Hyfo PDF

Package ‘hyfo’
April 4, 2020
Type Package
Title Hydrology and Climate Forecasting
Version 1.4.2
Date 2020-4-3
Description Focuses on data processing and visualization in hydrology and
climate forecasting. Main function includes data extraction, data downscaling,
data resampling, gap filler of precipitation, bias correction of forecasting
data, flexible time series plot, and spatial map generation. It is a good pre-
processing and post-processing tool for hydrological and hydraulic modellers.
License GPL-2
Depends R (>= 3.1.0), stats (>= 3.1.3), utils(>= 3.1.3),
Imports ggplot2 (>= 1.0.1), reshape2 (>= 1.4.1), zoo (>= 1.7-12),
rgdal (>= 0.8-16), plyr (>= 1.8.3), moments (>= 0.14), lmom (>=
2.5), maps(>= 2.3-9), maptools (>= 0.8-36), rgeos (>= 0.3-8),
ncdf4 (>= 1.14.1), MASS (>= 7.3-39), methods, data.table
Suggests gridExtra, knitr, rmarkdown
VignetteBuilder knitr
LazyData true
URL https://yuanchao-xu.github.io/hyfo/
BugReports https://github.com/Yuanchao-Xu/hyfo/issues
Repository CRAN
RoxygenNote 7.1.0
NeedsCompilation no
Author Yuanchao Xu [aut, cre]
Maintainer Yuanchao Xu <[email protected]>
Date/Publication 2020-04-04 12:50:09 UTC
1
2 R topics documented:
R topics documented:
applyBiasFactor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
biasCorrect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
biasFactor-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
biasFactor.hyfo-class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
checkBind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
collectData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
collectData_csv_anarbe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
collectData_excel_anarbe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
collectData_txt_anarbe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
coord2cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
downscaleNcdf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
extractPeriod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
fillGap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
getAnnual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
getAnnual_dataframe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
getBiasFactor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
getEnsem_comb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
getFrcEnsem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
getHisEnsem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
getLMom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
getMeanPreci . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
getMoment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
getNcdfVar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
getPreciBar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
getPreciBar_comb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
getSpatialMap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
getSpatialMap_comb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
getSpatialMap_mat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
list2Dataframe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
loadNcdf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
monthlyPreci . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
plotTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
plotTS_comb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
resample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
shp2cat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
testCat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
testdl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
tgridData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
writeNcdf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Index 57
applyBiasFactor 3
applyBiasFactor Apply bias factor to different forecasts for multi/operational/real time

bias correction.
Description
When you do multi/operational/real time bias correction. It’s too expensive to input hindcast and
obs every time. Especially when you have a long period of hindcast and obs, but only a short period
of frc, it’s too unecessary to read and compute hindcast and obs everytime. Therefore, biasFactor
is designed. Using getBiasFactor, you can get the biasFactor with hindcast and observation, then
you can use applyBiasFactor to apply the biasFactor to different forecasts.
Usage
applyBiasFactor(frc, biasFactor, obs = NULL)
## S4 method for signature 'data.frame,biasFactor'

## S4 method for signature 'list,biasFactor.hyfo'

Arguments
frc a hyfo grid data output or a dataframe(time series) consists of Date column and
one or more value columns, representing the frc data. Check details for more
information.
biasFactor a file containing all the information of the calibration, will be applied to different
forecasts.
obs for some methods, observation input is necessary. obs is a hyfo grid data output
or a dataframe (time series) consists of Date column and one or more value
columns, representing the observation data. Default value is NULL.
Details
Information about the method and how biasCorrect works can be found in biasCorrect
why use biasFactor
As for forecasting, for daily data, there is usually no need to have different bias factor every different
day. You can calculate one bisa factor using a long period of hindcast and obs, and apply that factor
to different frc.
For example,
You have 10 years of hindcast and observation. you want to do bias correction for some forecasting
product, e.g. system 4. For system 4, each month, you will get a new forecast about the future 6
months. So if you want to do the real time bias correction, you have to take the 10 years of hindcast
and observation data with you, and run biasCorrect every time you get a new forecast. That’s too
expensive.
4 applyBiasFactor
For some practical use in forecasting, there isn’t a so high demand for accuracy. E.g., Maybe for
February and March, you can use the same biasFactor, no need to do the computation again.
It is a generic function, if in your case you need to debug, please see ?debug() for how to debug
S4 method.
Author(s)
Yuanchao Xu <[email protected] >
References
Bias correction methods come from biasCorrection from dowscaleR
• Santander Meteorology Group (2015). downscaleR: Climate data manipulation and statistical
downscaling. R package version 0.6-0. https://github.com/SantanderMetGroup/downscaleR/wiki
• R.A.I. Wilcke, T. Mendlik and A. Gobiet (2013) Multi-variable error correction of regional
climate models. Climatic Change, 120, 871-887
• A. Amengual, V. Homar, R. Romero, S. Alonso, and C. Ramis (2012) A Statistical Adjustment
of Regional Climate Model Outputs to Local Scales: Application to Platja de Palma, Spain. J.
Clim., 25, 939-957
• C. Piani, J. O. Haerter and E. Coppola (2009) Statistical bias correction for daily precipitation
in regional climate models over Europe, Theoretical and Applied Climatology, 99, 187-192
• O. Gutjahr and G. Heinemann (2013) Comparing precipitation bias correction methods for
high-resolution regional climate simulations using COSMO-CLM, Theoretical and Applied
Climatology, 114, 511-529
See Also
biasCorrect for method used in bias correction. getBiasFactor, for the first part.
Examples
######## hyfo grid file biascorrection

