What are the Best Machine Learning Packages in R?

The most common question asked by prospective data scientists is – “What is the best programming
language for Machine Learning?” The answer to this question always results in a debate whether to
choose R, Python or MATLAB for Machine Learning. Nobody can answer the question as to whether
Python or R is best language for Machine Learning. However, the programming language one should
choose for machine learning directly depends on the requirements of a given data problem, the likes
and preferences of the data scientist and the context of machine learning activities they want to
perform.

R is the preeminent choice among data professionals who want to understand and explore data, using
statistical methods and graphs. It has several machine learning packages and advanced
implementations for the top machine learning algorithms – which every data scientist must be familiar
with, to explore, model and prototype the given data. R is an open source language to which people
have contributed, from around the world. Starting from data collection and cleaning to reproducible
research – you will find a Black Box written by someone else, which you can directly use in your
program. This Black Box is known as Package in R. A Package in R is nothing but collection of pre-
written codes which can be reused.

As per CRAN there are around 8,341 packages that are currently available. Apart from CRAN, there
are other repositories which contribute multiple packages. The simple straightforward syntax to install
any of these machine learning packages is: install.packages (“Name_Of_R_Package”).

Few basic packages without which your life as a data scientist, will be tough
include dplyr, ggplot2, reshape2 etc. In this article we will be more focused on packages used in the
field of Machine Learning.

1. MICE Package – Takes care of your Missing Values

If missing values are something which haunts you then MICE package is the real friend of yours.

When we face an issue of missing values we generally go ahead with basic imputations such as
replacing with 0, replacing with mean, replacing with mode etc. but each of these methods are not
versatile and could result into a possible data discrepancy.

MICE package helps you to impute missing values by using multiple techniques, depending on the kind
of data you are working with.

Let’s take an example on using MICE Package.

dataset <- data.frame(var1=rnorm(20,0,1), var2=rnorm(20,5,1))

dataset[c(2,5,7,10),1] <- NA

dataset[c(4,8,19),2] <- NA

summary(dataset)
Till now we have created a random dataframe and introduced few missing values in the data
intentionally. Now it’s time to see MICE at work and forget the worry

install.pckages(“mice”)

require(mice)

dataset2 <- mice(dataset)

dataset2<-complete(dataset2)

summary(dataset2)

We have used the default parameters of MICE package for the example, but you can read and change
the parameters as per your requirements.

2. rpart package: Lets partition your data

(rpart) package in R language, is used to build classification or regression models using a two-stage
procedure and the resultant models is represented in the form of binary trees. The basic way to plot
any regression or classification tree using the rpart package is to call the plot() function. The results
might not be pretty by just using the basic plot() function, so there is an alternative i.e.
the prp() function which is powerful and flexible. prp() function in rpart.plot package is often referred
to as the authentic Swiss army knife for plotting regression trees.

rpart() function helps establish a relationship between a dependant and independent variables so that
a business can understand the variance in the dependant variables based on the independent
variables. For instance, if an eLearning company has to find out how their sales (dependant variables)
have been impacted due to promotions on Social Media, WOM, Newspapers, Referral Sites, etc.
then rpart package has several functions that can help with this analysis phenomenon.

rpart stands for Recursive Partitioning and Regression Trees. Using rpart you can run Regression as
well as classification. If we talk about syntax, it is pretty simple-

rpart(formula, data=, method=,control=)

o where formula contains the combination of dependent & independent variables; data is
the name of your dataset, method depends on the objective i.e. for classification tree, it
 will beclass; and control is specific to your requirement for example, we want a minimum
number variable to split a node etc.

Let’s consider iris dataset, which looks like -

Assuming our objective is to predict Species using a decision tree, it can be achieved by a simple line
of code

rpart_tree <- rpart(formula = Species~., data=iris, method = ‘class’)

summary(rpart_tree)

plot(rpart_tree)

Let see how does our built tree look like:

Here you can see the splits of different nodes and predicted class.

To predict for a new dataset, you have simple function predict(tree_name,new_data) which will give
you the predicted classes.

3. PARTY: Let’s again partition your data

PARTY package in R is used for recursive partitioning and this package reflects the continuous
development of ensemble methods.
PARTY is yet another package to build decision trees based on Conditional Inference
algorithm. ctree() is the main function of PARTY package which is used extensively, which reduces the
training time and bias.

