undefined columns.
With column names that are more difficult for the reshape function to automatically parse, it is
sometimes necessary to add the "varying" argument which tells reshape to group particular
variables in wide format for the transformation into long format. This argument takes a list of
vectors of variable names or indices.
reshape(df.wide, idvar="identifier",
varying=list(c(3,5,7), c(4,6,8)), direction="long")
In reshaping long, the "v.names" argument can be provided to rename the resulting varying
variables.
Sometimes the specification of "varying" can be avoided by use of the "sep" argument which tells
reshape what part of the variable name specifies the value argument and which specifies the time
argument.
Reshaping data
Often data comes in tables. Generally one can divide this tabular data in wide and long formats. In
a wide format, each variable has its own column.
Person Height [cm] Age [yr]
Alison 178 20
Bob 174 45
Carl 182 31
However, sometimes it is more convenient to have a long format, in which all variables are in one
column and the values are in a second column.
Person Variable Value
Alison Height [cm] 178
Bob Height [cm] 174
Carl Height [cm] 182
Alison Age [yr] 20
Bob Age [yr] 45
Carl Age [yr] 31
Base R, as well as third party packages can be used to simplify this process. For each of the
options, the mtcars dataset will be used. By default, this dataset is in a long format. In order for the
packages to work, we will insert the row names as the first column.
mtcars # shows the dataset

data <- data.frame(observation=row.names(mtcars),mtcars)
Base R
There are two functions in base R that can be used to convert between wide and long format:
stack() and unstack().
long <- stack(data)

long # this shows the long format
wide <- unstack(long)
wide # this shows the wide format
However, these functions can become very complex for more advanced use cases. Luckily, there
are other options using third party packages.
The tidyr package

This package uses gather() to convert from wide to long and spread() to convert from long to wide.
library(tidyr)
long <- gather(data, variable, value, 2:12) # where variable is the name of the
# variable column, value indicates the name of the value column and 2:12 refers to
# the columns to be converted.
long # shows the long result
wide <- spread(long,variable,value)
wide # shows the wide result (~data)
The data.table package

The data.table package extends the reshape2 functions and uses the function melt() to go from
wide to long and dcast() to go from long to wide.
library(data.table)
long <- melt(data,'observation',2:12,'variable', 'value')
long # shows the long result
wide <- dcast(long, observation ~ variable)
wide # shows the wide result (~data)
Read Reshaping data between long and wide forms online:

https://riptutorial.com/r/topic/2904/reshaping-data-between-long-and-wide-forms
Chapter 98: RESTful R Services
Introduction
OpenCPU uses standard R packaging to develop, ship and deploy web applications.
Examples
opencpu Apps
The official website contain good exemple of apps: https://www.opencpu.org/apps.html
The following code is used to serve a R session:
library(opencpu)
opencpu$start(port = 5936)
After this code is executed, you can use URLs to access the functions of the R session. The result
could be XML, html, JSON or some other defined formats.
For exemple, the previous R session can be accessed by a cURL call:
#curl uses http post method for -X POST or -d "arg=value"

curl http://localhost:5936/ocpu/library/MASS/scripts/ch01.R -X POST
curl http://localhost:5936/ocpu/library/stats/R/rnorm -d "n=10&mean=5"
The call is asynchronous, meaning that the R session is not blocked while waiting for the call to
finish (contrary to shiny).
The call result is kept in a temporary session stored in /ocpu/tmp/
An exemple of how to retrieve the temporary session:
curl https://public.opencpu.org/ocpu/library/stats/R/rnorm -d n=5

/ocpu/tmp/x009f9e7630/R/.val
/ocpu/tmp/x009f9e7630/stdout
/ocpu/tmp/x009f9e7630/source
/ocpu/tmp/x009f9e7630/console
/ocpu/tmp/x009f9e7630/info
x009f9e7630 is the name of the session.
Pointing to /ocpu/tmp/x009f9e7630/R/.val will return the value resulting of rnorm(5),

/ocpu/tmp/x009f9e7630/R/console will return the content of the console of rnorm(5), etc..
Read RESTful R Services online: https://riptutorial.com/r/topic/8323/restful-r-services
Chapter 99: RMarkdown and knitr
presentation
Syntax
• Header:
YAML format, used when the script is compile to define general parameter and
○
metadata
Parameters
Parameter definition
title the title of the document
author The author of the document
date The date of the document: Can be "r format(Sys.time(), '%d %B, %Y')"
author The author of the document
The output format of the document: at least 10 format available. For html
output
document, html_output. For PDF document, pdf_document, ..
Remarks
Sub options parameters:

sub-option description html pdf word odt rtf md github ioslides slidy b
The LaTeX
package to
citation_package process X X X
citations, natbib,
biblatex or none
Let readers to
toggle the
code_folding display of R X
code, "none",
"hide", or "show"
Beamer color
colortheme X
theme to use
CSS file to use

css to style X X X
document
Graphics device
to use for figure
dev X X X X X X X
output (e.g.
"png")
Add a
countdown timer
duration X
(in minutes) to
footer of slides
Should figures
fig_caption be rendered with X X X X X X X
captions?
Default figure
fig_height, height and width
X X X X X X X X X X
fig_width (in inches) for
document
Syntax
highlighting:
"tango",
highlight X X X X X
"pygments",
"kate","zenburn",
"textmate"
File of content to
place in
document
includes X X X X X X X X
(in_header,
before_body,
after_body)
Should bullets
appear one at a
incremental time (on X X X
presenter
mouse clicks)?
keep_md Save a copy of X X X X X X
.md file that

contains knitr
output
Save a copy of
.tex file that
keep_tex X X
contains knitr
output
Engine to render
latex, or
latex_engine ""pdflatex", X X
"xelatex",
lualatex"
Directory of
dependency
lib_dir files to use X X X
(Bootstrap,
MathJax, etc.)
Set to local or a
URL to use a
local/URL
mathjax X X X
version of
MathJax to
render
Markdown
extensions to
md_extensions add to default X X X X X X X X X X
definition or R
Markdown
Add section
number_sections numbering to X X
headers
Additional
pandoc_args arguments to X X X X X X X X X X
pass to Pandoc
Preserve YAML
preserve_yaml front matter in X
final document?
docx file whose

styles should be
reference_docx copied when X
producing docx
output
Embed
self_contained dependencies X X X
into the doc
The lowest
heading level
slide_level X
that defines
individual slides
Use the smaller

smaller font size in the X
presentation?
Convert straight
quotes to curly,
smart dashes to em- X X X
dashes, ... to
ellipses, etc.
Pandoc
template to use
template X X X X X
when rendering
file
Bootswatch or
theme Beamer theme X X
to use for page
Add a table of
toc contents at start X X X X X X X
of document
The lowest level

of headings to
toc_depth X X X X X X
add to table of
contents
Float the table of

toc_float contents to the X
left of the main
content
Examples
Rstudio example
This is a script saved as .Rmd, on the contrary of r scripts saved as .R.
To knit the script, either use the render function or use the shortcut button in Rstudio.
---
title: "Rstudio exemple of a rmd file"
author: 'stack user'
date: "22 July 2016"
output: html_document
---
The header is used to define the general parameters and the metadata.
## R Markdown
This is an R Markdown document.

It is a script written in markdown with the possibility to insert chunk of R code in it.
To insert R code, it needs to be encapsulated into inverted quote.
Like that for a long piece of code:
```{r cars}
summary(cars)
```
And like ``r cat("that")`` for small piece of code.
## Including Plots
You can also embed plots, for example:
```{r echo=FALSE}
plot(pressure)
```
Adding a footer to an ioslides presentation
Adding a footer is not natively possible. Luckily, we can make use of jQuery and CSS to add a
footer to the slides of an ioslides presentation rendered with knitr. First of all we have to include
the jQuery plugin. This is done by the line
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script>
Now we can use jQuery to alter the DOM (document object model) of our presentation. In other
words: we alter the HTML structure of the document. As soon as the presentation is loaded (
$(document).ready(function() { ... })
), we select all slides, that do not have the class attributes .title-slide, .backdrop, or .segue and
add the tag <footer></footer> right before each slide is 'closed' (so before </slide>). The attribute
label carries the content that will be displayed later on.
All we have to do now is to layout our footer with CSS:
After each <footer> (footer::after):
• display the content of the attribute label

• use font size 12
• position the footer (20 pixels from the bottom of the slide and 60 pxs from the left)
(the other properties can be ignored but might have to be modified if the presentation uses a
different style template).
---
title: "Adding a footer to presentaion slides"
output: ioslides_presentation
---