########
# If your input is obtained by \code{loadNcdf}, you can also directly biascorrect

# the file.
# First load ncdf file.

filePath <- system.file("extdata", "tnc.nc", package = "hyfo")
varname <- getNcdfVar(filePath)
nc <- loadNcdf(filePath, varname)
data(tgridData)
#' # Since the example data, has some NA values, the process will include some warning #message,
# which can be ignored in this case.
applyBiasFactor 5
# Then we will use nc data as forecasting data, and use itself as hindcast data,
# use tgridData as observation.
biasFactor <- getBiasFactor(nc, tgridData)

newFrc <- applyBiasFactor(nc, biasFactor)
biasFactor <- getBiasFactor(nc, tgridData, method = 'eqm', extrapolate = 'constant',

preci = TRUE)
# This method needs obs input.
newFrc <- applyBiasFactor(nc, biasFactor, obs = tgridData)
biasFactor <- getBiasFactor(nc, tgridData, method = 'gqm', preci = TRUE)

######## Time series biascorrection

########
# Use the time series from testdl as an example, we take frc, hindcast and obs from testdl.
data(testdl)
# common period has to be extracted in order to better train the forecast.
datalist <- extractPeriod(testdl, startDate = '1994-1-1', endDate = '1995-10-1')
frc <- datalist[[1]]

hindcast <- datalist[[2]]
obs <- datalist[[3]]
# The data used here is just for example, so there could be negative data.
# default method is scaling

biasFactor <- getBiasFactor(hindcast, obs)
frc_new <- applyBiasFactor(frc, biasFactor)
# for precipitation data, extra process needs to be executed, so you have to tell
# the program to it is a precipitation data.
biasFactor <- getBiasFactor(hindcast, obs, preci = TRUE)

frc_new1 <- applyBiasFactor(frc, biasFactor)
# You can use other methods to biascorrect, e.g. delta method.

biasFactor <- getBiasFactor(hindcast, obs, method = 'delta')
# delta method needs obs input.
frc_new2 <- applyBiasFactor(frc, biasFactor, obs = obs)
#
biasFactor <- getBiasFactor(hindcast, obs, method = 'eqm', preci = TRUE)
# eqm needs obs input
6 biasCorrect
biasFactor <- getBiasFactor(hindcast, obs, method = 'gqm', preci = TRUE)

plotTS(obs, frc, frc_new, frc_new1, frc_new2, frc_new3, frc_new4, plot = 'cum')
# You can also give name to this input list.

TSlist <- list(obs, frc, frc_new, frc_new1, frc_new2, frc_new3, frc_new4)
names(TSlist) <- c('obs', 'frc', 'delta', 'delta_preci', 'scale', 'eqm', 'gqm')
plotTS(list = TSlist, plot = 'cum')
# If the forecasts you extracted only has incontinuous data for certain months and years, e.g.,
# for seasonal forecasting, forecasts only provide 3-6 months data, so the case can be
# for example Dec, Jan and Feb of every year from year 1999-2005.
# In such case, you need to extract certain months and years from observed time series.
# extractPeriod() can be then used.
# More examples can be found in the user manual on https://yuanchao-xu.github.io/hyfo/
biasCorrect Biascorrect the input timeseries or hyfo dataset
Description
Biascorrect the input time series or dataset, the input time series or dataset should consist of obser-
vation, hindcast, and forecast. observation and hindcast should belong to the same period, in order
to calibrate. Then the modified forecast will be returned. If the input is a time series, first column
should be date column and rest columns should be the value column. If the input is a hyfo dataset,
the dataset should be the result of loadNcdf, or a list file with the same format.
Usage
biasCorrect(
frc,
hindcast,
obs,
method = "scaling",
scaleType = "multi",
preci = FALSE,
prThreshold = 0,
extrapolate = "no"
)
biasCorrect 7
## S4 method for signature 'data.frame,data.frame,data.frame'

biasCorrect(
frc,
hindcast,
obs,
method = "scaling",
preci = FALSE,
prThreshold = 0,
extrapolate = "no"
)
## S4 method for signature 'list,list,list'