Similar to other predictive analytics functions in R, PARTY also has similar syntax i.e.

ctree(formula,data)

which will build your decision tree, taking the default values of various arguments into consideration
which can be tweaked based on requirements.

Let’s build a tree using the same example discussed above.

party_tree <- ctree(formula=Species~. , data = iris)

plot(party_tree)

Let see how the built tree looks like -

In this package also you have a predict function which will be used to predict classes for the new data
coming in.

4. CARET: Classification And REgression Training

Classification and REgression Training (CARET) package is developed with the intent to combine model
training and prediction. Data scientists can run several different algorithms for a given business
problem using the CARET package. Data scientists might not be aware as to which is the best algorithm
for a given problem. CARET package helps investigate the optimal parameters for an algorithm with
controlled experiments. The grid search method of the caret R package searches parameters by
combining various methods to estimate the performance of a given model. After looking at all the trial
combinations, the grid search method finds the combination that gives best results.

Data scientists can streamline the prices of building predictive models with the help of specialized
inbuilt functions for data splitting, feature selection, data pre-processing, variable importance
estimation, model tuning through resampling and model visualizations.
CARET package is one of the best packages in R. The developers of this package understood that it is
hard to know about the best suited algorithm for the given problem case. There can be situations
where you are using a particular model and doubting your data but the problem lies in the algorithm
you have chosen.

After installing CARET package, you can run names(getModelInfo()) and see that there are 217
possible methods which can be run through a single package.

To build any predictive model, CARET uses train() function; The syntax of train function looks like –

train(formula, data, method)

Where method is the predictive model you are trying to build. Let’s use the iris dataset and fit a linear
regression model to predict Sepal.Length

Lm_model <- train(Sepal.Length~Sepal.Width + Petal.Length + Petal.Width, data=iris, method =

summary(lm_model)

CARET package is just not for building models but it also takes care of splitting your data into test and
train, do transformation etc.

In short, this is the GoTo package in R - for your all Predictive Modeling related needs.

5. randomForest: Let’s combine multiple trees to build our own forest

Random Forest algorithm is one of the most widely used algorithms when it comes to Machine
Learning. R package randomForest is used to create large number of decision trees and then each
observation is inputted into the decision tree. The common output obtained for maximum of the
observations is considered as the final output. When using randomForest algorithm, data
scientists/analysts have to ensure that the variables must be numeric or factors. Factors cannot have
more than 32 levels when implementing randomForest.
As you must be aware that Random Forest takes random samples of variables as well as observations
and build multiple trees. These multiple trees are then combined at the end & votes are taken to
finally predict the class of the response variable.

Let’s use the iris data example to build a Random Forest using randomForest package.

Rf_fit<-randomForest(formula=Species~., data=iris)

You run a line similar to other packages and your Random Forest is ready to be used. Let see how does
this built Forest performs.

print(Rf_fit)

importance(Rf_fit)

You might need to play with different control parameters in randomForest e.g., Number of variables
in each tree, No. of trees you want to build etc. Generally, data scientists run multiple iterations and
select the best combination.

6. nnet: It’s all about hidden layers

This is the most widely used and easy to understand neural network package, but it is limited to a
single layer of nodes. However, several studies have shown that more nodes are not required as they
do not contribute in enhancing the performance of the model but rather increase the calculation time
and complexity of the model.

This package does not provide any specific set of methods for finding the number of nodes in the
hidden layer. So, when big data professionals implement nnet it is always suggested that they set it to
a value that lies between the number of input and output nodes. nnet packages provides
implementation for Artificial Neural Networks algorithm which works - based on the understanding of
how a human brain functions, given the input and output signals. ANNs find great applications in
forecasting for airlines. In fact, neural network structures provide better forecasts using the nnet
functions than the traditional forecasting methods like exponential smoothing, regression, etc.

R has multiple packages for building neural networks e.g, nnet, neuralnet, RSNNS. Let’s use
our iris data example again (I know you are bored of iris). Let’s try to predict Species using
the nnet now and see how does it look -
nnet_model <- nnet(Species~., data=iris, size = 10)

You can observe 10 hidden layers in the Neural Network output - this is because we gave size=10 while
building the Neural Net.