knitr::opts_chunk$set(echo = FALSE)
```
<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.2/jquery.min.js"></script>
<script>
$(document).ready(function() {
$('slide:not(.title-slide, .backdrop, .segue)').append('<footer label=\"My amazing
footer!\"></footer>');
})
</script>
<style>
footer:after {
content: attr(label);
font-size: 12pt;
position: absolute;
bottom: 20px;
left: 60px;
line-height: 1.9;
}
</style>
## Slide 1
This is slide 1.
## Slide 2
This is slide 2
# Test
## Slide 3
And slide 3.
The result will look like this:
Read RMarkdown and knitr presentation online: https://riptutorial.com/r/topic/2999/rmarkdown-

and-knitr-presentation
Chapter 100: RODBC
Examples
Connecting to Excel Files via RODBC
While RODBC is restricted to Windows computers with compatible architecture between R and any
target RDMS, one of its key flexibilities is to work with Excel files as if they were SQL databases.
require(RODBC)
con = odbcConnectExcel("myfile.xlsx") # open a connection to the Excel file
sqlTables(con)$TABLE_NAME # show all sheets
df = sqlFetch(con, "Sheet1") # read a sheet
df = sqlQuery(con, "select * from [Sheet1 $]") # read a sheet (alternative SQL syntax)
close(con) # close the connection to the file
SQL Server Management Database connection to get individual table
Another use of RODBC is in connecting with SQL Server Management Database. We need to
specify the 'Driver' i.e. SQL Server here, the database name "Atilla" and then use the sqlQuery to
extract either the full table or a fraction of it.
library(RODBC)
cn <- odbcDriverConnect(connection="Driver={SQL
Server};server=localhost;database=Atilla;trusted_connection=yes;")
tbl <- sqlQuery(cn, 'select top 10 * from table_1')
Connecting to relational databases
library(RODBC)
con <- odbcDriverConnect("driver={Sql Server};server=servername;trusted connection=true")
dat <- sqlQuery(con, "select * from table");
close(con)
This will connect to a SQL Server instance. For more information on what your connection string
should look like, visit connectionstrings.com
Also, since there's no database specified, you should make sure you fully qualify the object you're
wanting to query like this databasename.schema.objectname
Read RODBC online: https://riptutorial.com/r/topic/2471/rodbc
Chapter 101: roxygen2
Parameters
Parameter details
author Author of the package
examples The following lines will be examples on how to use the documented function
export To export the function - i.e. make it callable by users of the package
import Package(s) namespace(s) to import
importFrom Functions to import from the package (first name of the list)
param Parameter of the function to document
Examples
Documenting a package with roxygen2
Writing with roxygen2

roxygen2 is a package created by Hadley Wickham to facilitate documentation.
It allows to include the documentation inside the R script, in lines starting by #'. The different
parameters passed to the documentation start with an @, for example the creator of a package will
by written as follow:
#' @author The Author
For example, if we wanted to document the following function:
mean<-function(x) sum(x)/length(x)
We will want to write a small description to this function, and explain the parameters with the
following (each line will be explained and detailed after):
#' Mean
#'
#' A function to compute the mean of a vector
#' @param x A numeric vector
#' @keyword mean
#' @importFrom base sum
#' @export
#' @examples
#' mean(1:3)
#' \dontrun{ mean(1:1e99) }
mean<-function(x) sum(x)/length(x)
• The first line #' Mean is the title of the documentation, the following lines make the corpus.
• Each parameter of a function must be detailed through a relevant @param. @export indicated
that this function name should be exported, and thus can be called when the package is
loaded.
• @keyword provides relevant keywords when looking for help
• @importFrom lists all functions to import from a package that will be used in this function or in
you package. Note that importing the complete namespace of a package can be done with
@import
• The examples are then written below the @example tag.
The first one will be evaluated when the package is built;
○
The second one will not - usually to prevent long computations - due to the \dontrun
○
command.
Building the documentation

The documentation can be created using devtools::document(). Note also that devtools::check()
will automatically create a documentation and will report missing arguments in the documentation
of functions as warnings.
Read roxygen2 online: https://riptutorial.com/r/topic/5171/roxygen2
Chapter 102: Run-length encoding
Remarks
A run is a consecutive sequence of repeated values or observations. For repeated values, R's
"run-length encoding" concisely describes a vector in terms of its runs. Consider:
dat <- c(1, 2, 2, 2, 3, 1, 4, 4, 1, 1)
We have a length-one run of 1s; then a length-three run of 2s; then a length-one run of 3s; and so
on. R's run-length encoding captures all the lengths and values of a vector's runs.
Extensions
A run can also refer to consecutive observations in a tabular data. While R doesn't have a natural
way of encoding these, they can be handled with rleid from the data.table package (currently a
dead-end link).
Examples
Run-length Encoding with `rle`
Run-length encoding captures the lengths of runs of consecutive elements in a vector. Consider
an example vector:
dat <- c(1, 2, 2, 2, 3, 1, 4, 4, 1, 1)
The rle function extracts each run and its length:
r <- rle(dat)
r
# Run Length Encoding
# lengths: int [1:6] 1 3 1 1 2 2
# values : num [1:6] 1 2 3 1 4 1
The values for each run are captured in r$values:
r$values
# [1] 1 2 3 1 4 1
This captures that we first saw a run of 1's, then a run of 2's, then a run of 3's, then a run of 1's,
and so on.
The lengths of each run are captured in r$lengths:
r$lengths
# [1] 1 3 1 1 2 2
We see that the initial run of 1's was of length 1, the run of 2's that followed was of length 3, and
so on.
Identifying and grouping by runs in base R
One might want to group their data by the runs of a variable and perform some sort of analysis.
Consider the following simple dataset:
(dat <- data.frame(x = c(1, 1, 2, 2, 2, 1), y = 1:6))

# x y
# 1 1 1
# 2 1 2
# 3 2 3
# 4 2 4
# 5 2 5
# 6 1 6
The variable x has three runs: a run of length 2 with value 1, a run of length 3 with value 2, and a
run of length 1 with value 1. We might want to compute the mean value of variable y in each of the
runs of variable x (these mean values are 1.5, 4, and 6).
In base R, we would first compute the run-length encoding of the x variable using rle:
(r <- rle(dat$x))
# Run Length Encoding
# lengths: int [1:3] 2 3 1
# values : num [1:3] 1 2 1
The next step is to compute the run number of each row of our dataset. We know that the total
number of runs is length(r$lengths), and the length of each run is r$lengths, so we can compute
the run number of each of our runs with rep:
(run.id <- rep(seq_along(r$lengths), r$lengths))

# [1] 1 1 2 2 2 3
Now we can use tapply to compute the mean y value for each run by grouping on the run id:
data.frame(x=r$values, meanY=tapply(dat$y, run.id, mean))

# x meanY
# 1 1 1.5
# 2 2 4.0
# 3 1 6.0
Identifying and grouping by runs in data.table
The data.table package provides a convenient way to group by runs in data. Consider the
following example data:
library(data.table)
(DT <- data.table(x = c(1, 1, 2, 2, 2, 1), y = 1:6))
# x y
# 1: 1 1
# 2: 1 2
# 3: 2 3
# 4: 2 4
# 5: 2 5
# 6: 1 6
The variable x has three runs: a run of length 2 with value 1, a run of length 3 with value 2, and a
run of length 1 with value 1. We might want to compute the mean value of variable y in each of the
runs of variable x (these mean values are 1.5, 4, and 6).
The data.table rleid function provides an id indicating the run id of each element of a vector:
rleid(DT$x)
# [1] 1 1 2 2 2 3
One can then easily group on this run ID and summarize the y data:
DT[,mean(y),by=.(x, rleid(x))]
# x rleid V1
# 1: 1 1 1.5
# 2: 2 2 4.0
# 3: 1 3 6.0
Run-length encoding to compress and decompress vectors
Long vectors with long runs of the same value can be significantly compressed by storing them in
their run-length encoding (the value of each run and the number of times that value is repeated).
As an example, consider a vector of length 10 million with a huge number of 1's and only a small
number of 0's:
set.seed(144)
dat <- sample(rep(0:1, c(1, 1e5)), 1e7, replace=TRUE)
table(dat)
# 0 1
# 103 9999897
Storing 10 million entries will require significant space, but we can instead create a data frame with
the run-length encoding of this vector:
rle.df <- with(rle(dat), data.frame(values, lengths))

dim(rle.df)
# [1] 207 2
head(rle.df)
# values lengths
# 1 1 52818
# 2 0 1
# 3 1 219329
# 4 0 1
# 5 1 318306
# 6 0 1
From the run-length encoding, we see that the first 52,818 values in the vector are 1's, followed by
a single 0, followed by 219,329 consecutive 1's, followed by a 0, and so on. The run-length
encoding only has 207 entries, requiring us to store only 414 values instead of 10 million values.
As rle.df is a data frame, it can be stored using standard functions like write.csv.
Decompressing a vector in run-length encoding can be accomplished in two ways. The first
method is to simply call rep, passing the values element of the run-length encoding as the first
argument and the lengths element of the run-length encoding as the second argument:
decompressed <- rep(rle.df$values, rle.df$lengths)
We can confirm that our decompressed data is identical to our original data:
identical(decompressed, dat)
# [1] TRUE
The second method is to use R's built-in inverse.rle function on the rle object, for instance:
rle.obj <- rle(dat) # create a rle object here

class(rle.obj)
# [1] "rle"
dat.inv <- inverse.rle(rle.obj) # apply the inverse.rle on the rle object
We can confirm again that this produces exactly the original dat:
identical(dat.inv, dat)
# [1] TRUE
Read Run-length encoding online: https://riptutorial.com/r/topic/1133/run-length-encoding
Chapter 103: Scope of variables
Remarks
The most common pitfall with scope arises in parallelization. All variables and functions must be
passed into a new environment that is run on each thread.
Examples
Environments and Functions
Variables declared inside a function only exist (unless passed) inside that function.
x <- 1
foo <- function(x) {

y <- 3
z <- x + y
return(z)
}
Error: object 'y' not found
Variables passed into a function and then reassigned are overwritten, but only inside the function.
foo <- function(x) {

x <- 2
y <- 3
z <- x + y
return(z)
}
foo(1)
x
Variables assigned in a higher environment than a function exist within that function, without being
passed.
foo <- function() {

y <- 3
z <- x + y
return(z)
}
foo()
Sub functions
Functions called within a function (ie subfunctions) must be defined within that function to access
any variables defined in the local environment without being passed.
This fails:
bar <- function() {

z <- x + y
return(z)
}
foo <- function() {

y <- 3
z <- bar()
return(z)
}
foo()
Error in bar() : object 'y' not found
This works:
foo <- function() {
bar <- function() {

z <- x + y
return(z)
}
y <- 3
z <- bar()
return(z)
}
foo()
Global Assignment
Variables can be assigned globally from any environment using <<-. bar() can now access y.
bar <- function() {

z <- x + y
return(z)
}
foo <- function() {
y <<- 3
z <- bar()
return(z)
}
foo()
Global assignment is highly discouraged. Use of a wrapper function or explicitly calling variables
from another local environment is greatly preferred.
Explicit Assignment of Environments and Variables
Environments in R can be explicitly call and named. Variables can be explicitly assigned and call
to or from those environments.
A commonly created environment is one which encloses package:base or a subenvironment within

package:base.
e1 <- new.env(parent = baseenv())

e2 <- new.env(parent = e1)
Variables can be explicitly assigned and call to or from those environments.
assign("a", 3, envir = e1)

get("a", envir = e1)
Since e2 inherits from e1, a is 3 in both e1 and e2. However, assigning a within e2 does not change
the value of a in e1.
assign("a", 2, envir = e2)

Function Exit
The on.exit() function is handy for variable clean up if global variables must be assigned.
Some parameters, especially those for graphics, can only be set globally. This small function is
common when creating more specialized plots.
new_plot <- function(...) {
old_pars <- par(mar = c(5,4,4,2) + .1, mfrow = c(1,1))

on.exit(par(old_pars))
plot(...)
}
Packages and Masking
Functions and objects in different packages may have the same name. The package loaded later
will 'mask' the earlier package and a warning message will be printed. When calling the function by
name, the function from the most recently loaded package will be run. The earlier function can be
accessed explicitly.
library(plyr)
library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:plyr’:
arrange, count, desc, failwith, id, mutate, rename, summarise, summarize
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
When writing code, it is always best practice to call functions explicitly using package::function()
specifically to avoid this issue.
Read Scope of variables online: https://riptutorial.com/r/topic/3138/scope-of-variables
Chapter 104: Set operations
Remarks
A set contains only one copy of each distinct element. Unlike some other programming languages,
base R does not have a dedicated data type for sets. Instead, R treats a vector like a set by taking
only its distinct elements. This applies to the set operators, setdiff, intersect, union, setequal and
%in%. For v %in% S, only S is treated as a set, however, not the vector v.
For a true set data type in R, the Rcpp package provides some options.
Examples
Set operators for pairs of vectors
Comparing sets
In R, a vector may contain duplicated elements:
v = "A"
w = c("A", "A")
However, a set contains only one copy of each element. R treats a vector like a set by taking only
its distinct elements, so the two vectors above are regarded as the same:
setequal(v, w)
# TRUE
Combining sets
The key functions have natural names:
x = c(1, 2, 3)
y = c(2, 4)
union(x, y)
# 1 2 3 4
intersect(x, y)
# 2
setdiff(x, y)
# 1 3
These are all documented on the same page, ?union.
Set membership for vectors
The %in% operator compares a vector with a set.
v = "A"
w = c("A", "A")
w %in% v
# TRUE TRUE
v %in% w
# TRUE
Each element on the left is treated individually and tested for membership in the set associated
with the vector on the right (consisting of all its distinct elements).
Unlike equality tests, %in% always returns TRUE or FALSE:
c(1, NA) %in% c(1, 2, 3, 4)

# TRUE FALSE
The documentation is at ?`%in%`.
Cartesian or "cross" products of vectors
To find every vector of the form (x, y) where x is drawn from vector X and y from Y, we use
expand.grid:
X = c(1, 1, 2)
Y = c(4, 5)
expand.grid(X, Y)
# Var1 Var2
# 1 1 4
# 2 1 4
# 3 2 4
# 4 1 5
# 5 1 5
# 6 2 5
The result is a data.frame with one column for each vector passed to it. Often, we want to take the
Cartesian product of sets rather than to expand a "grid" of vectors. We can use unique, lapply and
do.call:
m = do.call(expand.grid, lapply(list(X, Y), unique))
# Var1 Var2
# 1 1 4
# 2 2 4
# 3 1 5
# 4 2 5
Applying functions to combinations
If you then want to apply a function to each resulting combination f(x,y), it can be added as
another column:
m$p = with(m, Var1*Var2)

# Var1 Var2 p
# 1 1 4 4
# 2 2 4 8
# 3 1 5 5
# 4 2 5 10
This approach works for as many vectors as we need, but in the special case of two, it is
sometimes a better fit to have the result in a matrix, which can be achieved with outer:
uX = unique(X)
uY = unique(Y)
outer(setNames(uX, uX), setNames(uY, uY), `*`)
# 4 5
# 1 4 5
# 2 8 10
For related concepts and tools, see the combinatorics topic.
Make unique / drop duplicates / select distinct elements from a vector
unique drops duplicates so that each element in the result is unique (only appears once):
x = c(2, 1, 1, 2, 1)
unique(x)
# 2 1
Values are returned in the order they first appeared.
duplicated tags each duplicated element:
duplicated(x)
# FALSE FALSE TRUE TRUE TRUE
anyDuplicated(x) > 0L is a quick way of checking whether a vector contains any duplicates.
Measuring set overlaps / Venn diagrams for vectors
To count how many elements of two sets overlap, one could write a custom function:
xtab_set <- function(A, B){

both <- union(A, B)
inA <- both %in% A
inB <- both %in% B
return(table(inA, inB))
}
A = 1:20
B = 10:30
xtab_set(A, B)
# inB
# inA FALSE TRUE
# FALSE 0 10
# TRUE 9 11
A Venn diagram, offered by various packages, can be used to visualize overlap counts across
multiple sets.
Read Set operations online: https://riptutorial.com/r/topic/1383/set-operations
Chapter 105: Shiny
Examples
Create an app
Shiny is an R package developed by RStudio that allows the creation of web pages to interactively
display the results of an analysis in R.
There are two simple ways to create a Shiny app:
• in one .R file, or
• in two files: ui.R and server.R.
A Shiny app is divided into two parts:
• ui: A user interface script, controlling the layout and appearance of the application.
• server: A server script which contains code to allow the application to react.
One file
library(shiny)
# Create the UI
ui <- shinyUI(fluidPage(
# Application title
titlePanel("Hello World!")
))
# Create the server function

server <- shinyServer(function(input, output){})
# Run the app

shinyApp(ui = ui, server = server)
Two files
Create ui.R file
library(shiny)
# Define UI for application

shinyUI(fluidPage(
# Application title
titlePanel("Hello World!")
))
Create server.R file
library(shiny)
# Define server logic

shinyServer(function(input, output){})
Radio Button
You can create a set of radio buttons used to select an item from a list.
It's possible to change the settings :
• selected : The initially selected value (character(0) for no selection)

• inline : horizontal or vertical
• width
It is also possible to add HTML.
library(shiny)
ui <- fluidPage(
radioButtons("radio",
label = HTML('<FONT color="red"><FONT size="5pt">Welcome</FONT></FONT><br>
<b>Your favorite color is red ?</b>'),
choices = list("TRUE" = 1, "FALSE" = 2),
selected = 1,
inline = T,
width = "100%"),
fluidRow(column(3, textOutput("value"))))
server <- function(input, output){

output$value <- renderPrint({
if(input$radio == 1){return('Great !')}
else{return("Sorry !")}})}
Checkbox Group
Create a group of checkboxes that can be used to toggle multiple choices independently. The
server will receive the input as a character vector of the selected values.
library(shiny)
ui <- fluidPage(
checkboxGroupInput("checkGroup1", label = h3("This is a Checkbox group"),
choices = list("1" = 1, "2" = 2, "3" = 3),
selected = 1),
fluidRow(column(3, verbatimTextOutput("text_choice")))
)

output$text_choice <- renderPrint({
return(paste0("You have chosen the choice ",input$checkGroup1))})
}
• label : title
• choices : selected values
• selected : The initially selected value (NULL for no selection)
• inline : horizontal or vertical
• width
Select box
Create a select list that can be used to choose a single or multiple items from a list of values.
library(shiny)
ui <- fluidPage(
selectInput("id_selectInput",
label = HTML('<B><FONT size="3">What is your favorite color ?</FONT></B>'),
multiple = TRUE,
choices = list("red" = "red", "green" = "green", "blue" = "blue", "yellow" =
"yellow"),
selected = NULL),
br(), br(),
fluidRow(column(3, textOutput("text_choice"))))
output$text_choice <- renderPrint({
return(input$id_selectInput)})
}
• label : title
• choices : selected values
• selected : The initially selected value (NULL for no selection)
• multiple : TRUE or FALSE
• width
• size
• selectize: TRUE or FALSE (for use or not selectize.js, change the display)
Launch a Shiny app
You can launch an application in several ways, depending on how you create you app. If your app
is divided in two files ui.R and server.R or if all of your app is in one file.
1. Two files app