biasCorrect(
frc,
hindcast,
obs,
method = "scaling",
preci = FALSE,
prThreshold = 0,
extrapolate = "no"
)
Arguments
frc a hyfo grid data output or a dataframe (time series) consists of Date column and
one or more value columns, representing the forecast to be calibrated.
hindcast a hyfo grid data output or a dataframe(time series) consists of Date column and
one or more value columns, representing the hindcast data. This data will be
used in the calibration of the forecast, so it’s better to have the same date period
as observation data. Check details for more information.
obs a hyfo grid data output or a dataframe (time series) consists of Date column and
one or more value columns, representing the observation data.
method bias correct method, including ’delta’, ’scaling’..., default is ’scaling’
scaleType only when the method "scaling" is chosen, scaleType will be available. Two
different types of scaling method, ’add’ and ’multi’, which means additive and
multiplicative scaling method. More info check details. Default scaleType is
’multi’.
preci If the precipitation is biascorrected, then you have to assign preci = TRUE. Since
for precipitation, some biascorrect methods may not apply to, or some methods
are specially for precipitation. Default is FALSE, refer to details.
prThreshold The minimum value that is considered as a non-zero precipitation. Default to 0
(assuming mm). If you want to use precipitation biascorrect, you should con-
sider carefully how to set this threshold, usually is 1. But you can try with
different numbers to see the results.
8 biasCorrect
extrapolate When use ’eqm’ method, and ’no’ is set, modified frc is bounded by the range of
obs. If ’constant’ is set, modified frc is not bounded by the range of obs. Default
is ’no’.
Details
Since climate forecast is based on global condition, when downscaling to different regions, it may
include some bias, biascorrection is used then to fix the bias.
Hindcast
In order to bias correct, we need to pick up some data from the forecast to train with the observation,
which is called hindcast in this function. Using hindcast and observation, the program can analyze
the bias and correct the bias in the forecast.
Hindcast should have EVERY attributes that forecast has.
Hindcast is also called re-forecast, is the forecast of the past. E.g. you have a forecast from year
2000-2010, assuming now you are in 2005. So from 2000-2005, this period is the hindcast period,
and 2005-2010, this period is the forecast period.
Hindcast can be the same as forecast, i.e., you can use forecast itself as hindcast to train the bias
correction.
How it works
Forecast product has to be calibrated, usually the system is doing forecast in real time. So, e.g., if the
forecast starts from year 2000, assuming you are in year 2003, then you will have 3 years’ hindcast
data (year 2000-2003), which can be used to calibrate. And your forecast period is (2003-2004)
E.g. you have observation from 2001-2002, this is your input obs. Then you can take the same
period (2001-2002) from the forecast, which is the hindcast period. For forecast, you can take any
period. The program will evaluate the obs and hindcast, to get the modification of the forecast, and
then add the modification to the forecast data.
The more categorized input, the more accurate result you will get. E.g., if you want to bias correct
a forecast for winter season. So you’d better to extract all the winter period in the hindcast and
observation to train. extractPeriod can be used for this purpose.
method
Different methods used in the bias correction. Among which, delta, scaling can be applied to
different kinds of parameters, with no need to set preci; eqm has two conditions for rainfall data
and other data, it needs user to input preci = TRUE/FALSE to point to different conditions; gqm is
designed for rainfall data, so preci = TRUE needs to be set.
delta
This method consists on adding to the observations the mean change signal (delta method). This
method is applicable to any kind of variable but it is preferable to avoid it for bounded variables
(e.g. precipitation, wind speed, etc.) because values out of the variable range could be obtained
(e.g. negative wind speeds...)
scaling
This method consists on scaling the simulation with the difference (additive) or quotient (multiplica-
tive) between the observed and simulated means in the train period. The additive or multiplicative
correction is defined by parameter scaling.type (default is additive). The additive version is
biasCorrect 9
preferably applicable to unbounded variables (e.g. temperature) and the multiplicative to variables
with a lower bound (e.g. precipitation, because it also preserves the frequency).
eqm
Empirical Quantile Mapping. This is a very extended bias correction method which consists on cal-
ibrating the simulated Cumulative Distribution Function (CDF) by adding to the observed quantiles
both the mean delta change and the individual delta changes in the corresponding quantiles. This
method is applicable to any kind of variable.
It can keep the extreme value, if you choose constant extrapolation method. But then you will face
the risk that the extreme value is an error.
gqm
Gamma Quantile Mapping. This method is described in Piani et al. 2010 and is applicable only
to precipitation. It is based on the initial assumption that both observed and simulated intensity
distributions are well approximated by the gamma distribution, therefore is a parametric q-q map
that uses the theorical instead of the empirical distribution.
It can somehow filter some extreme values caused by errors, while keep the extreme value. Seems
more reasonable. Better have a long period of training, and the if the forecast system is relatively
stable.
S4 method.
Author(s)
References
Clim., 25, 939-957
Examples

########
10 biasCorrect

# the file.

data(tgridData)
# Since the example data, has some NA values, the process will include some warning #message,
newFrc <- biasCorrect(nc, nc, tgridData)
newFrc <- biasCorrect(nc, nc, tgridData, scaleType = 'add')
newFrc <- biasCorrect(nc, nc, tgridData, method = 'eqm', extrapolate = 'constant',
preci = TRUE)
newFrc <- biasCorrect(nc, nc, tgridData, method = 'gqm', preci = TRUE)

########
data(testdl)

# default method is scaling, with 'multi' scaleType

frc_new <- biasCorrect(frc, hindcast, obs)
# the program that it is a precipitation data.
frc_new1 <- biasCorrect(frc, hindcast, obs, preci = TRUE)
# You can use other scaling methods to biascorrect.