Unfortunately, there is no direct way to plot the built neural networks but there are plenty of custom
functions contributed on GitHub which you can use.To build the above shown network we have used
- https://gist.githubusercontent.com/fawda123/7471137/raw/466c1474d0a505ff044412703516c34f
1a4684a5/nnet_plot_update.r

7. e1071: Let the vectors support your model

Wondering if this of junk value? Not at all! This is a very vital package in R language that has specialized
functions for implementing Naïve Bayes (conditional probability), SVM, Fourier Transforms, Bagged
Clustering, Fuzzy Clustering, etc. In fact, the first R interface for SVM implementation was in e1071 R
package - for instance, if a data scientist is trying to find out what is the probability that a person who
buys an iPhone 6S also buys an iPhone 6S Case.

This kind of analysis is based on conditional probability, so data scientists can make use of e1071 R
package which has specialized functions for implementing Naive Bayes Classifier.

Support Vector Machines are there to rescue you when you have a dataset which is not separable in
the given dimensions and you need to promote your data to higher dimensions in order to classify or
regress it.

Support Vector Machine a.k.a SVM uses Kernel Functions (To optimize mathematical operations) and
maximize the margin between two classes.

Similar to other functions discussed above, syntax for SVM is also similar:

svm_model <- svm(Species ~Sepal.Length + Sepal.Width, data=iris)

In order to visualize the classified SVM, we need to use plot() function with the data also

plot(svm_model, data = iris[,c(1,2,5)])

There are multiple parameters which you would have to change to get the best accuracy e.g, kernel,
cost, gamma, coefficients etc.

To get a bet classifier using SVM you will have to experiment with many of these factors, for example
kernel can take multiple values like – linear, Gaussian, Cosine etc.

8. kernLab: kernel trick packaged well

Kernlab takes advantage of the S4 object model in R language, so that data scientists can use kernel-
based machine learning algorithms. Kernlab has implementations for SVM, kernel feature analysis,
dot product primitives, ranking algorithm, Gaussian processes and a spectral clustering algorithm.
Kernel based machine learning methods are used when it is challenging to solve clustering,
classification and regression problems - in the space in which the observations are made.

Kernlab package is widely used in the implementation of SVM which eases pattern recognition to a
great extent. It has various kernel functions like – tanhdot (hyperbolic tangent kernel Function),
polydot (polynomial kernel function), laplacedot (laplacian kernel function) and many more to
perform pattern recognition.

Till now you might have understood the power of Kernel functions used in SVM. If Kernel functions
are not there, then SVM is not possible altogether.

SVM is not the only technique which uses Kernel Trick but there are plenty of other kernel-based
algorithms which are quite popular and useful, e.g., RVM, Kernel based PCA, Dimensionality reduction
etc.

kernLab package is a house to ~20 of such algorithms which work on the power of Kernels.

kernLab has its own predefined kernels but user has flexibility to build and use their own kernel
functions.

Let’s initialize our own Radial Basis Function with a sigma value of 0.01
 Myrbf <- rbfdot(sigma = 0.01)

Myrbf

If you want to see the class of Myrbf, you can do it by simply running class() function over the created
object

Every kernel object accepts two vectors and returns dot product of them. Let’s create two vectors and
see their dot products -

x<-rnorm(10)

y<-rnorm(10)

Myrbf(x,y)

Here we created two random normal variables x & y with 10 values each and computed their dot
product using Myrbf kernel.

Let’s see an example of SVM using Myrbf kernel

We’ll be using iris data again to understand the working of SVM using kernLab -

Kernlab_svm <- ksvm(Species ~ Sepal.Length + Sepal.Width, data = iris, kernel = Myrbf, C=4)

Kernlab_svm

Let’s use the built Support Vector Machine and see how did it predicted:

predited<-predict(Kernlab_svm,iris)

table(predicted = predicted, true = iris$Species)

Closing Note:

Every package or function in R has some default values associated with it, before applying any
algorithm you must know about the various options available. Passing default values will throw you
some result but you can’t be sure that the output is the most optimized or accurate one.

There are many other machine learning packages available in the CRAN repository like igraph,
glmnet, gbm, tree, CORElearn, mboost, etc. which are used in different industries to build
performance efficient models. We have observed the scenarios where changing just one parameter
can modify the output completely. So, don’t rely on default values of parameters – thoroughly
understand your data and problem requirements before applying any algorithm.