Your two files ui.R and server.Rhave to be in the same folder. You could then launch your app by
running in the console the shinyApp() function and by passing the path of the directory that
contains the Shiny app.
shinyApp("path_to_the_folder_containing_the_files")
You can also launch the app directly from Rstudio by pressing the Run App button that appear on
Rstudio when you an ui.R or server.R file open.
Or you can simply write runApp() on the console if your working directory is Shiny App directory.
2. One file app

If you create your in one R file you can also launch it with the shinyApp() function.
• inside of your code :
library(shiny)
ui <- fluidPage() #Create the ui

server <- function(input, output){} #create the server
shinyApp(ui = ui, server = server) #run the App
• in the console by adding path to a .R file containing the Shiny application with the paramter
appFile:
shinyApp(appFile="path_to_my_R_file_containig_the_app")
Control widgets
Function Widget
actionButton Action Button
checkboxGroupInput A group of check boxes
checkboxInput A single check box
dateInput A calendar to aid date selection
dateRangeInput A pair of calendars for selecting a date range
fileInput A file upload control wizard
helpText Help text that can be added to an input form
numericInput A field to enter numbers
radioButtons A set of radio buttons
selectInput A box with choices to select from
sliderInput A slider bar
submitButton A submit button
textInput A field to enter text
library(shiny)
# Create the UI
ui <- shinyUI(fluidPage(
titlePanel("Basic widgets"),
fluidRow(
column(3,
h3("Buttons"),
actionButton("action", label = "Action"),
br(),
br(),
submitButton("Submit")),
column(3,
h3("Single checkbox"),
checkboxInput("checkbox", label = "Choice A", value = TRUE)),
column(3,
checkboxGroupInput("checkGroup",
label = h3("Checkbox group"),
choices = list("Choice 1" = 1,
"Choice 2" = 2, "Choice 3" = 3),
selected = 1)),
column(3,
dateInput("date",
label = h3("Date input"),
value = "2014-01-01"))
),
fluidRow(
column(3,
dateRangeInput("dates", label = h3("Date range"))),
column(3,
fileInput("file", label = h3("File input"))),
column(3,
h3("Help text"),
helpText("Note: help text isn't a true widget,",
"but it provides an easy way to add text to",
"accompany other widgets.")),
column(3,
numericInput("num",
label = h3("Numeric input"),
value = 1))
),
fluidRow(
column(3,
radioButtons("radio", label = h3("Radio buttons"),
choices = list("Choice 1" = 1, "Choice 2" = 2,
"Choice 3" = 3),selected = 1)),
column(3,
selectInput("select", label = h3("Select box"),
choices = list("Choice 1" = 1, "Choice 2" = 2,
"Choice 3" = 3), selected = 1)),
column(3,
sliderInput("slider1", label = h3("Sliders"),
min = 0, max = 100, value = 50),
sliderInput("slider2", "",
min = 0, max = 100, value = c(25, 75))
),
column(3,
textInput("text", label = h3("Text input"),
value = "Enter text..."))
)
))
# Create the server function

server <- shinyServer(function(input, output){})
# Run the app

Debugging
debug() and debugonce() won't work well in the context of most Shiny debugging. However,
browser() statements inserted in critical places can give you a lot of insight into how your Shiny
code is (not) working. See also: Debugging using browser()
Showcase mode
Showcase mode displays your app alongside the code that generates it and highlights lines of
code in server.R as it runs them.
There are two ways to enable Showcase mode:
• Launch Shiny app with the argument display.mode = "showcase", e.g., runApp("MyApp",
display.mode = "showcase").
• Create file called DESCRIPTION in your Shiny app folder and add this line in it: DisplayMode:
Showcase.
Reactive Log Visualizer

Reactive Log Visualizer provides an interactive browser-based tool for visualizing reactive
dependencies and execution in your application. To enable Reactive Log Visualizer, execute
options(shiny.reactlog=TRUE) in R console and or add that line of code in your server.R file. To
start Reactive Log Visualizer, hit Ctrl+F3 on Windows or Command+F3 on Mac when your app is
running. Use left and right arrow keys to navigate in Reactive Log Visualizer.
Read Shiny online: https://riptutorial.com/r/topic/2044/shiny
Chapter 106: Solving ODEs in R
Syntax
• ode(y, times, func, parms, method, ...)
Parameters
Parameter Details
y (named) numeric vector: the initial (state) values for the ODE system
time sequence for which output is wanted; the first value of times must be the
times
initial time
name of the function that computes the values of the derivatives in the ODE
func
system
parms (named) numeric vector: parameters passed to func
method the integrator to use, by default: lsoda
Remarks
Note that it is necessary to return the rate of change in the same ordering as the specification of
the state variables. In example "The Lorenz model" this means, that in the function "Lorenz"
command
return(list(c(dX, dY, dZ)))
has the same order as the definition of the state variables
yini <- c(X = 1, Y = 1, Z = 1)
Examples
The Lorenz model
The Lorenz model describes the dynamics of three state variables, X, Y and Z. The model
equations are:
The initial conditions are:
and a, b and c are three parameters with
library(deSolve)
## -----------------------------------------------------------------------------
## Define R-function
## ----------------------------------------------------------------------------
Lorenz <- function (t, y, parms) {

with(as.list(c(y, parms)), {
dX <- a * X + Y * Z
dY <- b * (Y - Z)
dZ <- -X * Y + c * Y - Z
return(list(c(dX, dY, dZ)))

})
}
## -----------------------------------------------------------------------------
## Define parameters and variables
## -----------------------------------------------------------------------------
parms <- c(a = -8/3, b = -10, c = 28)

yini <- c(X = 1, Y = 1, Z = 1)
times <- seq(from = 0, to = 100, by = 0.01)
## -----------------------------------------------------------------------------
## Solve the ODEs
## -----------------------------------------------------------------------------
out <- ode(y = yini, times = times, func = Lorenz, parms = parms)
## -----------------------------------------------------------------------------
## Plot the results
## -----------------------------------------------------------------------------
plot(out, lwd = 2)
plot(out[,"X"], out[,"Y"],
type = "l", xlab = "X",
ylab = "Y", main = "butterfly")
Lotka-Volterra or: Prey vs. predator
library(deSolve)
## -----------------------------------------------------------------------------
## -----------------------------------------------------------------------------
LV <- function(t, y, parms) {

dP <- rG * P * (1 - P/K) - rI * P * C
dC <- rI * P * C * AE - rM * C
return(list(c(dP, dC), sum = C+P))

})
}
## -----------------------------------------------------------------------------
## -----------------------------------------------------------------------------
parms <- c(rI = 0.2, rG = 1.0, rM = 0.2, AE = 0.5, K = 10)

yini <- c(P = 1, C = 2)
times <- seq(from = 0, to = 200, by = 1)
## -----------------------------------------------------------------------------
## Solve the ODEs
## -----------------------------------------------------------------------------
out <- ode(y = yini, times = times, func = LV, parms = parms)
## -----------------------------------------------------------------------------
## Plot the results
## -----------------------------------------------------------------------------
matplot(out[ ,1], out[ ,2:4], type = "l", xlab = "time", ylab = "Conc",
main = "Lotka-Volterra", lwd = 2)
legend("topright", c("prey", "predator", "sum"), col = 1:3, lty = 1:3)
ODEs in compiled languages - definition in R
library(deSolve)
## -----------------------------------------------------------------------------
## -----------------------------------------------------------------------------
eps <- 0.01;

M <- 10
k <- M * eps^2/2
L <- 1
L0 <- 0.5
r <- 0.1
w <- 10
g <- 1
parameter <- c(eps = eps, M = M, k = k, L = L, L0 = L0, r = r, w = w, g = g)
yini <- c(xl = 0, yl = L0, xr = L, yr = L0,

ul = -L0/L, vl = 0,
ur = -L0/L, vr = 0,
lam1 = 0, lam2 = 0)
times <- seq(from = 0, to = 3, by = 0.01)
## -----------------------------------------------------------------------------
## -----------------------------------------------------------------------------
caraxis_R <- function(t, y, parms) {

yb <- r * sin(w * t)
xb <- sqrt(L * L - yb * yb)
Ll <- sqrt(xl^2 + yl^2)
Lr <- sqrt((xr - xb)^2 + (yr - yb)^2)
dxl <- ul; dyl <- vl; dxr <- ur; dyr <- vr
dul <- (L0-Ll) * xl/Ll + 2 * lam2 * (xl-xr) + lam1*xb

dvl <- (L0-Ll) * yl/Ll + 2 * lam2 * (yl-yr) + lam1*yb - k * g
dur <- (L0-Lr) * (xr-xb)/Lr - 2 * lam2 * (xl-xr)

dvr <- (L0-Lr) * (yr-yb)/Lr - 2 * lam2 * (yl-yr) - k * g
c1 <- xb * xl + yb * yl
c2 <- (xl - xr)^2 + (yl - yr)^2 - L * L
return(list(c(dxl, dyl, dxr, dyr, dul, dvl, dur, dvr, c1, c2)))
})
}
ODEs in compiled languages - definition in C
sink("caraxis_C.c")
cat("
/* suitable names for parameters and state variables */
#include <R.h>
#include <math.h>
static double parms[8];
#define eps parms[0]

#define m parms[1]
#define k parms[2]
#define L parms[3]
#define L0 parms[4]
#define r parms[5]
#define w parms[6]
#define g parms[7]
/*----------------------------------------------------------------------
initialising the parameter common block
----------------------------------------------------------------------
*/
void init_C(void (* daeparms)(int *, double *)) {
int N = 8;
daeparms(&N, parms);
}
/* Compartments */
#define xl y[0]
#define yl y[1]
#define xr y[2]
#define yr y[3]
#define lam1 y[8]
#define lam2 y[9]
/*----------------------------------------------------------------------
the residual function
----------------------------------------------------------------------
*/
void caraxis_C (int *neq, double *t, double *y, double *ydot,
double *yout, int* ip)
{
double yb, xb, Lr, Ll;
yb = r * sin(w * *t) ;
xb = sqrt(L * L - yb * yb);
Ll = sqrt(xl * xl + yl * yl) ;
Lr = sqrt((xr-xb)*(xr-xb) + (yr-yb)*(yr-yb));
ydot[0] = y[4];
ydot[1] = y[5];
ydot[2] = y[6];
ydot[3] = y[7];
ydot[4] = (L0-Ll) * xl/Ll + lam1*xb + 2*lam2*(xl-xr) ;

ydot[5] = (L0-Ll) * yl/Ll + lam1*yb + 2*lam2*(yl-yr) - k*g;
ydot[6] = (L0-Lr) * (xr-xb)/Lr - 2*lam2*(xl-xr) ;
ydot[7] = (L0-Lr) * (yr-yb)/Lr - 2*lam2*(yl-yr) - k*g ;
ydot[8] = xb * xl + yb * yl;
ydot[9] = (xl-xr) * (xl-xr) + (yl-yr) * (yl-yr) - L*L;
}
", fill = TRUE)
sink()
system("R CMD SHLIB caraxis_C.c")
dyn.load(paste("caraxis_C", .Platform$dynlib.ext, sep = ""))
dllname_C <- dyn.load(paste("caraxis_C", .Platform$dynlib.ext, sep = ""))[[1]]
ODEs in compiled languages - definition in fortran
sink("caraxis_fortran.f")
cat("
c----------------------------------------------------------------
c Initialiser for parameter common block
c----------------------------------------------------------------
subroutine init_fortran(daeparms)
external daeparms
integer, parameter :: N = 8
double precision parms(N)
common /myparms/parms
call daeparms(N, parms)

return
end
c----------------------------------------------------------------
c rate of change
c----------------------------------------------------------------
subroutine caraxis_fortran(neq, t, y, ydot, out, ip)
implicit none
integer neq, IP(*)
double precision t, y(neq), ydot(neq), out(*)
double precision eps, M, k, L, L0, r, w, g
common /myparms/ eps, M, k, L, L0, r, w, g
double precision xl, yl, xr, yr, ul, vl, ur, vr, lam1, lam2
double precision yb, xb, Ll, Lr, dxl, dyl, dxr, dyr
double precision dul, dvl, dur, dvr, c1, c2
c expand state variables

xl = y(1)
yl = y(2)
xr = y(3)
yr = y(4)
ul = y(5)
vl = y(6)
ur = y(7)
vr = y(8)
lam1 = y(9)
lam2 = y(10)
yb = r * sin(w * t)
xb = sqrt(L * L - yb * yb)
Ll = sqrt(xl**2 + yl**2)
Lr = sqrt((xr - xb)**2 + (yr - yb)**2)
dxl = ul
dyl = vl
dxr = ur
dyr = vr
dul = (L0-Ll) * xl/Ll + 2 * lam2 * (xl-xr) + lam1*xb

dvl = (L0-Ll) * yl/Ll + 2 * lam2 * (yl-yr) + lam1*yb - k*g
dur = (L0-Lr) * (xr-xb)/Lr - 2 * lam2 * (xl-xr)
dvr = (L0-Lr) * (yr-yb)/Lr - 2 * lam2 * (yl-yr) - k*g
c1 = xb * xl + yb * yl
c2 = (xl - xr)**2 + (yl - yr)**2 - L * L
c function values in ydot

ydot(1) = dxl
ydot(2) = dyl
ydot(3) = dxr
ydot(4) = dyr
ydot(5) = dul
ydot(6) = dvl
ydot(7) = dur
ydot(8) = dvr
ydot(9) = c1
ydot(10) = c2
return
end
", fill = TRUE)
sink()
system("R CMD SHLIB caraxis_fortran.f")
dyn.load(paste("caraxis_fortran", .Platform$dynlib.ext, sep = ""))
dllname_fortran <- dyn.load(paste("caraxis_fortran", .Platform$dynlib.ext, sep = ""))[[1]]
ODEs in compiled languages - a benchmark test
When you compiled and loaded the code in the three examples before (ODEs in compiled
languages - definition in R, ODEs in compiled languages - definition in C and ODEs in compiled
languages - definition in fortran) you are able to run a benchmark test.
R <- function(){
out <- ode(y = yini, times = times, func = caraxis_R,
parms = parameter)
}
C <- function(){
out <- ode(y = yini, times = times, func = "caraxis_C",
initfunc = "init_C", parms = parameter,
dllname = dllname_C)
}
fortran <- function(){

out <- ode(y = yini, times = times, func = "caraxis_fortran",
initfunc = "init_fortran", parms = parameter,
dllname = dllname_fortran)
}
Check if results are equal:
all.equal(tail(R()), tail(fortran()))
all.equal(R()[,2], fortran()[,2])
all.equal(R()[,2], C()[,2])
Make a benchmark (Note: On your machine the times are, of course, different):
bench <- microbenchmark::microbenchmark(

R(),
fortran(),
C(),
times = 1000
)
summary(bench)

R() 31508.928 33651.541 36747.8733 36062.2475 37546.8025 132996.564 1000 b
fortran() 570.674 596.700 686.1084 637.4605 730.1775 4256.555 1000 a
C() 562.163 590.377 673.6124 625.0700 723.8460 5914.347 1000 a
We see clearly, that R is slow in contrast to the definition in C and fortran. For big models it's worth
to translate the problem in a compiled language. The package cOde is one possibility to translate
ODEs from R to C.
Read Solving ODEs in R online: https://riptutorial.com/r/topic/7448/solving-odes-in-r
Chapter 107: Spark API (SparkR)
Remarks
The SparkR package let's you work with distributed data frames on top of a Spark cluster. These
allow you to do operations like selection, filtering, aggregation on very large datasets. SparkR
overview SparkR package documentation
Examples
Setup Spark context
Setup Spark context in R

To start working with Sparks distributed dataframes, you must connect your R program with an
existing Spark Cluster.
library(SparkR)
sc <- sparkR.init() # connection to Spark context
sqlContext <- sparkRSQL.init(sc) # connection to SQL context
Here are infos how to connect your IDE to a Spark cluster.
Get Spark Cluster

There is an Apache Spark introduction topic with install instructions. Basically, you can employ a
Spark Cluster locally via java (see instructions) or use (non-free) cloud applications (e.g. Microsoft
Azure [topic site], IBM).
Cache data
What:
Caching can optimize computation in Spark. Caching stores data in memory and is a special case
of persistence. Here is explained what happens when you cache an RDD in Spark.
Why:
Basically, caching saves an interim partial result - usually after transformations - of your original
data. So, when you use the cached RDD, the already transformed data from memory is accessed
without recomputing the earlier transformations.
How:
Here is an example how to quickly access large data (here 3 GB big csv) from in-memory storage
when accessing it more then once:
library(SparkR)
# next line is needed for direct csv import:
Sys.setenv('SPARKR_SUBMIT_ARGS'='"--packages" "com.databricks:spark-csv_2.10:1.4.0" "sparkr-
shell"')
sc <- sparkR.init()
sqlContext <- sparkRSQL.init(sc)
# loading 3 GB big csv file:

train <- read.df(sqlContext, "/train.csv", source = "com.databricks.spark.csv", inferSchema =
"true")
cache(train)
system.time(head(train))
# output: time elapsed: 125 s. This action invokes the caching at this point.
system.time(head(train))
# output: time elapsed: 0.2 s (!!)
Create RDDs (Resilient Distributed Datasets)
From dataframe:
mtrdd <- createDataFrame(sqlContext, mtcars)
From csv:
For csv's, you need to add the csv package to the environment before initiating the Spark context:
Sys.setenv('SPARKR_SUBMIT_ARGS'='"--packages" "com.databricks:spark-csv_2.10:1.4.0" "sparkr-

shell"') # context for csv import read csv ->
sc <- sparkR.init()
sqlContext <- sparkRSQL.init(sc)
Then, you can load the csv either by infering the data schema of the data in the columns:
train <- read.df(sqlContext, "/train.csv", header= "true", source =

"com.databricks.spark.csv", inferSchema = "true")
Or by specifying the data schema beforehand:
customSchema <- structType(

structField("margin", "integer"),
structField("gross", "integer"),
structField("name", "string"))
train <- read.df(sqlContext, "/train.csv", header= "true", source =

"com.databricks.spark.csv", schema = customSchema)
Read Spark API (SparkR) online: https://riptutorial.com/r/topic/5349/spark-api--sparkr-
Chapter 108: spatial analysis
Examples
Create spatial points from XY data set
When it comes to geographic data, R shows to be a powerful tool for data handling, analysis and
visualisation.
Often, spatial data is avaliable as an XY coordinate data set in tabular form. This example will
show how to create a spatial data set from an XY data set.
The packages rgdal and sp provide powerful functions. Spatial data in R can be stored as
Spatial*DataFrame (where * can be Points, Lines or Polygons).
This example uses data which can be downloaded at OpenGeocode.
At first, the working directory has to be set to the folder of the downloaded CSV data set.
Furthermore, the package rgdal has to be loaded.
setwd("D:/GeocodeExample/")
library(rgdal)
Afterwards, the CSV file storing cities and their geographical coordinates is loaded into R as a
data.frame
xy <- read.csv("worldcities.csv", stringsAsFactors = FALSE)
Often, it is useful to get a glimpse of the data and its structure (e.g. column names, data types
etc.).
head(xy)
str(xy)
This shows that the latitude and longitude columns are interpreted as character values, since they
hold entries like "-33.532". Yet, the later used function SpatialPointsDataFrame() which creates the
spatial data set requires the coordinate values to be of the data type numeric. Thus the two
columns have to be converted.
xy$latitude <- as.numeric(xy$latitude)

xy$longitude <- as.numeric(xy$longitude)
Few of the values cannot be converted into numeric data and thus, NA values are created. They
have to be removed.
xy <- xy[!is.na(xy$longitude),]
Finally, the XY data set can be converted into a spatial data set. This requires the coordinates and
the specification of the Coordinate Refrence System (CRS) in which the coordinates are stored.
xySPoints <- SpatialPointsDataFrame(coords = c(xy[,c("longitude", "latitude")]),

proj4string = CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs"),
data = xy
)
The basic plot function can easily be used to sneak peak the produced spatial points.
plot(xySPoints, pch = ".")
Importing a shape file (.shp)
rgdal
ESRI shape files can easily be imported into R by using the function readOGR() from the rgdal
package.
library(rgdal)
shp <- readORG(dsn = "/path/to/your/file", layer = "filename")
It is important to know, that the dsn must not end with / and the layer does not allow the file ending
(e.g. .shp)
raster
Another possible way of importing shapefiles is via the raster library and the shapefile function:
library(raster)
shp <- shapefile("path/to/your/file.shp")
Note how the path definition is different from the rgdal import statement.
tmap
tmap package provides a nice wrapper for the rgdal::readORG function.
library(tmap)
sph <- read_shape("path/to/your/file.shp")
Read spatial analysis online: https://riptutorial.com/r/topic/2093/spatial-analysis
Chapter 109: Speeding up tough-to-vectorize
code
Examples
Speeding tough-to-vectorize for loops with Rcpp
Consider the following tough-to-vectorize for loop, which creates a vector of length len where the
first element is specified (first) and each element x_i is equal to cos(x_{i-1} + 1):
repeatedCosPlusOne <- function(first, len) {