frc_new2 <- biasCorrect(frc, hindcast, obs, scaleType = 'add')
biasFactor-class 11
#
frc_new3 <- biasCorrect(frc, hindcast, obs, method = 'eqm', preci = TRUE)
frc_new4 <- biasCorrect(frc, hindcast, obs, method = 'gqm', preci = TRUE)

biasFactor-class An S4 class, representing the biasFactor of single time series biasCor-

rection.
Description
An S4 class, representing the biasFactor of single time series biasCorrection.
Slots
biasFactor list of biasFactor, containing all the information for computing.
method the biascorrection method
preci if the data is precipitation
scaleType ’Valid when ’scaling’ method is selected, ’multi’ or ’add’.
extrapolate Valid when ’eqm’ method is selected, ’constant’ or ’no’
memberDim members contained.
prThreshold precipitation threshold, under which the precipitation is considered as 0.
12 checkBind
biasFactor.hyfo-class An S4 class, representing the biasFactor of hyfo file.
Description
An S4 class, representing the biasFactor of hyfo file.
Slots
lonLatDim lists of biasFactor
checkBind Check data for bind function.
Description
check if the data is available for rbind() or cbind()
Usage
checkBind(data, bind)
Arguments
data A list containing different sublists ready to be processed by do.call('rbind')
or do.call('cbind')
bind A string showing which bind you are going to use can be ’rbind’ or ’cbind’
Value
data can be processed by bind function; data cannot be processed by bind function
Examples
data <- list(c(1,1,1),c(2,2,2))
bind <- 'rbind'
checkBind(data,bind)
data(testdl)
## Not run:
checkBind(testdl, 'rbind')
## End(Not run)
# Since the colnames in testdl are not the same, so it cannot be bound.
#
collectData 13
collectData Collect data from different csv files.
Description
Collect data from different csv files.
Usage
collectData(folderName, fileType = NULL, range = NULL, sheetIndex = 1)
Arguments
folderName A string showing the path of the folder holding different csv files.
fileType A string showing the file type, e.g. "txt", "csv", "excel".
range A vector containing startRow, endRow, startColumn, endColumn, e.g., c(2,15,2,3)
sheetIndex A number showing the sheetIndex in the excel file, if fileType is excel, sheetIndex
has to be provided, default is 1.
Value
The collected data from different files in the folder.
Examples
#use internal data as an example.

folder <- file.path(path.package("hyfo"), 'extdata')
# file may vary with different environment, it if doesn't work, use local way to get
# folder path.
a <- collectData(folder, fileType = 'csv', range = c(10, 20, 1,2))
collectData_csv_anarbe
Collect data from csv for Anarbe case.
Description
Collect data from the gauging stations in spain, catchement Anarbe
14 collectData_excel_anarbe
Usage
collectData_csv_anarbe(folderName, output = TRUE)
Arguments
folderName A string showing the path of the folder holding different csv files.
output A boolean showing whether the output is given, default is T.
Value
The collected data from different csv files.
Source
http://meteo.navarra.es/estaciones/mapadeestaciones.cfm
References
• http://meteo.navarra.es/estaciones/mapadeestaciones.cfm
• R Core Team (2015). R: A language and environment for statistical computing. R Foundation
for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
Examples

file <- system.file("extdata", "1999.csv", package = "hyfo")
folder <- strsplit(file, '1999')[[1]][1]
a <- collectData_csv_anarbe(folder)
collectData_excel_anarbe
Collect data from different excel files
Description
Collect data from different excel files
Usage
collectData_excel_anarbe(folderName, keyword = NULL, output = TRUE)
collectData_txt_anarbe 15
Arguments
folderName A string showing the folder path.
keyword A string showing the extracted column, e.g., waterLevel, waterBalance.
output A boolean showing whether the output is given.
Value
The collected data from different excel files.
References
for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.
collectData_txt_anarbe
collect data from different txt.
Description
collect data from different txt.
Usage
collectData_txt_anarbe(
folderName,
output = TRUE,
rangeWord = c("Ene ", -1, "Total ", -6)
)
Arguments
folderName A string showing the folder path.
output A boolean showing whether the result is given.
rangeWord A list containing the keyword and the shift. defaut is set to be used in spain
gauging station.
Value
The collected data from different txt files.
Source
http://www4.gipuzkoa.net/oohh/web/esp/02.asp
16 coord2cell
References
• http://www4.gipuzkoa.net/oohh/web/esp/02.asp
Examples
## Not run:
file <- system.file("extdata", "1999.csv", package = "hyfo")
folder <- strsplit(file, '1999')[[1]][1]
a <- collectData_txt_anarbe(folder)
## End(Not run)
coord2cell Change lon lat coordinates to cell coordinates
Description
Change lon lat coordinates to cell coordinates
Usage
coord2cell(coord, lon, lat)
Arguments
coord input lon lat coordinate

lon dataset lon array
lat dataset lat array
Value
A cell coordinate
downscaleNcdf 17
downscaleNcdf Downscale NetCDF file
Description
Downscale NetCDF file
Usage
downscaleNcdf(gridData, year = NULL, month = NULL, lon = NULL, lat = NULL)
Arguments
gridData A hyfo list file from loadNcdf
year A vector of the target year. e.g. year = 2000, year = 1980:2000
month A vector of the target month. e.g. month = 2, month = 3:12
lon A vector of the range of the downscaled longitude, should contain a max value
and a min value. e.g. lon = c(-1.5,2,5)
lat A vector of the range of the downscaled latitude, should contain a max value
and a min value. e.g. lat = c(32,2,36)
Value
A downscaled hyfo list file.
References
• Santander MetGroup (2015). ecomsUDG.Raccess: R interface to the ECOMS User Data
Gateway. R package version 2.2-6. http://meteo.unican.es/ecoms-udg
Examples
# First open the test NETcDF file.
# Then if you don't know the variable name, you can use \code{getNcdfVar} to get variable name
# Then write to your work directory
nc1 <- downscaleNcdf(nc, year = 2006, lon = c(-2, -0.5), lat = c(43.2, 43.7))
nc2 <- downscaleNcdf(nc, year = 2005, month = 3:8, lon = c(-2, -0.5), lat = c(43.2, 43.7))

18 extractPeriod
extractPeriod Extract period from list or dataframe.
Description
Extract common period or certain period from a list of different dataframes of time series, or from
a dataframe. NOTE: all the dates in the datalist should follow the format in ?as.Datebase.
Usage
extractPeriod(
data,
startDate = NULL,
endDate = NULL,
commonPeriod = FALSE,
year = NULL,
month = NULL
)
## S4 method for signature 'data.frame'

extractPeriod(
data,
startDate = NULL,
endDate = NULL,
year = NULL,
month = NULL
)
## S4 method for signature 'list'

extractPeriod(
data,
startDate = NULL,
endDate = NULL,
year = NULL,
month = NULL
)
Arguments
data A list of different dataframes of time series, or a dataframe with first column
Date, the rest columns value.
startDate A Date showing the start of the extract period, default as NULL, check details.
endDate A Date showing the end of the extract period, default as NULL, check details.
extractPeriod 19
commonPeriod A boolean showing whether the common period is extracted. If chosen, start-
Date and endDate should be NULL.
year extract certain year in the entire time series. if you want to extract year 2000, set
year = 2000
month extract certain months in a year. e.g. if you want to extract Jan, Feb of each year,
set month = c(1,2).
Details
startDate and endDate
If startDate and endDate are assigned, then certain period between startDate and endDate will be
returned, for both datalist input and dataframe input.
If startDate and endDate are NOT assigned, then,
if input is a datalist, the startDate and endDate of the common period of different datalists will be
assigned to the startDate and endDate.
if input is a dataframe, the startDate and endDate of the input dataframe will be assigned to the
startDate and endDate . Since different value columns share a common Date column in a dataframe
input.
year and month
For year crossing month input, hyfo will take from the year before. E.g. if month = c(10,11,12,1),
and year = 1999, hyfo will take month 10, 11 and 12 from year 1998, and month 1 from 1999.You
DO NOT have to set year = 1998 : 1999.
Well, if you set year = 1998 : 1999, hyfo will take month 10, 11 and 12 from year 1997, and month
1 from 1998, then, take month 10, 11 and 12 from year 1998, month 1 from 1999. So you only have
to care about the latter year.
S4 method.
Value
A list or a dataframe with all the time series inside containing the same period.
References
• Achim Zeileis and Gabor Grothendieck (2005). zoo: S3 Infrastructure for Regular and Irregu-
lar Time Series. Journal of Statistical Software, 14(6), 1-27. URL https://www.jstatsoft.org/v14/i06/
Examples
# Generate timeseries datalist. Each data frame consists of a Date and a value.
AAA <- data.frame(

# date column
Date = seq(as.Date('1990-10-28'),as.Date('1997-4-1'),1),
# value column
AAA = sample(1:100,length(seq(as.Date('1990-10-28'),as.Date('1997-4-1'),1)), repl = TRUE))
20 fillGap
BBB <- data.frame(

BBB = sample(1:100,length(seq(as.Date('1993-3-28'),as.Date('1999-1-1'),1)), repl = TRUE))
CCC <- data.frame(

CCC = sample(1:100,length(seq(as.Date('1988-2-2'),as.Date('1996-1-1'),1)), repl = TRUE))
list <- list(AAA, BBB, CCC)# dput() and dget() can be used to save and load list file.
list_com <- extractPeriod(list, commonPeriod = TRUE)
# list_com is the extracted datalist.

str(list_com)
# If startDate and endDate is provided, the record between them will be extracted.
# make sure startDate is later than any startDate in each dataframe and endDate is
# earlier than any endDate in each dataframe.
data(testdl)
datalist_com1 <- extractPeriod(testdl, startDate = '1994-1-1', endDate = '1995-10-1')
dataframe <- list2Dataframe(datalist_com1)