x <- numeric(len)
x[1] <- first
for (i in 2:len) {
x[i] <- cos(x[i-1] + 1)
}
return(x)
}
This code involves a for loop with a fast operation (cos(x[i-1]+1)), which often benefit from
vectorization. However, it is not trivial to vectorize this operation with base R, since R does not
have a "cumulative cosine of x+1" function.
One possible approach to speeding this function would be to implement it in C++, using the Rcpp
package:
library(Rcpp)
cppFunction("NumericVector repeatedCosPlusOneRcpp(double first, int len) {
NumericVector x(len);
x[0] = first;
for (int i=1; i < len; ++i) {
x[i] = cos(x[i-1]+1);
}
return x;
}")
This often provides significant speedups for large computations while yielding the exact same
results:
all.equal(repeatedCosPlusOne(1, 1e6), repeatedCosPlusOneRcpp(1, 1e6))

# [1] TRUE
system.time(repeatedCosPlusOne(1, 1e6))
# 1.274 0.015 1.310
system.time(repeatedCosPlusOneRcpp(1, 1e6))
# 0.028 0.001 0.030
In this case, the Rcpp code generates a vector of length 1 million in 0.03 seconds instead of 1.31
seconds with the base R approach.
Speeding tough-to-vectorize for loops by byte compiling
Following the Rcpp example in this documentation entry, consider the following tough-to-vectorize
function, which creates a vector of length len where the first element is specified (first) and each
element x_i is equal to cos(x_{i-1} + 1):
repeatedCosPlusOne <- function(first, len) {

x <- numeric(len)
x[1] <- first
for (i in 2:len) {
x[i] <- cos(x[i-1] + 1)
}
return(x)
}
One simple approach to speeding up such a function without rewriting a single line of code is byte
compiling the code using the R compile package:
library(compiler)
repeatedCosPlusOneCompiled <- cmpfun(repeatedCosPlusOne)
The resulting function will often be significantly faster while still returning the same results:
all.equal(repeatedCosPlusOne(1, 1e6), repeatedCosPlusOneCompiled(1, 1e6))

# [1] TRUE
system.time(repeatedCosPlusOne(1, 1e6))
# 1.175 0.014 1.201
system.time(repeatedCosPlusOneCompiled(1, 1e6))
# 0.339 0.002 0.341
In this case, byte compiling sped up the tough-to-vectorize operation on a vector of length 1 million
from 1.20 seconds to 0.34 seconds.
Remark
The essence of repeatedCosPlusOne, as the cumulative application of a single function, can be

expressed more transparently with Reduce:
iterFunc <- function(init, n, func) {

funcs <- replicate(n, func)
Reduce(function(., f) f(.), funcs, init = init, accumulate = TRUE)
}
repeatedCosPlusOne_vec <- function(first, len) {
iterFunc(first, len - 1, function(.) cos(. + 1))
}
repeatedCosPlusOne_vecmay be regarded as a "vectorization" of repeatedCosPlusOne. However, it can

be expected to be slower by a factor of 2:
microbenchmark(
repeatedCosPlusOne(1, 1e4),
repeatedCosPlusOne_vec(1, 1e4)
)
#> Unit: milliseconds
#> expr min lq mean median uq max
neval cld
#> repeatedCosPlusOne(1, 10000) 8.349261 9.216724 10.22715 10.23095 11.10817 14.33763
100 a
#> repeatedCosPlusOne_vec(1, 10000) 14.406291 16.236153 17.55571 17.22295 18.59085 24.37059
100 b
Read Speeding up tough-to-vectorize code online: https://riptutorial.com/r/topic/1203/speeding-up-

tough-to-vectorize-code
Chapter 110: Split function
Examples
Basic usage of split
split allows to divide a vector or a data.frame into buckets with regards to a factor/group
variables. This ventilation into buckets takes the form of a list, that can then be used to apply
group-wise computation (for loops or lapply/sapply).
First example shows the usage of split on a vector:
Consider following vector of letters:
testdata <- c("e", "o", "r", "g", "a", "y", "w", "q", "i", "s", "b", "v", "x", "h", "u")
Objective is to separate those letters into voyels and consonants, ie split it accordingly to letter type.
Let's first create a grouping vector:
vowels <- c('a','e','i','o','u','y')

letter_type <- ifelse(testdata %in% vowels, "vowels", "consonants")
Note that letter_type has the same length that our vector testdata. Now we can split this test
data in the two groups, vowels and consonants :
split(testdata, letter_type)
#$consonants
#[1] "r" "g" "w" "q" "s" "b" "v" "x" "h"
#$vowels
#[1] "e" "o" "a" "y" "i" "u"
Hence, the result is a list which names are coming from our grouping vector/factor letter_type.
split has also a method to deal with data.frames.
Consider for instance iris data:
data(iris)
By using split, one can create a list containing one data.frame per iris specie (variable: Species):
> liris <- split(iris, iris$Species)

> names(liris)
[1] "setosa" "versicolor" "virginica"
> head(liris$setosa)
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3.0 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
5 5.0 3.6 1.4 0.2 setosa
6 5.4 3.9 1.7 0.4 setosa
(contains only data for setosa group).
One example operation would be to compute correlation matrix per iris specie; one would then use
lapply:
> (lcor <- lapply(liris, FUN=function(df) cor(df[,1:4])))
$setosa
Sepal.Length 1.0000000 0.7425467 0.2671758 0.2780984
Sepal.Width 0.7425467 1.0000000 0.1777000 0.2327520
Petal.Length 0.2671758 0.1777000 1.0000000 0.3316300
Petal.Width 0.2780984 0.2327520 0.3316300 1.0000000
$versicolor
Sepal.Length 1.0000000 0.5259107 0.7540490 0.5464611
Sepal.Width 0.5259107 1.0000000 0.5605221 0.6639987
Petal.Length 0.7540490 0.5605221 1.0000000 0.7866681
Petal.Width 0.5464611 0.6639987 0.7866681 1.0000000
$virginica
Sepal.Length 1.0000000 0.4572278 0.8642247 0.2811077
Sepal.Width 0.4572278 1.0000000 0.4010446 0.5377280
Petal.Length 0.8642247 0.4010446 1.0000000 0.3221082
Petal.Width 0.2811077 0.5377280 0.3221082 1.0000000
Then we can retrieve per group the best pair of correlated variables: (correlation matrix is
reshaped/melted, diagonal is filtered out and selecting best record is performed)
> library(reshape)
> (topcor <- lapply(lcor, FUN=function(cormat){
correlations <- melt(cormat,variable_name="correlatio);
filtered <- correlations[correlations$X1 != correlations$X2,];
filtered[which.max(filtered$correlation),]
}))
$setosa
X1 X2 correlation
2 Sepal.Width Sepal.Length 0.7425467
$versicolor
X1 X2 correlation
12 Petal.Width Petal.Length 0.7866681
$virginica
X1 X2 correlation
3 Petal.Length Sepal.Length 0.8642247
Note that one computations are performed on such groupwise level, one may be interested in
stacking the results, which can be done with:
> (result <- do.call("rbind", topcor))
X1 X2 correlation
setosa Sepal.Width Sepal.Length 0.7425467
versicolor Petal.Width Petal.Length 0.7866681
virginica Petal.Length Sepal.Length 0.8642247
Using split in the split-apply-combine paradigm
A popular form of data analysis is split-apply-combine, in which you split your data into groups,
apply some sort of processing on each group, and then combine the results.
Let's consider a data analysis where we want to obtain the two cars with the best miles per gallon
(mpg) for each cylinder count (cyl) in the built-in mtcars dataset. First, we split the mtcars data
frame by the cylinder count:
(spl <- split(mtcars, mtcars$cyl))

# $`4`
# mpg cyl disp hp drat wt qsec vs am gear carb
# Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1
# Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2
# Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2
# Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1
# ...
#
# $`6`
# Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4
# Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4
# Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1
# Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1
# ...
#
# $`8`
# Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2
# Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4
# Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3
# Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3
# ...
This has returned a list of data frames, one for each cylinder count. As indicated by the output, we
could obtain the relevant data frames with spl$`4`, spl$`6`, and spl$`8` (some might find it more
visually appealing to use spl$"4" or spl[["4"]] instead).
Now, we can use lapply to loop through this list, applying our function that extracts the cars with
the best 2 mpg values from each of the list elements:
(best2 <- lapply(spl, function(x) tail(x[order(x$mpg),], 2)))

# $`4`
# Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1
# Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1
#
# $`6`
# Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4
# Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1
#
# $`8`
# Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2
# Pontiac Firebird 19.2 8 400 175 3.08 3.845 17.05 0 0 3 2
Finally, we can combine everything together using rbind. We want to call rbind(best2[["4"]],
best2[["6"]], best2[["8"]]), but this would be tedious if we had a huge list. As a result, we use:
do.call(rbind, best2)
# 4.Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1
# 4.Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1
# 6.Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4
# 6.Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1
# 8.Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2
# 8.Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2
This returns the result of rbind (argument 1, a function) with all the elements of best2 (argument 2,
a list) passed as arguments.
With simple analyses like this one, it can be more compact (and possibly much less readable!) to
do the whole split-apply-combine in a single line of code:
do.call(rbind, lapply(split(mtcars, mtcars$cyl), function(x) tail(x[order(x$mpg),], 2)))
It is also worth noting that the lapply(split(x,f), FUN) combination can be alternatively framed
using the ?by function:
by(mtcars, mtcars$cyl, function(x) tail(x[order(x$mpg),], 2))

do.call(rbind, by(mtcars, mtcars$cyl, function(x) tail(x[order(x$mpg),], 2)))
Read Split function online: https://riptutorial.com/r/topic/1073/split-function
Chapter 111: sqldf
Examples
Basic Usage Examples
sqldf()from the package sqldf allows the use of SQLite queries to select and manipulate data in
R. SQL queries are entered as character strings.
To select the first 10 rows of the "diamonds" dataset from the package ggplot2, for example:
data("diamonds")
head(diamonds)
# A tibble: 6 x 10
carat cut color clarity depth table price x y z
<dbl> <ord> <ord> <ord> <dbl> <dbl> <int> <dbl> <dbl> <dbl>
1 0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43
2 0.21 Premium E SI1 59.8 61 326 3.89 3.84 2.31
3 0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31
4 0.29 Premium I VS2 62.4 58 334 4.20 4.23 2.63
5 0.31 Good J SI2 63.3 58 335 4.34 4.35 2.75
6 0.24 Very Good J VVS2 62.8 57 336 3.94 3.96 2.48
require(sqldf)
sqldf("select * from diamonds limit 10")

1 0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43
2 0.21 Premium E SI1 59.8 61 326 3.89 3.84 2.31
3 0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31
4 0.29 Premium I VS2 62.4 58 334 4.20 4.23 2.63
5 0.31 Good J SI2 63.3 58 335 4.34 4.35 2.75
6 0.24 Very Good J VVS2 62.8 57 336 3.94 3.96 2.48
7 0.24 Very Good I VVS1 62.3 57 336 3.95 3.98 2.47
8 0.26 Very Good H SI1 61.9 55 337 4.07 4.11 2.53
9 0.22 Fair E VS2 65.1 61 337 3.87 3.78 2.49
10 0.23 Very Good H VS1 59.4 61 338 4.00 4.05 2.39
To select the first 10 rows where for the color "E":
sqldf("select * from diamonds where color = 'E' limit 10")

1 0.23 Ideal E SI2 61.5 55 326 3.95 3.98 2.43
2 0.21 Premium E SI1 59.8 61 326 3.89 3.84 2.31
3 0.23 Good E VS1 56.9 65 327 4.05 4.07 2.31
4 0.22 Fair E VS2 65.1 61 337 3.87 3.78 2.49
5 0.20 Premium E SI2 60.2 62 345 3.79 3.75 2.27
6 0.32 Premium E I1 60.9 58 345 4.38 4.42 2.68
7 0.23 Very Good E VS2 63.8 55 352 3.85 3.92 2.48
8 0.23 Very Good E VS1 60.7 59 402 3.97 4.01 2.42
9 0.23 Very Good E VS1 59.5 58 402 4.01 4.06 2.40
10 0.23 Good E VS1 64.1 59 402 3.83 3.85 2.46
Notice in the example above that quoted strings within the SQL query are quoted using '' if the
overall query is quoted with "" (this also works in reverse).
Suppose that we wish to add a new column to count the number of Premium cut diamonds over 1
carat:
sqldf("select count(*) from diamonds where carat > 1 and color = 'E'")
count(*)
1 1892
Results of created values can also be returned as new columns:
sqldf("select *, count(*) as cnt_big_E_colored_stones from diamonds where carat > 1 and color
= 'E' group by clarity")

cnt_big_E_colored_stones
1 1.30 Fair E I1 66.5 58 2571 6.79 6.75 4.50
65
2 1.28 Ideal E IF 60.7 57 18700 7.09 6.99 4.27
28
3 2.02 Very Good E SI1 59.8 59 18731 8.11 8.20 4.88
499
4 2.03 Premium E SI2 61.5 59 18477 8.24 8.16 5.04
666
5 1.51 Ideal E VS1 61.5 57 18729 7.34 7.40 4.53
158
6 1.72 Very Good E VS2 63.4 56 18557 7.65 7.55 4.82
318
7 1.20 Ideal E VVS1 61.8 56 16256 6.78 6.87 4.22
52
8 1.55 Ideal E VVS2 62.5 55 18188 7.38 7.40 4.62
106
If one would be interested what is the max price of the diamond according to the cut:
sqldf("select cut, max(price) from diamonds group by cut")
cut max(price)
1 Fair 18574
2 Good 18788
3 Ideal 18806
4 Premium 18823
5 Very Good 18818
Read sqldf online: https://riptutorial.com/r/topic/2100/sqldf
Chapter 112: Standardize analyses by writing
standalone R scripts
Introduction
If you want to routinely apply an R analysis to a lot of separate data files, or provide a repeatable
analysis method to other people, an executable R script is a user-friendly way to do so. Instead of
you or your user having to call R and execute your script inside R via source(.) or a function call,
your user may simply call the script itself as if it was a program.
Remarks
To represent the standard input-/output channels, use the functions file("stdin") (input from
terminal or other program via pipe), stdout() (standard output) and stderr() (standard error). Note
that while there is the function stdin(), it can not be used when supplying a ready-made script to
R, because it will read the next lines of that script instead of user input.
Examples
The basic structure of standalone R program and how to call it
The first standalone R script

Standalone R scripts are not executed by the program R (R.exe under Windows), but by a program
called Rscript (Rscript.exe), which is included in your R installation by default.
To hint at this fact, standalone R scripts start with a special line called Shebang line, which holds
the following content: #!/usr/bin/env Rscript. Under Windows, an additional measure is needed,
which is detailled later.
The following simple standalone R script saves a histogram under the file name "hist.png" from
numbers it receives as input:
#!/usr/bin/env Rscript
# User message (\n = end the line)

cat("Input numbers, separated by space:\n")
# Read user input as one string (n=1 -> Read only one line)
input <- readLines(file('stdin'), n=1)
# Split the string at each space (\\s == any space)
input <- strsplit(input, "\\s")[[1]]
# convert the obtained vector of strings to numbers
input <- as.numeric(input)
# Open the output picture file
png("hist.png",width=400, height=300)
# Draw the histogram
hist(input)
# Close the output file
dev.off()
You can see several key elements of a standalone R script. In the first line, you see the Shebang
line. Followed by that, cat("....\n") is used to print a message to the user. Use file("stdin")
whenever you want to specify "User input on console" as a data origin. This can be used instead
of a file name in several data reading functions (scan, read.table, read.csv,...). After the user input
is converted from strings to numbers, the plotting begins. There, it can be seen, that plotting
commands which are meant to be written to a file must be enclosed in two commands. These are
in this case png(.) and dev.off(). The first function depends on the desired output file format (other
common choices being jpeg(.) and pdf(.)). The second function, dev.off() is always required. It
writes the plot to the file and ends the plotting process.
Preparing a standalone R script

Linux/Mac
The standalone script's file must first be made executable. This can happen by right-clicking the
file, opening "Properties" in the opening menu and checking the "Executable" checkbox in the
"Permissions" tab. Alternatively, the command
chmod +x PATH/TO/SCRIPT/SCRIPTNAME.R
can be called in a Terminal.
Windows
For each standalone script, a batch file must be written with the following contents:
"C:\Program Files\R-XXXXXXX\bin\Rscript.exe" "%~dp0\XXXXXXX.R" %*
A batch file is a normal text file, but which has a *.bat extension except a *.txt extension. Create
it using a text editor like notepad (not Word) or similar and put the file name into quotation marks
"FILENAME.bat") in the save dialog. To edit an existing batch file, right-click on it and select "Edit".
You have to adapt the code shown above everywhere XXX... is written:
• Insert the correct folder where your R installation resides

• Insert the correct name of your script and place it into the same directory as this batch file.
Explanation of the elements in the code: The first part "C:\...\Rscript.exe" tells Windows where to
find the Rscript.exe program. The second part "%~dp0\XXX.R" tells Rscript to execute the R script
you've written which resides in the same folder as the batch file (%~dp0 stands for the batch file
folder). Finally, %* forwards any command line arguments you give to the batch file to the R script.
If you double-click on the batch file, the R script is executed. If you drag files on the batch file, the
corresponding file names are given to the R script as command line arguments.
Using littler to execute R scripts
littler (pronounced little r) (cran) provides, besides other features, two possibilities to run R scripts
from the command line with littler's r command (when one works with Linux or MacOS).
Installing littler
From R:
install.packages("littler")
The path of r is printed in the terminal, like
You could link to the 'r' binary installed in

'/home/*USER*/R/x86_64-pc-linux-gnu-library/3.4/littler/bin/r'
from '/usr/local/bin' in order to use 'r' for scripting.
To be able to call r from the system's command line, a symlink is needed:
ln -s /home/*USER*/R/x86_64-pc-linux-gnu-library/3.4/littler/bin/r /usr/local/bin/r
Using apt-get (Debian, Ubuntu):
sudo apt-get install littler
Using littler with standard .r scripts

With r from littler it is possible to execute standalone R scripts without any changes to the script.
Example script:
# User message (\n = end the line)

cat("Input numbers, separated by space:\n")
# Read user input as one string (n=1 -> Read only one line)
input <- readLines(file('stdin'), n=1)
# Split the string at each space (\\s == any space)
input <- strsplit(input, "\\s")[[1]]
# convert the obtained vector of strings to numbers
input <- as.numeric(input)
# Open the output picture file

png("hist.png",width=400, height=300)
# Draw the histogram
hist(input)
# Close the output file
dev.off()
Note that no shebang is at the top of the scripts. When saved as for example hist.r, it is directly
callable from the system command:
r hist.r
Using littler on shebanged scripts

It is also possible to create executable R scripts with littler, with the use of the shebang
#!/usr/bin/env r
at the top of the script. The corresponding R script has to be made executable with chmod +X
/path/to/script.r and is directly callable from the system terminal.
Read Standardize analyses by writing standalone R scripts online:

https://riptutorial.com/r/topic/9937/standardize-analyses-by-writing-standalone-r-scripts
Chapter 113: String manipulation with stringi
package
Remarks
To install package simply run:
install.packages("stringi")
to load it:
require("stringi")
Examples
Count pattern inside string
With fixed pattern
stri_count_fixed("babab", "b")
# [1] 3
stri_count_fixed("babab", "ba")
# [1] 2
stri_count_fixed("babab", "bab")
# [1] 1
Natively:
length(gregexpr("b","babab")[[1]])
# [1] 3
length(gregexpr("ba","babab")[[1]])
# [1] 2
length(gregexpr("bab","babab")[[1]])
# [1] 1
function is vectorized over string and pattern:
stri_count_fixed("babab", c("b","ba"))
# [1] 3 2
stri_count_fixed(c("babab","bbb","bca","abc"), c("b","ba"))
# [1] 3 0 1 0
A base R solution:
sapply(c("b","ba"),function(x)length(gregexpr(x,"babab")[[1]]))
# b ba
# 3 2
With regex
First example - find a and any character after
Second example - find a and any digit after
stri_count_regex("a1 b2 a3 b4 aa", "a.")

# [1] 3
stri_count_regex("a1 b2 a3 b4 aa", "a\\d")
# [1] 2
Duplicating strings
stri_dup("abc",3)
# [1] "abcabcabc"
A base R solution that does the same would look like this:
paste0(rep("abc",3),collapse = "")
# [1] "abcabcabc"
Paste vectors
stri_paste(LETTERS,"-", 1:13)
# [1] "A-1" "B-2" "C-3" "D-4" "E-5" "F-6" "G-7" "H-8" "I-9" "J-10" "K-11" "L-12" "M-
13"
# [14] "N-1" "O-2" "P-3" "Q-4" "R-5" "S-6" "T-7" "U-8" "V-9" "W-10" "X-11" "Y-12" "Z-
13"
Natively, we could do this in R via:
> paste(LETTERS,1:13,sep="-")
#[1] "A-1" "B-2" "C-3" "D-4" "E-5" "F-6" "G-7" "H-8" "I-9" "J-10" "K-11" "L-12" "M-
13"
#[14] "N-1" "O-2" "P-3" "Q-4" "R-5" "S-6" "T-7" "U-8" "V-9" "W-10" "X-11" "Y-12" "Z-
13"
Splitting text by some fixed pattern
Split vector of texts using one pattern:
stri_split_fixed(c("To be or not to be.", "This is very short sentence.")," ")

# [[1]]
# [1] "To" "be" "or" "not" "to" "be."
#
# [[2]]
# [1] "This" "is" "very" "short" "sentence."
Split one text using many patterns:
stri_split_fixed("Apples, oranges and pineaplles.",c(" ", ",", "s"))

# [[1]]
# [1] "Apples," "oranges" "and" "pineaplles."
#
# [[2]]
# [1] "Apples" " oranges and pineaplles."
#
# [[3]]
# [1] "Apple" ", orange" " and pineaplle" "."
Read String manipulation with stringi package online: https://riptutorial.com/r/topic/1670/string-

manipulation-with-stringi-package
Chapter 114: strsplit function
Syntax
• strsplit(
• x
• split
• fixed = FALSE
• perl = FALSE
• useBytes = FALSE)
Examples
Introduction
strsplit is a useful function for breaking up a vector into an list on some character pattern. With
typical R tools, the whole list can be reincorporated to a data.frame or part of the list might be used
in a graphing exercise.
Here is a common usage of strsplit: break a character vector along a comma separator:
temp <- c("this,that,other", "hat,scarf,food", "woman,man,child")

# get a list split by commas
myList <- strsplit(temp, split=",")
# print myList
myList
[[1]]
[1] "this" "that" "other"
[[2]]
[1] "hat" "scarf" "food"
[[3]]
[1] "woman" "man" "child"
As hinted above, the split argument is not limited to characters, but may follow a pattern dictated
by a regular expression. For example, temp2 is identical to temp above except that the separators
have been altered for each item. We can take advantage of the fact that the split argument
accepts regular expressions to alleviate the irregularity in the vector.
temp2 <- c("this, that, other", "hat,scarf ,food", "woman; man ; child")
myList2 <- strsplit(temp2, split=" ?[,;] ?")
myList2
[[1]]
[1] "this" "that" "other"
[[2]]
[1] "hat" "scarf" "food"
[[3]]
[1] "woman" "man" "child"
Notes:
1. breaking down the regular expression syntax is out of scope for this example.
2. Sometimes matching regular expressions can slow down a process. As with many R
functions that allow the use of regular expressions, the fixed argument is available to tell R to
match on the split characters literally.
Read strsplit function online: https://riptutorial.com/r/topic/2762/strsplit-function
Chapter 115: Subsetting
Introduction
Given an R object, we may require separate analysis for one or more parts of the data contained
in it. The process of obtaining these parts of the data from a given object is called subsetting.
Remarks
Missing values:
Missing values (NAs) used in subsetting with [ return NA since a NA index
picks an unknown element and so returns NA in the corresponding element..
The "default" type of NA is "logical" (typeof(NA)) which means that, as any "logical" vector used in
subsetting, will be recycled to match the length of the subsetted object. So x[NA] is equivalent to
x[as.logical(NA)] which is equivalent to x[rep_len(as.logical(NA), length(x))] and, consequently,
it returns a missing value (NA) for each element of x. As an example:
x <- 1:3
x[NA]
## [1] NA NA NA
While indexing with "numeric"/"integer" NA picks a single NA element (for each NA in index):
x[as.integer(NA)]
## [1] NA
x[c(NA, 1, NA, NA)]

## [1] NA 1 NA NA
Subsetting out of bounds:
The [ operator, with one argument passed, allows indices that are > length(x) and returns NA for
atomic vectors or NULL for generic vectors. In contrast, with [[ and when [ is passed more
arguments (i.e. subsetting out of bounds objects with length(dim(x)) > 2) an error is returned:
(1:3)[10]
## [1] NA
(1:3)[[10]]
## Error in (1:3)[[10]] : subscript out of bounds
as.matrix(1:3)[10]
## [1] NA
as.matrix(1:3)[, 10]
## Error in as.matrix(1:3)[, 10] : subscript out of bounds
list(1, 2, 3)[10]
## [[1]]
## NULL
list(1, 2, 3)[[10]]
## Error in list(1, 2, 3)[[10]] : subscript out of bounds
The behaviour is the same when subsetting with "character" vectors, that are not matched in the
"names" attribute of the object, too:
c(a = 1, b = 2)["c"]
## <NA>
## NA
list(a = 1, b = 2)["c"]
## <NA>
## NULL
Help topics:
See ?Extract for further information.
Examples
Atomic vectors
Atomic vectors (which excludes lists and expressions, which are also vectors) are subset using the
[ operator:
# create an example vector

v1 <- c("a", "b", "c", "d")
# select the third element

v1[3]
## [1] "c"
The [ operator can also take a vector as the argument. For example, to select the first and third
elements:
v1 <- c("a", "b", "c", "d")
v1[c(1, 3)]
## [1] "a" "c"
Some times we may require to omit a particular value from the vector. This can be achieved using
a negative sign(-) before the index of that value. For example, to omit to omit the first value from
v1, use v1[-1]. This can be extended to more than one value in a straight forward way. For
example, v1[-c(1,3)].
> v1[-1]
[1] "b" "c" "d"
> v1[-c(1,3)]
[1] "b" "d"
On some occasions, we would like to know, especially, when the length of the vector is large,
index of a particular value, if it exists:
> v1=="c"
[1] FALSE FALSE TRUE FALSE
> which(v1=="c")
[1] 3
If the atomic vector has names (a names attribute), it can be subset using a character vector of
names:
v <- 1:3
names(v) <- c("one", "two", "three")
v
## one two three
## 1 2 3
v["two"]
## two
## 2
The [[ operator can also be used to index atomic vectors, with differences in that it accepts a
indexing vector with a length of one and strips any names present:
v[[c(1, 2)]]
## Error in v[[c(1, 2)]] :
## attempt to select more than one element in vectorIndex
v[["two"]]
## [1] 2
Vectors can also be subset using a logical vector. In contrast to subsetting with numeric and
character vectors, the logical vector used to subset has to be equal to the length of the vector
whose elements are extracted, so if a logical vector y is used to subset x, i.e. x[y], if length(y) <
length(x) then y will be recycled to match length(x):
v[c(TRUE, FALSE, TRUE)]

## one three
## 1 3
v[c(FALSE, TRUE)] # recycled to 'c(FALSE, TRUE, FALSE)'

## two
## 2
v[TRUE] # recycled to 'c(TRUE, TRUE, TRUE)'

## one two three
## 1 2 3
v[FALSE] # handy to discard elements but save the vector's type and basic structure
## named integer(0)
Lists
A list can be subset with [:
l1 <- list(c(1, 2, 3), 'two' = c("a", "b", "c"), list(10, 20))
l1
## [[1]]
## [1] 1 2 3
##
## $two
## [1] "a" "b" "c"
##
## [[3]]
## [[3]][[1]]
## [1] 10
##
## [[3]][[2]]
## [1] 20
l1[1]
## [[1]]
## [1] 1 2 3
l1['two']
## $two
## [1] "a" "b" "c"
l1[[2]]
## [1] "a" "b" "c"
l1[['two']]
## [1] "a" "b" "c"
Note the result of l1[2] is still a list, as the [ operator selects elements of a list, returning a smaller
list. The [[ operator extracts list elements, returning an object of the type of the list element.
Elements can be indexed by number or a character string of the name (if it exists). Multiple
elements can be selected with [ by passing a vector of numbers or strings of names. Indexing with
a vector of length > 1 in [ and [[ returns a "list" with the specified elements and a recursive subset
(if available), respectively:
l1[c(3, 1)]
## [[1]]
## [[1]][[1]]
## [1] 10
##
## [[1]][[2]]
## [1] 20
##
##
## [[2]]
## [1] 1 2 3
Compared to:
l1[[c(3, 1)]]
## [1] 10
which is equivalent to:
l1[[3]][[1]]
## [1] 10
The $ operator allows you to select list elements solely by name, but unlike [ and [[, does not
require quotes. As an infix operator, $ can only take a single name:
l1$two
## [1] "a" "b" "c"
Also, the $ operator allows for partial matching by default:
l1$t
## [1] "a" "b" "c"
in contrast with [[ where it needs to be specified whether partial matching is allowed:
l1[["t"]]
## NULL
l1[["t", exact = FALSE]]
## [1] "a" "b" "c"
Setting options(warnPartialMatchDollar = TRUE), a "warning" is given when partial matching

happens with $:
l1$t
## [1] "a" "b" "c"
## Warning message:
## In l1$t : partial match of 't' to 'two'
Matrices
For each dimension of an object, the [ operator takes one argument. Vectors have one dimension
and take one argument. Matrices and data frames have two dimensions and take two arguments,
given as [i, j] where i is the row and j is the column. Indexing starts at 1.
## a sample matrix
mat <- matrix(1:6, nrow = 2, dimnames = list(c("row1", "row2"), c("col1", "col2", "col3")))
mat
# col1 col2 col3
# row1 1 3 5
# row2 2 4 6
mat[i,j] is the element in the i-th row, j-th column of the matrix mat. For example, an i value of 2
and a j value of 1 gives the number in the second row and the first column of the matrix. Omitting
i or j returns all values in that dimension.
mat[ , 3]
## row1 row2
## 5 6
mat[1, ]
# col1 col2 col3
# 1 3 5
When the matrix has row or column names (not required), these can be used for subsetting:
mat[ , 'col1']
# row1 row2
# 1 2
By default, the result of a subset will be simplified if possible. If the subset only has one dimension,
as in the examples above, the result will be a one-dimensional vector rather than a two-
dimensional matrix. This default can be overriden with the drop = FALSE argument to [:
## This selects the first row as a vector

class(mat[1, ])
# [1] "integer"
## Whereas this selects the first row as a 1x3 matrix:

class(mat[1, , drop = F])
# [1] "matrix"
Of course, dimensions cannot be dropped if the selection itself has two dimensions:
mat[1:2, 2:3] ## A 2x2 matrix

# col2 col3
# row1 3 5
# row2 4 6
Selecting individual matrix entries by their positions
It is also possible to use a Nx2 matrix to select N individual elements from a matrix (like how a
coordinate system works). If you wanted to extract, in a vector, the entries of a matrix in the (1st
row, 1st column), (1st row, 3rd column), (2nd row, 3rd column), (2nd row, 1st column) this can be
done easily by creating a index matrix with those coordinates and using that to subset the matrix:
mat
# col1 col2 col3
# row1 1 3 5
# row2 2 4 6
ind = rbind(c(1, 1), c(1, 3), c(2, 3), c(2, 1))

ind
# [,1] [,2]
# [1,] 1 1
# [2,] 1 3
# [3,] 2 3
# [4,] 2 1
mat[ind]
# [1] 1 5 6 2
In the above example, the 1st column of the ind matrix refers to rows in mat, the 2nd column of ind
refers to columns in mat.
Data frames
Subsetting a data frame into a smaller data frame can be accomplished the same as
subsetting a list.
> df3 <- data.frame(x = 1:3, y = c("a", "b", "c"), stringsAsFactors = FALSE)
> df3
## x y
## 1 1 a
## 2 2 b
## 3 3 c
> df3[1] # Subset a variable by number

## x
## 1 1
## 2 2
## 3 3
> df3["x"] # Subset a variable by name

## x
## 1 1
## 2 2
## 3 3
> is.data.frame(df3[1])
## TRUE
> is.list(df3[1])
## TRUE
Subsetting a dataframe into a column vector can be accomplished using double brackets [[ ]]
or the dollar sign operator $.
> df3[[2]] # Subset a variable by number using [[ ]]

## [1] "a" "b" "c"
> df3[["y"]] # Subset a variable by name using [[ ]]

## [1] "a" "b" "c"
> df3$x # Subset a variable by name using $

## [1] 1 2 3
> typeof(df3$x)
## "integer"
> is.vector(df3$x)
## TRUE
Subsetting a data as a two dimensional matrix can be accomplished using i and j terms.
> df3[1, 2] # Subset row and column by number

## [1] "a"
> df3[1, "y"] # Subset row by number and column by name
## [1] "a"
> df3[2, ] # Subset entire row by number

## x y
## 2 2 b
> df3[ , 1] # Subset all first variables

## [1] 1 2 3
> df3[ , 1, drop = FALSE]

## x
## 1 1
## 2 2
## 3 3
Note: Subsetting by j (column) alone simplifies to the variable's own type, but subsetting by i
alone returns a data.frame, as the different variables may have different types and classes. Setting
the drop parameter to FALSE keeps the data frame.
> is.vector(df3[, 2])

## TRUE
> is.data.frame(df3[2, ])
## TRUE
> is.data.frame(df3[, 2, drop = FALSE])

## TRUE
Other objects
The [ and [[ operators are primitive functions that are generic. This means that any object in R
(specifically isTRUE(is.object(x)) --i.e. has an explicit "class" attribute) can have its own specified
behaviour when subsetted; i.e. has its own methods for [ and/or [[.
For example, this is the case with "data.frame" (is.object(iris)) objects where [.data.frame and
[[.data.frame methods are defined and they are made to exhibit both "matrix"-like and "list"-like
subsetting. With forcing an error when subsetting a "data.frame", we see that, actually, a function
[.data.frame was called when we -just- used [.
iris[invalidArgument, ]
## Error in `[.data.frame`(iris, invalidArgument, ) :
## object 'invalidArgument' not found
Without further details on the current topic, an example[ method:
x = structure(1:5, class = "myClass")

x[c(3, 2, 4)]
## [1] 3 2 4
'[.myClass' = function(x, i) cat(sprintf("We'd expect '%s[%s]' to be returned but this a
custom `[` method and should have a `?[.myClass` help page for its behaviour\n",
deparse(substitute(x)), deparse(substitute(i))))
x[c(3, 2, 4)]
## We'd expect 'x[c(3, 2, 4)]' to be returned but this a custom `[` method and should have a
`?[.myClass` help page for its behaviour
## NULL
We can overcome the method dispatching of [ by using the equivalent non-generic .subset (and
.subset2 for [[). This is especially useful and efficient when programming our own "class"es and
want to avoid work-arounds (like unclass(x)) when computing on our "class"es efficiently (avoiding
method dispatch and copying objects):
.subset(x, c(3, 2, 4))

## [1] 3 2 4
Vector indexing
For this example, we will use the vector:
> x <- 11:20

> x
[1] 11 12 13 14 15 16 17 18 19 20
R vectors are 1-indexed, so for example x[1] will return 11. We can also extract a sub-vector of x
by passing a vector of indices to the bracket operator:
> x[c(2,4,6)]
[1] 12 14 16
If we pass a vector of negative indices, R will return a sub-vector with the specified indices
excluded:
> x[c(-1,-3)]
[1] 12 14 15 16 17 18 19 20
We can also pass a boolean vector to the bracket operator, in which case it returns a sub-vector
corresponding to the coordinates where the indexing vector is TRUE:
> x[c(rep(TRUE,5),rep(FALSE,5))]
[1] 11 12 13 14 15 16
If the indexing vector is shorter than the length of the array, then it will be repeated, as in:
> x[c(TRUE,FALSE)]
[1] 11 13 15 17 19
> x[c(TRUE,FALSE,FALSE)]
[1] 11 14 17 20
Elementwise Matrix Operations
Let A and B be two matrices of same dimension. The operators +,-,/,*,^ when used with matrices
of same dimension perform the required operations on the corresponding elements of the matrices
and return a new matrix of the same dimension. These operations are usually referred to as
element-wise operations.
Operator A op B Meaning
+ A+B Addition of corresponding elements of A and B
- A-B Subtracts the elements of B from the corresponding elements of A
/ A/B Divides the elements of A by the corresponding elements of B
* A*B Multiplies the elements of A by the corresponding elements of B
^ A^(-1) For example, gives a matrix whose elements are reciprocals of A
For "true" matrix multiplication, as seen in Linear Algebra, use %*%. For example, multiplication of A
with B is: A %*% B. The dimensional requirements are that the ncol() of A be the same as nrow() of B
Some Functions used with Matrices
Function Example Purpose
nrow() nrow(A) determines the number of rows of A
ncol() ncol(A) determines the number of columns of A
rownames() rownames(A) prints out the row names of the matrix A
colnames() colnames(A) prints out the column names of the matrix A
rowMeans() rowMeans(A) computes means of each row of the matrix A
colMeans() colMeans(A) computes means of each column of the matrix A
upper.tri() upper.tri(A) returns a vector whose elements are the upper
triangular matrix of square matrix A
lower.tri() lower.tri(A) returns a vector whose elements are the lower
triangular matrix of square matrix A
det() det(A) results in the determinant of the matrix A
solve() solve(A) results in the inverse of the non-singular matrix A
returns a diagonal matrix whose off-diagnal elemts are zeros

diag() diag(A)
and
Function Example Purpose
diagonals are the same as that of the square matrix A
t() t(A) returns the the transpose of the matrix A
eigen() eigen(A) retuens the eigenvalues and eigenvectors of the matrix A
returns TRUE or FALSE depending on whether A is a matrix or

is.matrix() is.matrix(A)
not.
as.matrix() as.matrix(x) creates a matrix out of the vector x
Read Subsetting online: https://riptutorial.com/r/topic/1686/subsetting
Chapter 116: Survival analysis
Examples
Random Forest Survival Analysis with randomForestSRC
Just as the random forest algorithm may be applied to regression and classification tasks, it can
also be extended to survival analysis.
In the example below a survival model is fit and used for prediction, scoring, and performance
analysis using the package randomForestSRC from CRAN.
require(randomForestSRC)
set.seed(130948) #Other seeds give similar comparative results

x1 <- runif(1000)
y <- rnorm(1000, mean = x1, sd = .3)
data <- data.frame(x1 = x1, y = y)
head(data)
x1 y
1 0.9604353 1.3549648
2 0.3771234 0.2961592
3 0.7844242 0.6942191
4 0.9860443 1.5348900
5 0.1942237 0.4629535
6 0.7442532 -0.0672639
(modRFSRC <- rfsrc(y ~ x1, data = data, ntree=500, nodesize = 5))
Sample size: 1000

Number of trees: 500
Minimum terminal node size: 5
Average no. of terminal nodes: 208.258
No. of variables tried at each split: 1
Total no. of variables: 1
Analysis: RF-R
Family: regr
Splitting rule: mse
% variance explained: 32.08
Error rate: 0.11
x1new <- runif(10000)

ynew <- rnorm(10000, mean = x1new, sd = .3)
newdata <- data.frame(x1 = x1new, y = ynew)
survival.results <- predict(modRFSRC, newdata = newdata)

survival.results
Sample size of test (predict) data: 10000
Number of grow trees: 500
Average no. of grow terminal nodes: 208.258
Total no. of grow variables: 1
Analysis: RF-R
Family: regr
% variance explained: 34.97
Test set error rate: 0.11
Introduction - basic fitting and plotting of parametric survival models with the
survival package
survival is the most commonly used package for survival analysis in R. Using the built-in lung
dataset we can get started with Survival Analysis by fitting a regression model with the survreg()
function, creating a curve with survfit(), and plotting predicted survival curves by calling the
predict method for this package with new data.
In the example below we plot 2 predicted curves and vary sex between the 2 sets of new data, to
visualize its effect:
require(survival)
s <- with(lung,Surv(time,status))
sWei <- survreg(s ~ as.factor(sex)+age+ph.ecog+wt.loss+ph.karno,dist='weibull',data=lung)
fitKM <- survfit(s ~ sex,data=lung)

plot(fitKM)
lines(predict(sWei, newdata = list(sex = 1,

age = 1,
ph.ecog = 1,
ph.karno = 90,
wt.loss = 2),
type = "quantile",
p = seq(.01, .99, by = .01)),
seq(.99, .01, by =-.01),
col = "blue")
lines(predict(sWei, newdata = list(sex = 2,

age = 1,
ph.ecog = 1,
ph.karno = 90,
wt.loss = 2),
type = "quantile",
p = seq(.01, .99, by = .01)),
seq(.99, .01, by =-.01),
col = "red")
Kaplan Meier estimates of survival curves and risk set tables with survminer
Base plot
install.packages('survminer')
biocLite("RTCGA.clinical") # data for examples
library(RTCGA.clinical)
survivalTCGA(BRCA.clinical, OV.clinical,
extract.cols = "admin.disease_code") -> BRCAOV.survInfo
library(survival)
fit <- survfit(Surv(times, patient.vital_status) ~ admin.disease_code,