# now we have a dataframe to extract certain months and years.
dataframe_new <- extractPeriod(dataframe, month = c(1,2,3))
dataframe_new <- extractPeriod(dataframe, month = c(12,1,2), year = 1995)
fillGap Fill gaps in the rainfall time series.
Description
Fill gaps in the rainfall time series.
Usage
fillGap(dataset, corPeriod = "daily")
Arguments
dataset A dataframe with first column the time, the rest columns are rainfall data of
different gauges
corPeriod A string showing the period used in the correlation computing, e.g. daily, monthly,
yearly.
fillGap 21
Details
the gap filler follows the rules below:
1. The correlation coefficient of every two columns (except time column) is calculated. the corre-
lation coefficient calculation can be based on ’daily’, ’monthly’, ’annual’, in each case, the daily
data, the monthly mean daily data and annual mean daily data of each column will be taken in the
correlation calculation.
Then the correlation matrix is got, then based on the matrix, for each column, the 1st, 2nd, 3rd,...
correlated column will be got. So if there is missing value in the column, it will get data from
orderly 1st, 2nd, 3rd column.
2. The simple linear regress is calculated between every two columns. When generating the linear
coefficient, the incept should be force to 0. i.e. y = a*x + b should be forec to y = a*x.
3. Gap filling. E.g., on a certain date, there is a missing value in column A, then the correlation
order is column B, column C, column D, which means A should take values from B firstly, if B is
also missing data, then C, then D.
Assuming finally value from column C is taken. Then according to step 2, A = a*C, then the final
value filled in column A is missing_in_A = a*value_in_C, a is the linear coeffcient.
Value
The filled dataframe
References
Gap fiiling method based on correlation and linear regression.
• Hirsch, Robert M., et al. "Statistical analysis of hydrologic data." Handbook of hydrology.
(1992): 17-1. Salas, Jose D. "Analysis and modeling of hydrologic time series." Handbook of
hydrology 19 (1993): 1-72.
Examples
b <- read.table(text = ' Date AAA BBB CCC DDD EEE
49 1999-12-15 24.8 21.4 25.6 35.0 17.4
50 1999-12-16 NA 0.6 1.5 6.3 2.5
51 1999-12-17 NA 16.3 20.3 NA 19.2
52 1999-12-18 13 1.6 NA 6.3 0.0
53 1999-12-19 10 36.4 12.5 26.8 24.9
54 1999-12-20 NA 0.0 0.0 0.2 0.0
55 1999-12-21 0.2 0.0 0.0 0.0 0.0
56 1999-12-22 0.0 0.0 0.0 0.0 0.0')
b1 <- fillGap(b) # if corPeriod is missing, 'daily' is taken as default.
data(testdl)
a <- extractPeriod(testdl, commonPeriod = TRUE)
a1 <- list2Dataframe(a)
a2 <- fillGap(a1)
a3 <- fillGap(a1, corPeriod = 'monthly')
22 getAnnual
getAnnual Get annual rainfall of different rainfall time series
Description
Get annual rainfall of different raninfall time series.
Usage
getAnnual(data, output = "series", minRecords = 355, ...)


Arguments
data A list containing different time series of different rainfall gauges. Or a dataframe
with first column Date and the rest columns the value of different gauging sta-
tions. Usually an output of list2Dataframe.
output A string showing the output output.
minRecords A number showing the minimum accept record number, e.g. for a normal
year(365 days), if minRecords = 360, it means if a year has less than 360 records
of a year, it will be ignored in the mean annual value calculation. Only valid
when output = "mean", default is 355.
... title,x,y showing the title and x and y axis of the plot. e.g. title = 'aaa'
Details
S4 method.
Value
The annual rainfall and the number of missing data of each year and each rainfall gauge, which will
also be plotted. If output "mean" is seleted, the mean annual rainfall will be returned.
getAnnual_dataframe 23
References
• H. Wickham. ggplot2: elegant graphics for data analysis. Springer New York, 2009.
• Hadley Wickham (2007). Reshaping Data with the reshape Package. Journal of Statistical
Software, 21(12), 1-20. URL http://www.jstatsoft.org/v21/i12/.
Examples
#datalist is provided by the package as a test.
data(testdl)
a <- getAnnual(testdl)
#set minRecords to control the calculation of annual rainfall.
b <- getAnnual(testdl, output = 'mean', minRecords = 350)
c <- getAnnual(testdl, output = 'mean', minRecords = 365)
a1 <- extractPeriod(testdl, comm = TRUE)

a2 <- list2Dataframe(a1)
getAnnual(a2)
a3 <- fillGap(a2)
getAnnual(a3)
getAnnual_dataframe Get annual rainfall of the input time series.
Description
Get annual rainfall of the input time series.
Usage
getAnnual_dataframe(dataset)
Arguments
dataset A dataframe containing one time series, e.g., rainfall from one gauging station.
the time should follow the format : "1990-1-1"
Value
The annual rainfall of each year of the input station.
24 getBiasFactor
getBiasFactor Get bias factor for multi/operational/real time bias correction.
Description
When you do multi/operational/real time bias correction. It’s too expensive to input hindcast and
obs every time. Especially when you have a long period of hindcast and obs, but only a short period
of frc, it’s too unecessary to read and compute hindcast and obs everytime. Therefore, biasFactor
is designed. Using getBiasFactor, you can get the biasFactor with hindcast and observation, then
you can use applyBiasFactor to apply the biasFactor to different forecasts.
Usage
getBiasFactor(
hindcast,
obs,
method = "scaling",
preci = FALSE,
prThreshold = 0,
extrapolate = "no"
)
## S4 method for signature 'data.frame,data.frame'