data = BRCAOV.survInfo)
library(survminer)
ggsurvplot(fit, risk.table = TRUE)
More advanced
ggsurvplot(
fit, # survfit object with calculated statistics.
risk.table = TRUE, # show risk table.
pval = TRUE, # show p-value of log-rank test.
conf.int = TRUE, # show confidence intervals for
# point estimaes of survival curves.
xlim = c(0,2000), # present narrower X axis, but not affect
# survival estimates.
break.time.by = 500, # break X axis in time intervals by 500.
ggtheme = theme_RTCGA(), # customize plot and risk table with a theme.
risk.table.y.text.col = T, # colour risk table text annotations.
risk.table.y.text = FALSE # show bars instead of names in text annotations
# in legend of risk table
)
Based on
http://r-addict.com/2016/05/23/Informative-Survival-Plots.html
Read Survival analysis online: https://riptutorial.com/r/topic/3788/survival-analysis
Chapter 117: Text mining
Examples
Scraping Data to build N-gram Word Clouds
The following example utilizes the tm text mining package to scrape and mine text data from the
web to build word clouds with symbolic shading and ordering.
require(RWeka)
require(tau)
require(tm)
require(tm.plugin.webmining)
require(wordcloud)
# Scrape Google Finance ---------------------------------------------------

googlefinance <- WebCorpus(GoogleFinanceSource("NASDAQ:LFVN"))
# Scrape Google News ------------------------------------------------------

lv.googlenews <- WebCorpus(GoogleNewsSource("LifeVantage"))
p.googlenews <- WebCorpus(GoogleNewsSource("Protandim"))
ts.googlenews <- WebCorpus(GoogleNewsSource("TrueScience"))
# Scrape NYTimes ----------------------------------------------------------

lv.nytimes <- WebCorpus(NYTimesSource(query = "LifeVantage", appid = nytimes_appid))
p.nytimes <- WebCorpus(NYTimesSource("Protandim", appid = nytimes_appid))
ts.nytimes <- WebCorpus(NYTimesSource("TrueScience", appid = nytimes_appid))
# Scrape Reuters ----------------------------------------------------------

lv.reutersnews <- WebCorpus(ReutersNewsSource("LifeVantage"))
p.reutersnews <- WebCorpus(ReutersNewsSource("Protandim"))
ts.reutersnews <- WebCorpus(ReutersNewsSource("TrueScience"))
# Scrape Yahoo! Finance ---------------------------------------------------

lv.yahoofinance <- WebCorpus(YahooFinanceSource("LFVN"))
# Scrape Yahoo! News ------------------------------------------------------

lv.yahoonews <- WebCorpus(YahooNewsSource("LifeVantage"))
p.yahoonews <- WebCorpus(YahooNewsSource("Protandim"))
ts.yahoonews <- WebCorpus(YahooNewsSource("TrueScience"))
# Scrape Yahoo! Inplay ----------------------------------------------------

lv.yahooinplay <- WebCorpus(YahooInplaySource("LifeVantage"))
# Text Mining the Results -------------------------------------------------

corpus <- c(googlefinance, lv.googlenews, p.googlenews, ts.googlenews, lv.yahoofinance,
lv.yahoonews, p.yahoonews,
ts.yahoonews, lv.yahooinplay) #lv.nytimes, p.nytimes, ts.nytimes,lv.reutersnews,
p.reutersnews, ts.reutersnews,
inspect(corpus)
wordlist <- c("lfvn", "lifevantage", "protandim", "truescience", "company", "fiscal",
"nasdaq")
ds0.1g <- tm_map(corpus, content_transformer(tolower))

ds1.1g <- tm_map(ds0.1g, content_transformer(removeWords), wordlist)
ds1.1g <- tm_map(ds1.1g, content_transformer(removeWords), stopwords("english"))
ds2.1g <- tm_map(ds1.1g, stripWhitespace)
ds3.1g <- tm_map(ds2.1g, removePunctuation)
ds4.1g <- tm_map(ds3.1g, stemDocument)
tdm.1g <- TermDocumentMatrix(ds4.1g)

dtm.1g <- DocumentTermMatrix(ds4.1g)
findFreqTerms(tdm.1g, 40)
findAssocs(dtm.1g, "skin", .75)

findAssocs(dtm.1g, "scienc", .5)
findAssocs(dtm.1g, "product", .75)
tdm89.1g <- removeSparseTerms(tdm.1g, 0.89)

tdm2.1g <- tdm92.1g
# Creates a Boolean matrix (counts # docs w/terms, not raw # terms)

tdm3.1g <- inspect(tdm2.1g)
tdm3.1g[tdm3.1g>=1] <- 1
# Transform into a term-term adjacency matrix

termMatrix.1gram <- tdm3.1g %*% t(tdm3.1g)
# inspect terms numbered 5 to 10

termMatrix.1gram[5:10,5:10]
termMatrix.1gram[1:10,1:10]
# Create a WordCloud to Visualize the Text Data ---------------------------

notsparse <- tdm2.1g
m = as.matrix(notsparse)
v = sort(rowSums(m),decreasing=TRUE)
d = data.frame(word = names(v),freq=v)
# Create the word cloud

pal = brewer.pal(9,"BuPu")
wordcloud(words = d$word,
freq = d$freq,
scale = c(3,.8),
random.order = F,
colors = pal)
Note the use of random.order and a sequential pallet from RColorBrewer, which allows the
programmer to capture more information in the cloud by assigning meaning to the order and
coloring of terms.
Above is the 1-gram case.
We can make a major leap to n-gram word clouds and in doing so we’ll see how to make almost
any text-mining analysis flexible enough to handle n-grams by transforming our TDM.
The initial difficulty you run into with n-grams in R is that tm, the most popular package for text
mining, does not inherently support tokenization of bi-grams or n-grams. Tokenization is the
process of representing a word, part of a word, or group of words (or symbols) as a single data
element called a token.
Fortunately, we have some hacks which allow us to continue using tm with an upgraded tokenizer.
There’s more than one way to achieve this. We can write our own simple tokenizer using the
textcnt() function from tau:
tokenize_ngrams <- function(x, n=3)

return(rownames(as.data.frame(unclass(textcnt(x,method="string",n=n)))))
or we can invoke RWeka's tokenizer within tm:
# BigramTokenize
BigramTokenizer <- function(x) NGramTokenizer(x, Weka_control(min = 2, max = 2))
From this point you can proceed much as in the 1-gram case:
# Create an n-gram Word Cloud ----------------------------------------------

tdm.ng <- TermDocumentMatrix(ds5.1g, control = list(tokenize = BigramTokenizer))
dtm.ng <- DocumentTermMatrix(ds5.1g, control = list(tokenize = BigramTokenizer))
# Try removing sparse terms at a few different levels

tdm89.ng <- removeSparseTerms(tdm.ng, 0.89)
notsparse <- tdm91.ng

m = as.matrix(notsparse)
v = sort(rowSums(m),decreasing=TRUE)
d = data.frame(word = names(v),freq=v)
# Create the word cloud

pal = brewer.pal(9,"BuPu")
wordcloud(words = d$word,
freq = d$freq,
scale = c(3,.8),
random.order = F,
colors = pal)
The example above is reproduced with permission from Hack-R's data science blog. Additional
commentary may be found in the original article.
Read Text mining online: https://riptutorial.com/r/topic/3579/text-mining
Chapter 118: The character class
Introduction
Characters are what other languages call 'string vectors.'
Remarks
Related topics
Patterns
• Regular Expressions (regex)

• Pattern Matching and Replacement
• strsplit function
Input and output
• Reading and writing strings
Examples
Coercion
To check whether a value is a character use the is.character() function. To coerce a variable to a
character use the as.character() function.
x <- "The quick brown fox jumps over the lazy dog"
class(x)
[1] "character"
is.character(x)
[1] TRUE
Note that numerics can be coerced to characters, but attempting to coerce a character to numeric
may result in NA.
as.numeric("2")
[1] 2
as.numeric("fox")
[1] NA
Warning message:
NAs introduced by coercion
Read The character class online: https://riptutorial.com/r/topic/9017/the-character-class
Chapter 119: The Date class
Remarks
Related topics
• Date and Time
Jumbled notes
• Date: Stores time as number of days since UNIX epoch on 1970-01-01. with negative values
for earlier dates.
• It is represented as an integer (however, it is not enforced in the internal representation)
• They are always printed following the rules of the current Gregorian calendar, even though
the calendar was not in use a long time ago.
• It doesn't keep track of timezones, so it should not be used to truncate the time out of POSIXct
or POSIXlt objects.
• sys.Date() returns an object of class Date
More notes
• lubridate's ymd, mdy, etc. are alternatives to as.Date that also parse to Date class; see Parsing
dates and datetimes from strings with lubridate.
• data.table's experimental IDate class is derived from and is mostly interchangeable with
Date, but is stored as integer instead of double.
Examples
Formatting Dates
To format Dates we use the format(date, format="%Y-%m-%d") function with either the POSIXct (given
from as.POSIXct()) or POSIXlt (given from as.POSIXlt())
d = as.Date("2016-07-21") # Current Date Time Stamp
format(d,"%a") # Abbreviated Weekday

## [1] "Thu"
format(d,"%A") # Full Weekday

## [1] "Thursday"
format(d,"%b") # Abbreviated Month

## [1] "Jul"
format(d,"%B") # Full Month
## [1] "July"
format(d,"%m") # 00-12 Month Format

## [1] "07"
format(d,"%d") # 00-31 Day Format

## [1] "21"
format(d,"%e") # 0-31 Day Format

## [1] "21"
format(d,"%y") # 00-99 Year

## [1] "16"
format(d,"%Y") # Year with Century

## [1] "2016"
For more, see ?strptime.
Dates
To coerce a variable to a date use the as.Date() function.
> x <- as.Date("2016-8-23")

> x
[1] "2016-08-23"
> class(x)
[1] "Date"
The as.Date() function allows you to provide a format argument. The default is %Y-%m-%d, which is
Year-month-day.
> as.Date("23-8-2016", format="%d-%m-%Y") # To read in an European-style date

[1] "2016-08-23"
The format string can be placed either within a pair of single quotes or double quotes. Dates are
usually expressed in a variety of forms such as: "d-m-yy" or "d-m-YYYY" or "m-d-yy" or "m-d-YYYY" or
"YYYY-m-d" or "YYYY-d-m". These formats can also be expressed by replacing "-" by "/". Furher,
dates are also expressed in the forms, say, "Nov 6, 1986" or "November 6, 1986" or "6 Nov, 1986"
or "6 November, 1986" and so on. The as.Date() function accepts all such character strings and
when we mention the appropriate format of the string, it always outputs the date in the form "YYYY-
m-d".
Suppose we have a date string "9-6-1962" in the format "%d-%m-%Y".
#
# It tries to interprets the string as YYYY-m-d
#
> as.Date("9-6-1962")
[1] "0009-06-19" #interprets as "%Y-%m-%d"
>
as.Date("9/6/1962")
[1] "0009-06-19" #again interprets as "%Y-%m-%d"
>
# It has no problem in understanding, if the date is in form YYYY-m-d or YYYY/m/d
#
> as.Date("1962-6-9")
[1] "1962-06-09" # no problem
> as.Date("1962/6/9")
[1] "1962-06-09" # no problem
>
By specifying the correct format of the input string, we can get the desired results. We use the
following codes for specifying the formats to the as.Date() function.
Format Code Meaning
%d day
%m month
%y year in 2-digits
%Y year in 4-digits
%b abbreviated month in 3 chars
%B full name of the month
Consider the following example specifying the format parameter:
> as.Date("9-6-1962",format="%d-%m-%Y")
[1] "1962-06-09"
>
The parameter name format can be omitted.
> as.Date("9-6-1962", "%d-%m-%Y")

[1] "1962-06-09"
>
Some times, names of the months abbreviated to the first three characters are used in the writing
the dates. In which case we use the format specifier %b.
> as.Date("6Nov1962","%d%b%Y")
[1] "1962-11-06"
>
Note that, there are no either '-' or '/' or white spaces between the members in the date string.
The format string should exactly match that input string. Consider the following example:
> as.Date("6 Nov, 1962","%d %b, %Y")
[1] "1962-11-06"
>
Note that, there is a comma in the date string and hence a comma in the format specification too.
If comma is omitted in the format string, it results in an NA. An example usage of %B format specifier
is as follows:
> as.Date("October 12, 2016", "%B %d, %Y")

[1] "2016-10-12"
>
> as.Date("12 October, 2016", "%d %B, %Y")
[1] "2016-10-12"
>
%y format is system specific and hence, should be used with caution. Other parameters used with
this function are origin and tz( time zone).
Parsing Strings into Date Objects
R contains a Date class, which is created with as.Date(), which takes a string or vector of strings,
and if the date is not in ISO 8601 date format YYYY-MM-DD, a formatting string of strptime-style
tokens.
as.Date('2016-08-01') # in ISO format, so does not require formatting string

## [1] "2016-08-01"
as.Date('05/23/16', format = '%m/%d/%y')

## [1] "2016-05-23"
as.Date('March 23rd, 2016', '%B %drd, %Y') # add separators and literals to format
## [1] "2016-03-23"
as.Date(' 2016-08-01 foo') # leading whitespace and all trailing characters are ignored
## [1] "2016-08-01"
as.Date(c('2016-01-01', '2016-01-02'))
# [1] "2016-01-01" "2016-01-02"
Read The Date class online: https://riptutorial.com/r/topic/9015/the-date-class
Chapter 120: The logical class
Introduction
Logical is a mode (and an implicit class) for vectors.
Remarks
Shorthand
TRUE, FALSE
and NA are the only values for logical vectors; and all three are reserved words. T and F
can be shorthand for TRUE and FALSE in a clean R session, but neither T nor F are reserved, so
assignment of non-default values to those names can set users up for difficulties.
Examples
Logical operators
There are two sorts of logical operators: those that accept and return vectors of any length
(elementwise operators: !, |, &, xor()) and those that only evaluate the first element in each
argument (&&, ||). The second sort is primarily used as the cond argument to the if function.
Logical Operator Meaning Syntax
! Not !x
& element-wise (vectorized) and x&y
&& and (single element only) x && y
| element-wise (vectorized) or x|y
|| or (single element only) x || y
xor element-wise (vectorized) exclusive OR xor(x,y)
Note that the || operator evaluates the left condition and if the left condition is TRUE the right side
is never evaluated. This can save time if the first is the result of a complex operation. The &&
operator will likewise return FALSE without evaluation of the second argument when the first
element of the first argument is FALSE.
> x <- 5
> x > 6 || stop("X is too small")
Error: X is too small
> x > 3 || stop("X is too small")
[1] TRUE
To check whether a value is a logical you can use the is.logical() function.
Coercion
To coerce a variable to a logical use the as.logical() function.
> x <- 2
> z <- x > 4
> z
[1] FALSE
> class(x)
[1] "numeric"
> as.logical(2)
[1] TRUE
When applying as.numeric() to a logical, a double will be returned. NA is a logical value and a
logical operator with an NA will return NA if the outcome is ambiguous.
Interpretation of NAs
See Missing values for details.
> TRUE & NA

[1] NA
> FALSE & NA
[1] FALSE
> TRUE || NA
[1] TRUE
> FALSE || NA
[1] NA
Read The logical class online: https://riptutorial.com/r/topic/9016/the-logical-class
Chapter 121: tidyverse
Examples
Creating tbl_df’s
A tbl_df (pronounced tibble diff) is a variation of a data frame that is often used in tidyverse
packages. It is implemented in the tibble package.
Use the as_data_frame function to turn a data frame into a tbl_df:
library(tibble)
mtcars_tbl <- as_data_frame(mtcars)
One of the most notable differences between data.frames and tbl_dfs is how they print:
# A tibble: 32 x 11
mpg cyl disp hp drat wt qsec vs am gear carb
* <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4
2 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4
3 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1
4 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1
5 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2
6 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1
7 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4
8 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2
9 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2
10 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4
• The printed output includes a summary of the dimensions of the table (32 x 11)
• It includes the type of each column (dbl)
• It prints a limited number of rows. (To change this use options(tibble.print_max = [number])).
Many functions in the dplyr package work naturally with tbl_dfs, such as group_by().
tidyverse: an overview
What is tidyverse?
tidyverse is the fast and elegant way to turn basic R into an enhanced tool, redesigned by
Hadley/Rstudio. The development of all packages included in tidyverse follow the principle rules of
The tidy tools manifesto. But first, let the authors describe their masterpiece:
The tidyverse is a set of packages that work in harmony because they share common
data representations and API design. The tidyverse package is designed to make it
easy to install and load core packages from the tidyverse in a single command.
The best place to learn about all the packages in the tidyverse and how they fit
together is R for Data Science. Expect to hear more about the tidyverse in the coming
months as I work on improved package websites, making citation easier, and providing
a common home for discussions about data analysis with the tidyverse.
(source))
How to use it?

Just with the ordinary R packages, you need to install and load the package.
install.package("tidyverse")
library("tidyverse")
The difference is, on a single command a couple of dozens of packages are installed/loaded. As a
bonus, one may rest assured that all the installed/loaded packages are of compatible versions.
What are those packages?

The commonly known and widely used packages:
• ggplot2: advanced data visualisation SO_doc

• dplyr: fast (Rcpp) and coherent approach to data manipulation SO_doc
• tidyr: tools for data tidying SO_doc
• readr: for data import.
• purrr: makes your pure functions purr by completing R's functional programming tools with
important features from other languages, in the style of the JS packages underscore.js,
lodash and lazy.js.
• tibble: a modern re-imagining of data frames.
• magrittr: piping to make code more readable SO_doc
Packages for manipulating specific data formats:
• hms: easily read times

• stringr: provide a cohesive set of functions designed to make working with strings as easy as
posssible
• lubridate: advanced date/times manipulations SO_doc
• forcats: advanced work with factors.
Data import:
• DBI: defines a common interface between the R and database management systems
(DBMS)
• haven: easily import SPSS, SAS and Stata files SO_doc
• httr: the aim of httr is to provide a wrapper for the curl package, customised to the demands
of modern web APIs
• jsonlite: a fast JSON parser and generator optimized for statistical data and the web
• readxl: read.xls and .xlsx files without need for dependency packages SO_doc
• rvest: rvest helps you scrape information from web pages SO_doc
• xml2: for XML
And modelling:
• modelr: provides functions that help you create elegant pipelines when modelling
• broom: easily extract the models into tidy data
Finally, tidyverse suggest the use of:
• knitr: the amazing general-purpose literate programming engine, with lightweight API's
designed to give users full control of the output without heavy coding work. SO_docs: one,
two
• rmarkdown: Rstudio's package for reproducible programming. SO_docs: one, two, three,
four
Read tidyverse online: https://riptutorial.com/r/topic/1395/tidyverse
Chapter 122: Time Series and Forecasting
Remarks
Forecasting and time-series analysis may be handled with commonplace functions from the stats
package, such as glm() or a large number of specialized packages. The CRAN Task View for
time-series analysis provides a detailed listing of key packages by topic with short descriptions.
Examples
Exploratory Data Analysis with time-series data
data(AirPassengers)
class(AirPassengers)
1 "ts"
In the spirit of Exploratory Data Analysis (EDA) a good first step is to look at a plot of your time-
series data:
plot(AirPassengers) # plot the raw data

abline(reg=lm(AirPassengers~time(AirPassengers))) # fit a trend line
For further EDA we examine cycles across years:
cycle(AirPassengers)
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
1949 1 2 3 4 5 6 7 8 9 10 11 12
1950 1 2 3 4 5 6 7 8 9 10 11 12
1951 1 2 3 4 5 6 7 8 9 10 11 12
1952 1 2 3 4 5 6 7 8 9 10 11 12
1953 1 2 3 4 5 6 7 8 9 10 11 12
1954 1 2 3 4 5 6 7 8 9 10 11 12
1955 1 2 3 4 5 6 7 8 9 10 11 12
1956 1 2 3 4 5 6 7 8 9 10 11 12
1957 1 2 3 4 5 6 7 8 9 10 11 12
1958 1 2 3 4 5 6 7 8 9 10 11 12
1959 1 2 3 4 5 6 7 8 9 10 11 12
1960 1 2 3 4 5 6 7 8 9 10 11 12
boxplot(AirPassengers~cycle(AirPassengers)) #Box plot across months to explore seasonal

effects
Creating a ts object