getBiasFactor(
hindcast,
obs,
method = "scaling",
preci = FALSE,
prThreshold = 0,
extrapolate = "no"
)
## S4 method for signature 'list,list'

getBiasFactor(
hindcast,
obs,
method = "scaling",
preci = FALSE,
prThreshold = 0,
extrapolate = "no"
)
getBiasFactor 25
Arguments
hindcast a hyfo grid data output or a dataframe(time series) consists of Date column and
one or more value columns, representing the hindcast data. This data will be
used in the calibration of the forecast, so it’s better to have the same date period
as observation data. Check details for more information.
obs a hyfo grid data output or a dataframe (time series) consists of Date column and
one or more value columns, representing the observation data.
method bias correct method, including ’delta’, ’scaling’...,default method is ’scaling’.
scaleType only when the method "scaling" is chosen, scaleType will be available. Two
different types of scaling method, ’add’ and ’multi’, which means additive and
multiplicative scaling method, default is ’multi’. More info check details.
preci If the precipitation is biascorrected, then you have to assign preci = TRUE. Since
for precipitation, some biascorrect methods may not apply to, or some methods
are specially for precipitation. Default is FALSE, refer to details.
prThreshold The minimum value that is considered as a non-zero precipitation. Default to 1
(assuming mm).
extrapolate When use ’eqm’ method, and ’no’ is set, modified frc is bounded by the range of
obs. If ’constant’ is set, modified frc is not bounded by the range of obs. Default
is ’no’.
Details
Information about the method and how biasCorrect works can be found in biasCorrect
why use biasFactor
As for forecasting, for daily data, there is usually no need to have different bias factor every different
day. You can calculate one bisa factor using a long period of hindcast and obs, and apply that factor
to different frc.
For example,
You have 10 years of hindcast and observation. you want to do bias correction for some forecasting
product, e.g. system 4. For system 4, each month, you will get a new forecast about the future 6
months. So if you want to do the real time bias correction, you have to take the 10 years of hindcast
and observation data with you, and run biasCorrect every time you get a new forecast. That’s too
expensive.
For some practical use in forecasting, there isn’t a so high demand for accuracy. E.g., Maybe for
February and March, you can use the same biasFactor, no need to do the computation again.
S4 method.
Author(s)

26 getBiasFactor
References
Clim., 25, 939-957
See Also
biasCorrect for method used in bias correction. applyBiasFactor, for the second part.
Examples

########

# the file.

data(tgridData)
# Since the example data, has some NA values, the process will include some warning #message,
biasFactor <- getBiasFactor(nc, tgridData)

biasFactor <- getBiasFactor(nc, tgridData, method = 'eqm', extrapolate = 'constant',

preci = TRUE)
# This method needs obs input.
newFrc <- applyBiasFactor(nc, biasFactor, obs = tgridData)
getBiasFactor 27
biasFactor <- getBiasFactor(nc, tgridData, method = 'gqm', preci = TRUE)


########
data(testdl)

# default method is scaling

biasFactor <- getBiasFactor(hindcast, obs)
frc_new <- applyBiasFactor(frc, biasFactor)
# the program to it is a precipitation data.
biasFactor <- getBiasFactor(hindcast, obs, preci = TRUE)

# You can use other methods to biascorrect, e.g. delta method.

biasFactor <- getBiasFactor(hindcast, obs, method = 'delta')
# delta method needs obs input.
#
biasFactor <- getBiasFactor(hindcast, obs, method = 'eqm', preci = TRUE)
# eqm needs obs input
biasFactor <- getBiasFactor(hindcast, obs, method = 'gqm', preci = TRUE)


28 getEnsem_comb
getEnsem_comb Combine ensembles together
Description
Combine ensembles together
Usage
getEnsem_comb(
...,
list = NULL,
nrow = 1,
legend = TRUE,
x = "",
y = "",
title = "",
output = FALSE
)
Arguments
... different ensembles generated by getHisEnsem(,output = 'ggplot') or getFrcEnsem(,output
= 'ggplot'), see details.
list If input is a list containing different ggplot data, use list = inputlist.
nrow A number showing the number of rows.
legend A boolean representing whether you want the legend. Sometimes when you
combine plots, there will be a lot of legends, if you don’t like it, you can turn it
off by setting legend = FALSE, default is TRUE.
x A string of x axis name.
y A string of y axis name.
title A string of the title.
output A boolean, if chosen TRUE, the output will be given.
getFrcEnsem 29
Value
A combined ensemble plot.
References
Examples
data(testdl)
a <- testdl[[1]]
# Choose example from "1994-2-4" to "1996-1-4"
b1<- getHisEnsem(a, example = c('1995-2-4', '1996-1-4'), plot = 'cum', output = 'ggplot',

name = 1)
b2 <- getHisEnsem(a, example = c('1995-4-4', '1996-3-4'), plot = 'cum', output = 'ggplot',