Time series data can be stored as a ts object. ts objects contain information about seasonal
frequency that is used by ARIMA functions. It also allows for calling of elements in the series by
date using the window command.
#Create a dummy dataset of 100 observations

x <- rnorm(100)
#Convert this vector to a ts object with 100 annual observations
x <- ts(x, start = c(1900), freq = 1)
#Convert this vector to a ts object with 100 monthly observations starting in July
x <- ts(x, start = c(1900, 7), freq = 12)
#Alternatively, the starting observation can be a number:

x <- ts(x, start = 1900.5, freq = 12)
#Convert this vector to a ts object with 100 daily observations and weekly frequency starting
in the first week of 1900
x <- ts(x, start = c(1900, 1), freq = 7)
#The default plot for a ts object is a line plot

plot(x)
#The window function can call elements or sets of elements by date
#Call the first 4 weeks of 1900

window(x, start = c(1900, 1), end = (1900, 4))
#Call only the 10th week in 1900

window(x, start = c(1900, 10), end = (1900, 10))
#Call all weeks including and after the 10th week of 1900
window(x, start = c(1900, 10))
It is possible to create ts objects with multiple series:
#Create a dummy matrix of 3 series with 100 observations each

x <- cbind(rnorm(100), rnorm(100), rnorm(100))
#Create a multi-series ts with annual observation starting in 1900

x <- ts(x, start = 1900, freq = 1)
#R will draw a plot for each series in the object

plot(x)
Read Time Series and Forecasting online: https://riptutorial.com/r/topic/2701/time-series-and-

forecasting
Chapter 123: Updating R and the package
library
Examples
On Windows
Default installation of R on Windows stored files (and thus library) on a dedicated folder per R
version on program files.
That means that by default, you would work with several versions of R in parallel and thus
separate libraries.
If this not what you want and you prefer to always work with a single R instance you wan't to
gradually update, it is recommended to modify the R installation folder. In wizard, just specify this
folder (I personally use c:\stats\R). Then, for any upgrade, one possibility is to overwrite this R.
Whether you also want to upgrade (all) packages is a delicate choice as it may break some of your
code (this appeared for me with the tmpackage). You may:
• First make a copy of all your library before upgrading packages

• Maintain your own source packages repository, for instance using package miniCRAN
If you want to upgrade all packages - without any check, you can call use packageStatus as in:
pkgs <- packageStatus() # choose mirror

upgrade(pkgs)
Finally, there exists a very convenient package to perform all operations, namely installr, even
coming with a dedicated gui. If you want to use gui, you must use Rgui and not load the package
in RStudio. Using the package with code is as simple as:
install.packages("installr") # install
setInternet2(TRUE) # only for R versions older than 3.3.0
installr::updateR() # updating R.
I refer to the great documentation https://www.r-statistics.com/tag/installr/ and specifically the step

by step process with screenshots on Windows:https://www.r-statistics.com/2015/06/a-step-by-
step-screenshots-tutorial-for-upgrading-r-on-windows/
Note that still I advocate using a single directory, ie. removing reference to the R version in
installation folder name.
Read Updating R and the package library online: https://riptutorial.com/r/topic/4088/updating-r-

and-the-package-library
Chapter 124: Updating R version
Introduction
Installing or Updating your Software will give access to new features and bug fixes. Updating your
R installation can be done in a couple of ways. One Simple way is go to R website and download
the latest version for your system.
Examples
Installing from R Website
To get the latest release go to https://cran.r-project.org/ and download the file for your operating
system. Open the downloaded file and follow the on-screen installation steps. All the settings can
be left on default unless you want to change a certain behaviour.
Updating from within R using installr Package
You can also update R from within R by using a handy package called installr.
Open R Console (NOT RStudio, this doesn't work from RStudio) and run the following code to
install the package and initiate update.
install.packages("installr")
library("installr")
updateR()
Deciding on the old packages
Once the installation is finished click the Finish button.
Now it asks if you want to copy your packages fro the older version of R to Newer version of R.
Once you choose yes all the package are copied to the newer version of R.
After that you can choose if you still want to keep the old packages or delete.
You can even move your Rprofile.site from older version to keep all your customised settings.
Updating Packages
You can update your installed packages once the updating of R is done.
Once its done Restart R and enjoy exploring.
Check R Version
You can check R Version using the console
version
Read Updating R version online: https://riptutorial.com/r/topic/10729/updating-r-version
Chapter 125: Using pipe assignment in your
own package %<>%: How to ?
Introduction
In order to use the pipe in a user-created package, it must be listed in the NAMESPACE like any
other function you choose to import.
Examples
Putting the pipe in a utility-functions file
One option for doing this is to export the pipe from within the package itself. This may be done in
the 'traditional' zzz.R or utils.R files that many packages utilise for useful little functions that are
not exported as part of the package. For example, putting:
#' Pipe operator

#'
#' @name %>%
#' @rdname pipe
#' @keywords internal
#' @export
#' @importFrom magrittr %>%
#' @usage lhs \%>\% rhs
NULL
Read Using pipe assignment in your own package %<>%: How to ? online:
https://riptutorial.com/r/topic/10547/using-pipe-assignment-in-your-own-package-------how-to--
Chapter 126: Using texreg to export models
in a paper-ready way
Introduction
The texreg package helps to export a model (or several models) in a neat paper-ready way. The
result may be exported as HTML or .doc (MS Office Word).
Remarks
Links
• CRAN page
Examples
Printing linear regression results
# models
fit1 <- lm(mpg ~ wt, data = mtcars)
fit2 <- lm(mpg ~ wt+hp, data = mtcars)
fit3 <- lm(mpg ~ wt+hp+cyl, data = mtcars)
# export to html
texreg::htmlreg(list(fit1,fit2,fit3),file='models.html')
# export to doc
texreg::htmlreg(list(fit1,fit2,fit3),file='models.doc')
The result looks like a table in a paper.
There are several additional handy parameters in texreg::htmlreg() function. Here is a use case
for the most helpful parameters.
# export to html
texreg::htmlreg(list(fit1,fit2,fit3),file='models.html',
single.row = T,
custom.model.names = LETTERS[1:3],
leading.zero = F,
digits = 3)
Which result in a table like this
Read Using texreg to export models in a paper-ready way online:

https://riptutorial.com/r/topic/9037/using-texreg-to-export-models-in-a-paper-ready-way
Chapter 127: Variables
Examples
Variables, data structures and basic Operations
In R, data objects are manipulated using named data structures. The names of the objects might
be called "variables" although that term does not have a specific meaning in the official R
documentation. R names are case sensitive and may contain alphanumeric characters(a-z,A-z,0-9
), the dot/period(.) and underscore(_). To create names for the data structures, we have to follow
the following rules:
• Names that start with a digit or an underscore (e.g. 1a), or names that are valid numerical
expressions (e.g. .11), or names with dashes ('-') or spaces can only be used when they are
quoted: `1a` and `.11`. The names will be printed with backticks:
list( '.11' ="a")

#$`.11`
#[1] "a"
• All other combinations of alphanumeric characters, dots and underscores can be used freely,
where reference with or without backticks points to the same object.
• Names that begin with . are considered system names and are not always visible using the
ls()-function.
There is no restriction on the number of characters in a variable name.
Some examples of valid object names are: foobar, foo.bar, foo_bar, .foobar
In R, variables are assigned values using the infix-assignment operator <-. The operator = can
also be used for assigning values to variables, however its proper use is for associating values
with parameter names in function calls. Note that omitting spaces around operators may create
confusion for users. The expression a<-1 is parsed as assignment (a <- 1) rather than as a logical
comparison (a < -1).
> foo <- 42

> fooEquals = 43
So foo is assigned the value of 42. Typing foo within the console will output 42, while typing
fooEquals will output 43.
> foo
[1] 42
> fooEquals
[1] 43
The following command assigns a value to the variable named x and prints the value
simultaneously:
> (x <- 5)
[1] 5
# actually two function calls: first one to `<-`; second one to the `()`-function
> is.function(`(`)
[1] TRUE # Often used in R help page examples for its side-effect of printing.
It is also possible to make assignments to variables using ->.
> 5 -> x
> x
[1] 5
>
Types of data structures

There are no scalar data types in R. Vectors of length-one act like scalars.
• Vectors: Atomic vectors must be sequence of same-class objects.: a sequence of numbers,

or a sequence of logicals or a sequence of characters. v <- c(2, 3, 7, 10), v2 <- c("a", "b",
"c") are both vectors.
• Matrices: A matrix of numbers, logical or characters. a <- matrix(data = c(1, 2, 3, 4, 5, 6,
7, 8, 9, 10, 11, 12), nrow = 4, ncol = 3, byrow = F). Like vectors, matrix must be made of
same-class elements. To extract elements from a matrix rows and columns must be
specified: a[1,2] returns [1] 5 that is the element on the first row, second column.
• Lists: concatenation of different elements mylist <- list (course = 'stat', date =
'04/07/2009', num_isc = 7, num_cons = 6, num_mat = as.character(c(45020, 45679, 46789,
43126, 42345, 47568, 45674)), results = c(30, 19, 29, NA, 25, 26 ,27) ). Extracting
elements from a list can be done by name (if the list is named) or by index. In the given
example mylist$results and mylist[[6]] obtains the same element. Warning: if you try
mylist[6], R wont give you an error, but it extract the result as a list. While mylist[[6]][2] is
permitted (it gives you 19), mylist[6][2] gives you an error.
• data.frame: object with columns that are vectors of equal length, but (possibly) different
types. They are not matrices. exam <- data.frame(matr = as.character(c(45020, 45679, 46789,
43126, 42345, 47568, 45674)), res_S = c(30, 19, 29, NA, 25, 26, 27), res_O = c(3, 3, 1, NA,
3, 2, NA), res_TOT = c(30,22,30,NA,28,28,27)). Columns can be read by name exam$matr,
exam[, 'matr'] or by index exam[1], exam[,1]. Rows can also be read by name exam['rowname',
] or index exam[1,]. Dataframes are actually just lists with a particular structure (rownames-
attribute and equal length components)
Common operations and some cautionary advice

Default operations are done element by element. See ?Syntax for the rules of operator precedence.
Most operators (and may other functions in base R) have recycling rules that allow arguments of
unequal length. Given these objects:
Example objects
> a <- 1
> b <- 2
> c <- c(2,3,4)
> d <- c(10,10,10)
> e <- c(1,2,3,4)
> f <- 1:6
> W <- cbind(1:4,5:8,9:12)
> Z <- rbind(rep(0,3),1:3,rep(10,3),c(4,7,1))
Some vector operations

> a+b # scalar + scalar
[1] 3
> c+d # vector + vector
[1] 12 13 14
> a*b # scalar * scalar
[1] 2
> c*d # vector * vector (componentwise!)
[1] 20 30 40
> c+a # vector + scalar
[1] 3 4 5
> c^2 #
[1] 4 9 16
> exp(c)
[1] 7.389056 20.085537 54.598150
Some vector operation Warnings!

> c+e # warning but.. no errors, since recycling is assumed to be desired.
[1] 3 5 7 6
Warning message:
In c + e : longer object length is not a multiple of shorter object length
R sums what it can and then reuses the shorter vector to fill in the blanks... The warning was given
only because the two vectors have lengths that are not exactly multiples. c+f # no warning
whatsoever.
Some Matrix operations Warning!

> Z+W # matrix + matrix #(componentwise)
> Z*W # matrix* matrix#(Standard product is always componentwise)
To use a matrix multiply: V %*% W
> W + a # matrix+ scalar is still componentwise
[,1] [,2] [,3]
[1,] 2 6 10
[2,] 3 7 11
[3,] 4 8 12
[4,] 5 9 13
> W + c # matrix + vector... : no warnings and R does the operation in a column-wise manner
[,1] [,2] [,3]
[1,] 3 8 13
[2,] 5 10 12
[3,] 7 9 14
[4,] 6 11 16
"Private" variables
A leading dot in a name of a variable or function in R is commonly used to denote that the variable
or function is meant to be hidden.
So, declaring the following variables
> foo <- 'foo'

> .foo <- 'bar'
And then using the ls function to list objects will only show the first object.
> ls()
[1] "foo"
However, passing all.names = TRUE to the function will show the 'private' variable
> ls(all.names = TRUE)

[1] ".foo" "foo"
Read Variables online: https://riptutorial.com/r/topic/9013/variables
Chapter 128: Web Crawling in R
Examples
Standard scraping approach using the RCurl package
We try to extract imdb top chart movies and ratings
R> library(RCurl)
R> library(XML)
R> url <- "http://www.imdb.com/chart/top"
R> top <- getURL(url)
R> parsed_top <- htmlParse(top, encoding = "UTF-8")
R> top_table <- readHTMLTable(parsed_top)[[1]]
R> head(top_table[1:10, 1:3])
Rank & Title IMDb Rating

1 1. The Shawshank Redemption (1994) 9.2
2 2. The Godfather (1972) 9.2
3 3. The Godfather: Part II (1974) 9.0
4 4. The Dark Knight (2008) 8.9
5 5. Pulp Fiction (1994) 8.9
6 6. The Good, the Bad and the Ugly (1966) 8.9
7 7. Schindler’s List (1993) 8.9
8 8. 12 Angry Men (1957) 8.9
9 9. The Lord of the Rings: The Return of the King (2003) 8.9
10 10. Fight Club (1999) 8.8
Read Web Crawling in R online: https://riptutorial.com/r/topic/4336/web-crawling-in-r
Chapter 129: Web scraping and parsing
Remarks
Scraping refers to using a computer to retrieve the code of a webpage. Once the code is obtained,
it must be parsed into a useful form for further use in R.
Base R does not have many of the tools required for these processes, so scraping and parsing are
typically done with packages. Some packages are most useful for scraping (RSelenium, httr, curl,
RCurl), some for parsing (XML, xml2), and some for both (rvest).
A related process is scraping a web API, which unlike a webpage returns data intended to be
machine-readable. Many of the same packages are used for both.
Legality
Some websites object to being scraped, whether due to increased server loads or concerns about
data ownership. If a website forbids scraping in it Terms of Use, scraping it is illegal.
Examples
Basic scraping with rvest
rvestis a package for web scraping and parsing by Hadley Wickham inspired by Python's
Beautiful Soup. It leverages Hadley's xml2 package's libxml2 bindings for HTML parsing.
As part of the tidyverse, rvest is piped. It uses
• xml2::read_html to scrape the HTML of a webpage,

• which can then be subset with its html_node and html_nodes functions using CSS or XPath
selectors, and
• parsed to R objects with functions like html_text and html_table.
To scrape the table of milestones from the Wikipedia page on R, the code would look like
library(rvest)
url <- 'https://en.wikipedia.org/wiki/R_(programming_language)'
# scrape HTML from website

url %>% read_html() %>%
# select HTML tag with class="wikitable"
html_node(css = '.wikitable') %>%
# parse table into data.frame
html_table() %>%
# trim for printing
dplyr::mutate(Description = substr(Description, 1, 70))
## Release Date Description
## 1 0.16 This is the last alpha version developed primarily by Ihaka
## 2 0.49 1997-04-23 This is the oldest source release which is currently availab
## 3 0.60 1997-12-05 R becomes an official part of the GNU Project. The code is h
## 4 0.65.1 1999-10-07 First versions of update.packages and install.packages funct
## 5 1.0 2000-02-29 Considered by its developers stable enough for production us
## 6 1.4 2001-12-19 S4 methods are introduced and the first version for Mac OS X
## 7 2.0 2004-10-04 Introduced lazy loading, which enables fast loading of data
## 8 2.1 2005-04-18 Support for UTF-8 encoding, and the beginnings of internatio
## 9 2.11 2010-04-22 Support for Windows 64 bit systems.
## 10 2.13 2011-04-14 Adding a new compiler function that allows speeding up funct
## 11 2.14 2011-10-31 Added mandatory namespaces for packages. Added a new paralle
## 12 2.15 2012-03-30 New load balancing functions. Improved serialization speed f
## 13 3.0 2013-04-03 Support for numeric index values 231 and larger on 64 bit sy
While this returns a data.frame, note that as is typical for scraped data, there is still further data
cleaning to be done: here, formatting dates, inserting NAs, and so on.
Note that data in a less consistently rectangular format may take looping or other further munging
to successfully parse. If the website makes use of jQuery or other means to insert content,
read_html may be insufficient to scrape, and a more robust scraper like RSelenium may be
necessary.
Using rvest when login is required
I common problem encounter when scrapping a web is how to enter a userid and password to log
into a web site.
In this example which I created to track my answers posted here to stack overflow. The overall
flow is to login, go to a web page collect information, add it a dataframe and then move to the next
page.
library(rvest)
#Address of the login webpage

login<-
"https://stackoverflow.com/users/login?ssrc=head&returnurl=http%3a%2f%2fstackoverflow.com%2f"
#create a web session with the desired login address

pgsession<-html_session(login)
pgform<-html_form(pgsession)[[2]] #in this case the submit is the 2nd form
filled_form<-set_values(pgform, email="*****", password="*****")
submit_form(pgsession, filled_form)
#pre allocate the final results dataframe.

results<-data.frame()
#loop through all of the pages with the desired info

for (i in 1:5)
{
#base address of the pages to extract information from
url<-"http://stackoverflow.com/users/**********?tab=answers&sort=activity&page="
url<-paste0(url, i)
page<-jump_to(pgsession, url)
#collect info on the question votes and question title
summary<-html_nodes(page, "div .answer-summary")
question<-matrix(html_text(html_nodes(summary, "div"), trim=TRUE), ncol=2, byrow = TRUE)
#find date answered, hyperlink and whether it was accepted

dateans<-html_node(summary, "span") %>% html_attr("title")
hyperlink<-html_node(summary, "div a") %>% html_attr("href")
accepted<-html_node(summary, "div") %>% html_attr("class")
#create temp results then bind to final results

rtemp<-cbind(question, dateans, accepted, hyperlink)
results<-rbind(results, rtemp)
}
#Dataframe Clean-up
names(results)<-c("Votes", "Answer", "Date", "Accepted", "HyperLink")
results$Votes<-as.integer(as.character(results$Votes))
results$Accepted<-ifelse(results$Accepted=="answer-votes default", 0, 1)
The loop in this case is limited to only 5 pages, this needs to change to fit your application. I
replaced the user specific values with ******, hopefully this will provide some guidance for you
problem.
Read Web scraping and parsing online: https://riptutorial.com/r/topic/2890/web-scraping-and-

parsing
Chapter 130: Writing functions in R
Examples
Named functions
R is full of functions, it is after all a functional programming language, but sometimes the precise
function you need isn't provided in the Base resources. You could conceivably install a package
containing the function, but maybe your requirements are just so specific that no pre-made
function fits the bill? Then you're left with the option of making your own.
A function can be very simple, to the point of being being pretty much pointless. It doesn't even
need to take an argument:
one <- function() { 1 }

one()
[1] 1
two <- function() { 1 + 1 }

two()
[1] 2
What's between the curly braces { } is the function proper. As long as you can fit everything on a
single line they aren't strictly needed, but can be useful to keep things organized.
A function can be very simple, yet highly specific. This function takes as input a vector (vec in this
example) and outputs the same vector with the vector's length (6 in this case) subtracted from
each of the vector's elements.
vec <- 4:9

subtract.length <- function(x) { x - length(x) }
subtract.length(vec)
[1] -2 -1 0 1 2 3
Notice that length() is in itself a pre-supplied (i.e. Base) function. You can of course use a
previously self-made function within another self-made function, as well as assign variables and
perform other operations while spanning several lines:
vec2 <- (4:7)/2
msdf <- function(x, multiplier=4) {

mult <- x * multiplier
subl <- subtract.length(x)
data.frame(mult, subl)
}
msdf(vec2, 5)
mult subl
1 10.0 -2.0
2 12.5 -1.5
3 15.0 -1.0
4 17.5 -0.5
multiplier=4 makes sure that 4 is the default value of the argument multiplier, if no value is given
when calling the function 4 is what will be used.
The above are all examples of named functions, so called simply because they have been given
names (one, two, subtract.length etc.)
Anonymous functions
An anonymous function is, as the name implies, not assigned a name. This can be useful when
the function is a part of a larger operation, but in itself does not take much place. One frequent
use-case for anonymous functions is within the *apply family of Base functions.
Calculate the root mean square for each column in a data.frame:
df <- data.frame(first=5:9, second=(0:4)^2, third=-1:3)
apply(df, 2, function(x) { sqrt(sum(x^2)) })

first second third
15.968719 18.814888 3.872983
Create a sequence of step-length one from the smallest to the largest value for each row in a
matrix.
x <- sample(1:6, 12, replace=TRUE)

mat <- matrix(x, nrow=3)
apply(mat, 1, function(x) { seq(min(x), max(x)) })
An anonymous function can also stand on its own:
(function() { 1 })()
[1] 1
is equivalent to
f <- function() { 1 })
f()
[1] 1
RStudio code snippets
This is just a small hack for those who use self-defined functions often.
Type "fun" RStudio IDE and hit TAB.
The result will be a skeleton of a new function.
name <- function(variables) {
One can easily define their own snippet template, i.e. like the one below
name <- function(df, x, y) {

require(tidyverse)
out <-
return(out)
}
The option is Edit Snippets in the Global Options -> Code menu.
Passing column names as argument of a function
Sometimes one would like to pass names of columns from a data frame to a function. They may
be provided as strings and used in a function using [[. Let's take a look at the following example,
which prints to R console basic stats of selected variables:
basic.stats <- function(dset, vars){

for(i in 1:length(vars)){
print(vars[i])
print(summary(dset[[vars[i]]]))
}
}
basic.stats(iris, c("Sepal.Length", "Petal.Width"))
As a result of running above given code, names of selected variables and their basic summary
statistics (minima, first quantiles, medians, means, third quantiles and maxima) are printed in R
console. The code dset[[vars[i]]] selects i-th element from the argument vars and selects a
corresponding column in declared input data set dset. For example, declaring
iris[["Sepal.Length"]] alone would print the Sepal.Length column from the iris data set as a
vector.
Read Writing functions in R online: https://riptutorial.com/r/topic/7937/writing-functions-in-r
Chapter 131: xgboost
Examples
Cross Validation and Tuning with xgboost
library(caret) # for dummyVars

library(RCurl) # download https data
library(Metrics) # calculate errors
library(xgboost) # model
###############################################################################
# Load data from UCI Machine Learning Repository (http://archive.ics.uci.edu/ml/datasets.html)
urlfile <- 'https://archive.ics.uci.edu/ml/machine-learning-databases/adult/adult.data'
x <- getURL(urlfile, ssl.verifypeer = FALSE)
adults <- read.csv(textConnection(x), header=F)
# adults <-read.csv('https://archive.ics.uci.edu/ml/machine-learning-
databases/adult/adult.data', header=F)
names(adults)=c('age','workclass','fnlwgt','education','educationNum',
'maritalStatus','occupation','relationship','race',
'sex','capitalGain','capitalLoss','hoursWeek',
'nativeCountry','income')
# clean up data
adults$income <- ifelse(adults$income==' <=50K',0,1)
# binarize all factors
library(caret)
dmy <- dummyVars(" ~ .", data = adults)
adultsTrsf <- data.frame(predict(dmy, newdata = adults))
###############################################################################
# what we're trying to predict adults that make more than 50k
outcomeName <- c('income')
# list of features
predictors <- names(adultsTrsf)[!names(adultsTrsf) %in% outcomeName]
# play around with settings of xgboost - eXtreme Gradient Boosting (Tree) library
# https://github.com/tqchen/xgboost/wiki/Parameters
# max.depth - maximum depth of the tree
# nrounds - the max number of iterations
# take first 10% of the data only!

trainPortion <- floor(nrow(adultsTrsf)*0.1)
trainSet <- adultsTrsf[ 1:floor(trainPortion/2),]

testSet <- adultsTrsf[(floor(trainPortion/2)+1):trainPortion,]
smallestError <- 100

for (depth in seq(1,10,1)) {
for (rounds in seq(1,20,1)) {
# train
bst <- xgboost(data = as.matrix(trainSet[,predictors]),
label = trainSet[,outcomeName],
max.depth=depth, nround=rounds,
objective = "reg:linear", verbose=0)
gc()
# predict
predictions <- predict(bst, as.matrix(testSet[,predictors]),
outputmargin=TRUE)
err <- rmse(as.numeric(testSet[,outcomeName]), as.numeric(predictions))
if (err < smallestError) {

smallestError = err
print(paste(depth,rounds,err))
}
}
}
cv <- 30
trainSet <- adultsTrsf[1:trainPortion,]
cvDivider <- floor(nrow(trainSet) / (cv+1))
smallestError <- 100

for (depth in seq(1,10,1)) {
for (rounds in seq(1,20,1)) {
totalError <- c()
indexCount <- 1
for (cv in seq(1:cv)) {
# assign chunk to data test
dataTestIndex <- c((cv * cvDivider):(cv * cvDivider + cvDivider))
dataTest <- trainSet[dataTestIndex,]
# everything else to train
dataTrain <- trainSet[-dataTestIndex,]
bst <- xgboost(data = as.matrix(dataTrain[,predictors]),

label = dataTrain[,outcomeName],
max.depth=depth, nround=rounds,
objective = "reg:linear", verbose=0)
gc()
predictions <- predict(bst, as.matrix(dataTest[,predictors]),
outputmargin=TRUE)
err <- rmse(as.numeric(dataTest[,outcomeName]),

as.numeric(predictions))
totalError <- c(totalError, err)
}
if (mean(totalError) < smallestError) {
smallestError = mean(totalError)
print(paste(depth,rounds,smallestError))
}
}
}
###########################################################################
# Test both models out on full data set
trainSet <- adultsTrsf[ 1:trainPortion,]
# assign everything else to test

testSet <- adultsTrsf[(trainPortion+1):nrow(adultsTrsf),]

max.depth=4, nround=19, objective = "reg:linear", verbose=0)
pred <- predict(bst, as.matrix(testSet[,predictors]), outputmargin=TRUE)
rmse(as.numeric(testSet[,outcomeName]), as.numeric(pred))
max.depth=3, nround=20, objective = "reg:linear", verbose=0)
pred <- predict(bst, as.matrix(testSet[,predictors]), outputmargin=TRUE)
rmse(as.numeric(testSet[,outcomeName]), as.numeric(pred))
Read xgboost online: https://riptutorial.com/r/topic/3239/xgboost
Credits
S.
Chapters Contributors
No
42-, akraf, Ale, Andrea Cirillo, Andrew Brēza, Axeman,

Community, Craig Vermeer, d.b, dotancohen, Francesco Dondi,
Frank, G5W, George Bonebright, GForce, Giorgos K, Gregor,
Getting started with
1 H. Pauwelyn, kartoffelsalat, kdopen, Konrad Rudolph, L.V.Rao,
R Language
lmckeogh, Lovy, Matt, mnoronha, pitosalas, polka, Rahul Saini,
RetractedAndRetired, russellpierce, Steve_Corrin, theArun,
Thomas, torina, user2100721, while
*apply family of Benjamin, FisherDisinformation, Gavin Simpson, jcb, Karolis

2 functions Koncevičius, kneijenhuijs, Maximilian Kohl, nrussell, omar,
(functionals) Robert, seasmith, zacdav
42-, Dirk Eddelbuettel, ikashnitsky, Karolis Koncevičius, Nikos

3 .Rprofile
Alexandris, Stedy, Thomas
Aggregating data
4 Florian, Frank
frames
Analyze tweets with

5 Umberto
R
6 ANOVA Ben Bolker, DataTx, kneijenhuijs
7 Arima Models Andrew Bryk, Steve_Corrin
Batanichek, FisherDisinformation, Matt Sandgren, Robert,

8 Arithmetic Operators
russellpierce, Tensibai
9 Bar Chart L.V.Rao
42-, Alexey Shiklomanov, catastrophic-failure,

10 Base Plotting FisherDisinformation, Frank, Giorgos K, K.Daisey, maRtin,
MichaelChirico, RamenChef, Robert, symbolrush
11 Bibliography in RMD J_F, RamenChef
12 boxplot Carlos Cinelli, Christophe D., Karolis Koncevičius, L.V.Rao
13 caret highBandWidth, Steve_Corrin
42-, AkselA, David Heckmann, dayne, Frank, Gregor, Jaap,

14 Classes
kneijenhuijs, L.V.Rao, Nathan Werth, Steve_Corrin
15 Cleaning data Derek Corcoran
16 Code profiling Ben Bolker, Glen Moutrie, Jav, SymbolixAU, USER_1
17 Coercion d.b
Color schemes for

18 ikashnitsky, munirbe
graphics
Column wise
19 akrun
operation
20 Combinatorics Frank, Karolis Koncevičius
Control flow
21 Benjamin, David Arenburg, nrussell, Robert, Steve_Corrin
structures
Creating packages
22 Frank, Lovy
with devtools
Creating reports with

23 ikashnitsky, Karolis Koncevičius, Martin Schmelzer
RMarkdown
alistaire, bartektartanus, Jaap, Karsten W., lmo, Rich Scriven,

24 Creating vectors
Robert, Robin Gertenbach, smci, takje
25 Data acquisition ikashnitsky
Alex, Andrea Ianni , Batanichek, Carlos Cinelli, Christophe D.,

DataTx, David Arenburg, David Robinson, dayne, Frank,
26 Data frames
Gregor, Hack-R, kaksat, R. Schifini, scoa, Sumedh, Thomas,
Tomás Barcellos, user2100721
akrun, Allen Wang, bartektartanus, cderv, David, David

Arenburg, Dean MacGregor, Eric Lecoutre, Frank, Jaap, jogo, L
27 data.table Co, leogama, Mallick Hossain, micstr, Nathan Werth, oshun,
Peter Humburg, Sowmya S. Manian, stanekam, Steve_Corrin,
Sumedh, Tensibai, user2100721, Uwe
AkselA, alistaire, Angelo, coatless, David Leal, Dean

28 Date and Time MacGregor, Frank, kneijenhuijs, MichaelChirico, scoa,
SymbolixAU, takje, theArun, thelatemail
Date-time classes
AkselA, alistaire, coatless, Frank, MichaelChirico, SymbolixAU,
29 (POSIXct and
thelatemail
POSIXlt)
30 Debugging James Elderfield, russellpierce
31 Distribution FisherDisinformation, Frank, L.V.Rao, tenCupMaximum
Functions
4444, Alihan Zıhna, ikashnitsky, Robert, skoh, Sumedh,

32 dplyr
theArun
Expression: parse +
33 YCR
eval
Extracting and
Listing Files in
34 catastrophic-failure, Jeff
Compressed
Archives
42-, Benjamin, dash2, Frank, Gavin Simpson, JulioSergio,

35 Factors kneijenhuijs, Nathan Werth, omar, Rich Scriven, Robert,
Steve_Corrin
Fault-
36 tolerant/resilient Rappster
code
Feature Selection in
37 R -- Removing Joy
Extraneous Features
38 Formula 42-, Axeman, Qaswed, Sathish
Fourier Series and

39 Hack-R
Transformations
Functional
40 Karolis Koncevičius
programming
Generalized linear
41 Ben Bolker, YCR
models
42 Get user input Ashish, DeveauP
akraf, Alex, alistaire, Andrea Cirillo, Artem Klevtsov, Axeman,

baptiste, blmoore, Boern, gitblame, ikashnitsky, Jaap, jmax, loki
43 ggplot2
, Matt, Mine Cetinkaya-Rundel, Paolo, smci, Steve_Corrin,
Sumedh, Taylor Ostberg, theArun, void, YCR, Yun Ching
GPU-accelerated
44 cdeterman
computing
45 Hashmaps nrussell, russellpierce
heatmap and
46 AndreyAkinshin, Nanami
heatmap.2
Hierarchical
47 Frank, G5W, Tal Galili
clustering with hclust
Hierarchical Linear
48 Ben Bolker
Modeling
I/O for database

49 Frank, JHowIX, SommerEngineering
tables
I/O for foreign tables 42-, Alex, alistaire, Andrea Cirillo, Carlos Cinelli, Charmgoggles
50 (Excel, SAS, SPSS, , Crops, Frank, Jaap, Jeromy Anglim, kaksat, Ken S.,
Stata) kitman0804, lmo, Miha, Parfait, polka, Thomas
I/O for geographic

51 data (shapefiles, Alex, Frank, ikashnitsky
etc.)
52 I/O for raster images Frank, loki
I/O for R's binary

53 Frank, ikashnitsky, Mario, russellpierce, zacdav, zx8754
format
Implement State
54 Machine Pattern David Leal
using S4 Class
55 Input and output Frank
56 Inspecting packages Frank, Sowmya S. Manian
Aaghaz Hussain, akraf, alko989, Andrew Brēza, Artem Klevtsov

, Arun Balakrishnan, Christophe D., CL., Frank, gitblame, Hack-
R, hongsy, Jaap, kaksat, kneijenhuijs, lmckeogh, loki, Marc
57 Installing packages
Brinkmann, Miha, Peter Humburg, Pragyaditya Das, Raj
Padmanabhan, seasmith, SymbolixAU, theArun, user890739,
xamgore, zx8754
Introduction to 4444, AkselA, alistaire, beetroot, Carson, Frank, Hack-R,

58
Geographical Maps HypnoGenX, Robert, russellpierce, SymbolixAU, symbolrush
59 Introspection Jason
60 JSON SymbolixAU
Amstell, Ben Bolker, Carl, Carlos Cinelli, David Robinson,

Linear Models
61 fortune_p, Frank, highBandWidth, ikashnitsky, jaySf, Robert,
(Regression)
russellpierce, thelatemail, USER_1, WAF
Andrea Ianni , BarkleyBG, dayne, Frank, Hack-R, Hairizuan

62 Lists
Noorazman, Peter Humburg, RamenChef
63 lubridate alistaire, Angelo, Frank, gitblame, Hendrik, scoa
64 Machine learning loki
65 Matrices dayne, Frank
Meta:
66 Documentation Frank, Gregor, Stephen Leppik, Steve_Corrin
Guidelines
Amit Kohli, Artem Klevtsov, Axeman, Eric Lecoutre, Frank,

67 Missing values Gregor, Jaap, kitman0804, lmo, seasmith, Steve_Corrin,
theArun, user2100721
Modifying strings by
68 Alex, David Leal, Frank
substitution
Natural language
69 CptNemo
processing
Network analysis
70 with the igraph Boysenb3rry
package
Non-standard
71 evaluation and PAC
standard evaluation
Numeric classes and

72 Frank, Steve_Corrin
storage modes
Object-Oriented
73 Jon Ericson, rcorty
Programming in R
74 Parallel processing Artem Klevtsov, jameselmore, K.Daisey, lmo, loki, russellpierce
Abdou, Alex, Artem Klevtsov, David Arenburg, David Leal,

Pattern Matching Frank, Gavin Simpson, Jaap, NWaters, R. Schifini,
75
and Replacement SommerEngineering, Steve_Corrin, Tensibai, thelatemail,
user2100721
Performing a
76 Stephen Leppik, tenCupMaximum
Permutation Test
42-, Alexandru Papiu, Alihan Zıhna, alistaire, AndreyAkinshin,

Artem Klevtsov, Atish, Axeman, Benjamin, Carlos Cinelli,
Pipe operators CMichael, DrPositron, Franck Dernoncourt, Frank, Gal Dreiman
77
(%>% and others) , Gavin Simpson, Gregor, ikashnitsky, James McCalden, Kay
Brodersen, Matt, polka, RamenChef, Ryan Hilbert, Sam Firke,
seasmith, Shawn Mehan, Simplans, Spacedman, SymbolixAU,
thelatemail, tomw, TriskalJM, user2100721
Pivot and unpivot

78 Sun Bee
with data.table
Probability
79 Pankaj Sharma
Distributions with R
80 Publishing Frank
R code vectorization
81 Axeman, David Arenburg, snaut
best practices
82 R in LaTeX with knitr JHowIX
R Markdown
83 Notebooks (from dmail
RStudio)
R memento by
84 Lovy
examples
Random Forest
85 G5W
Algorithm
Random Numbers bartektartanus, FisherDisinformation, Karolis Koncevičius, Miha

86
Generator , mnoronha
87 Randomization TARehman
Raster and Image

88 Frank, loki
Analysis
89 Rcpp Artem Klevtsov, coatless, Dirk Eddelbuettel
Reading and writing 42-, 4444, abhiieor, cdrini, dotancohen, Frank, Gregor, kdopen,
90
strings Rich Scriven, Thomas, Uwe
a.powell, Aaghaz Hussain, abhiieor, Alex, alistaire, Andrea

Cirillo, bartektartanus, Carl Witthoft, Carlos Cinelli, catastrophic-
failure, cdrini, Charmgoggles, Crops, DaveRGP, David
Reading and writing
Arenburg, Dawny33, Derwin McGeary, EDi, Eric Lecoutre,
tabular data in plain-
91 FoldedChromatin, Frank, Gavin Simpson, gitblame, Hairizuan
text files (CSV, TSV,
Noorazman, herbaman, ikashnitsky, Jaap, Jeromy Anglim,
etc.)
JHowIX, joeyreid, Jordan Kassof, K.Daisey, kitman0804,
kneijenhuijs, lmo, loki, Miha, PAC, polka, russellpierce, Sam
Firke, stats-hb, Thomas, Uwe, zacdav, zelite, zx8754
92 Recycling Frank, USER_1
Regular Expression
93 Alexey Shiklomanov
Syntax in R
Regular Expressions
94 42-, Benjamin, David Leal, etienne, Frank, MichaelChirico, PAC
(regex)
95 Reproducible R Charmgoggles, Frank, ikashnitsky
Charmgoggles, Frank, Jeromy Anglim, SymbolixAU,

96 Reshape using tidyr
user2100721
Reshaping data Charmgoggles, David Arenburg, demonplus, Frank, Jeromy

97 between long and Anglim, kneijenhuijs, lmo, Steve_Corrin, SymbolixAU, takje,
wide forms user2100721, zx8754
98 RESTful R Services YCR
RMarkdown and
99 Martin Schmelzer, YCR
knitr presentation
100 RODBC akrun, Hack-R, Parfait, Tim Coker
101 roxygen2 DeveauP, PAC
102 Run-length encoding Frank, josliber, Psidom
103 Scope of variables Artem Klevtsov, K.Daisey, RamenChef
104 Set operations DeveauP, FisherDisinformation, Frank
alistaire, CClaire, Christophe D., JvH, russellpierce,

105 Shiny
SymbolixAU, tuomastik, zx8754
106 Solving ODEs in R J_F
107 Spark API (SparkR) Maximilian Kohl
108 spatial analysis beetroot, ikashnitsky, loki, maRtin
Speeding up tough-
109 egnha, josliber
to-vectorize code
Eric Lecoutre, etienne, josliber, Sathish, Tensibai, thelatemail,

110 Split function
user2100721
111 sqldf Hack-R, Miha
Standardize
112 analyses by writing akraf, herbaman
standalone R scripts
String manipulation
113 bartektartanus, FisherDisinformation
with stringi package
114 strsplit function lmo
42-, Agriculturist, alexis_laz, alistaire, dayne, Frank, Gavin

115 Subsetting Simpson, Gregor, L.V.Rao, Mario, mrip, RamenChef, smci,
user2100721, zx8754
116 Survival analysis 42-, Axeman, Hack-R, Marcin Kosiński
117 Text mining Hack-R
118 The character class Frank, Steve_Corrin
alistaire, coatless, Frank, L.V.Rao, MichaelChirico,

119 The Date class
Steve_Corrin
120 The logical class 42-, Frank, Gregor, L.V.Rao, Steve_Corrin
David Robinson, egnha, Frank, ikashnitsky, RamenChef,

121 tidyverse
Sumedh
Time Series and Andras Deak, Andrew Bryk, coatless, Hack-R, JGreenwell,
122
Forecasting Pankaj Sharma, Steve_Corrin, μ Muthupandian
Updating R and the

123 Eric Lecoutre
package library
124 Updating R version dmail
Using pipe
assignment in your
125 RobertMc
own package %<>%:
How to ?
Using texreg to
126 export models in a Frank, ikashnitsky
paper-ready way
127 Variables 42-, Ale, Axeman, Craig Vermeer, Frank, L.V.Rao, lmckeogh
128 Web Crawling in R Pankaj Sharma
Web scraping and

129 alistaire, Dave2e
parsing
Writing functions in
130 AkselA, ikashnitsky, kaksat
R
131 xgboost Hack-R

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What are the main topics covered in the document?

What are the main topics covered in the document?

What is the *apply family of functions used for?

What is the *apply family of functions used for?

R Language

Chapter 1: Getting started with R Language 2

Editing R Docs on Stack Overflow 2

For OSX / macOS 3

For Debian, Ubuntu and derivatives 3

For Red Hat and Fedora 3

Interactive mode and R scripts 4

The interactive mode 4

The first plot 6

Chapter 2: *apply family of functions (functionals) 9

Members of the *apply Family 9

Use anonymous functions with apply 10

Bulk File Loading 11

Combining multiple `data.frames` (`lapply`, `mapply`) 11

Built-in functionals: lapply(), sapply(), and mapply() 13

Using user-defined functionals 14

.Rprofile - the first chunk of code executed 16

Setting your R home directory 16

Setting page size options 16

set the default help type 16

set a site library 16

Set a CRAN mirror 17

Setting the location of your library 17

Custom shortcuts or functions 17

Pre-loading the most useful packages 17

Chapter 4: Aggregating data frames 19

Aggregating with base R 19

Aggregating with dplyr 20

Aggregating with data.table 21

Chapter 5: Analyze tweets with R 23

Get text of tweets 24

Basic usage of aov() 25

Basic usage of Anova() 25

Chapter 7: Arima Models 27

Modeling an AR1 Process with Arima 27

Chapter 8: Arithmetic Operators 36

Range and addition 36

Addition and subtraction 37

Chapter 9: Bar Chart 40

Chapter 10: Base Plotting 48

Empirical Cumulative Distribution Function 63

Getting Started with R_Plots 64

Chapter 11: Bibliography in RMD 66

Specifying a bibliography and cite authors 67

Chapter 12: boxplot 71

Create a box-and-whisker plot with boxplot() {graphics} 71

Simple boxplot (Sepal.Length) 72

Boxplot of sepal length grouped by species 72

Change groups names 74

Proximity of the box 76

See the summaries which the boxplots are based plot=FALSE 76

Additional boxplot style parameters. 77

Chapter 14: Classes 82

Vectors and lists 83

Chapter 15: Cleaning data 85