name = 2)
getEnsem_comb(b1, b2)
getEnsem_comb(list = list(b1, b2), nrow = 2)
getFrcEnsem Extract time series from forecasting data.
Description
getFrcEnsem extract timeseries from forecasting data, if forecasting data has a member session an
ensemble time sereis will be returned, if forecasting data doesn’t have a member session, a singe
time series will be returned.
Usage
getFrcEnsem(
dataset,
cell = "mean",
plot = "norm",
output = "data",
30 getFrcEnsem
name = NULL,
mv = 0,
coord = NULL,
...
)
Arguments
dataset A list containing different information, should be the result of loadNcdf
cell A vector containing the locaton of the cell, e.g. c(2, 3), default is "mean", rep-
resenting the spatially averaged value. Check details for more information.
plot A string showing whether the plot will be shown, e.g., ’norm’ means normal
plot (without any process), ’cum’ means cummulative plot, default is ’norm’.
For other words there will be no plot.
output A string showing which type of output you want. Default is "data", if "ggplot",
the data that can be directly plotted by ggplot2 will be returned, which is eas-
ier for you to make series plots afterwards. NOTE: If output = 'ggplot', the
missing value in the data will be replaced by mv, if assigned, default mv is 0.
name If output = 'ggplot', name has to be assigned to your output, in order to dif-
ferentiate different outputs in the later multiplot using getEnsem_comb.
mv A number showing representing the missing value. When calculating the cumu-
lative value, missing value will be replaced by mv, default is 0.
coord A coordinate of longitude and latitude. e.g. corrd = c(lon, lat). If coord is
assigned, cell argument will no longer be used.
Details
cell representing the location of the cell, NOTE: this location means the index of the cell, IT IS
NOT THE LONGITUDE AND LATITUDE. e.g., cell = c(2,3), the program will take the 2nd
longitude and 3rd latitude, by the increasing order. Longitude comes first.
name Assuming you have two ggplot outputs, you want to plot them together. In this situation, you
need a name column to differentiate one ggplot output from the other. You can assigne this name by
the argument directly, If name is not assigned and output = 'ggplot' is selected, then the system
time will be selected as name column.
Value
A ensemble time series extracted from forecating data.
References
getHisEnsem 31
Examples

a <- getFrcEnsem(nc)
# If there is no member session in the dataset, a single time sereis will be extracted.
a1 <- getFrcEnsem(tgridData)
# The default output is spatially averaged, if there are more than one cells in the dataset,
# the mean value of the cells will be calculated. While if you are interested in special cell,
# you can assign the cell value. You can also directly use longitude and latitude to extract
# time series.
getSpatialMap(nc, 'mean')
a <- getFrcEnsem(nc, cell = c(6,2))
# From the map, cell = c(6, 2) means lon = -1.4, lat = 43.2, so you can use corrd to locate
# your research area and extract time series.
b <- getFrcEnsem(nc, coord = c(-1.4, 43.2))
getHisEnsem Get ensemble forecast from historical data.
Description
getHisEnsem use historical data as the forecasting input time series.
Usage
getHisEnsem(
TS,
example,
interval = 365,
buffer = 0,
plot = "norm",
output = "data",
name = NULL,
mv = 0,
...
)
32 getHisEnsem
Arguments
TS A time series dataframe, with first column Date, and second column value.
example A vector containing two strings showing the start and end date, which represent
the forecasting period. Check details for more information.
the program will extract every possible period in TS you provided to generate
the ensemble. Check details for more information.
interval A number representing the interval of each ensemble member. NOTE: "interval"
takes 365 as a year, and 30 as a month, regardless of leap year and months with
31 days. So if you want the interval to be 2 years, set interval = 730, which
equals 2 * 365 ; if two months, set interval = 60; 2 days, interval = 2, for
other numbers that cannot be divided by 365 or 30 without remainder, it will
treat the number as days.By defualt interval is set to be 365, a year.
buffer A number showing how many days are used as buffer period for models. Check
details for more information.
plot A string showing whether the plot will be shown, e.g., ’norm’ means normal
plot (without any process), ’cum’ means cummulative plot, default is ’norm’.
For other words there will be no plot.
the data that can be directly plotted by ggplot2 will be returned, which is eas-
ier for you to make series plots afterwards. NOTE: If output = 'ggplot', the
missing value in the data will be replaced by mv, if assigned, default mv is 0.
ferentiate different outputs in the later multiplot using getEnsem_comb.
mv A number showing representing the missing value. When calculating the cumu-
lative value, missing value will be replaced by mv, default is 0.
Details
example E.g., if you have a time series from 2000 to 2010. Assuming you are in 2003, you want to
forecast the period from 2003-2-1 to 2003-4-1. Then for each year in your input time series, every
year from 1st Feb to 1st Apr will be extracted to generate the ensemble forecasts. In this case your
input example should be example = c('2003-2-1','2003-4-1')
interval doesn’t care about leap year and the months with 31 days, it will take 365 as a year, and
30 as a month. e.g., if the interval is from 1999-2-1 to 1999-3-1, you should just set interval to 30,
although the real interval is 28 days.
example and interval controls how the ensemble will be generated. e.g. if the time series is from
1990-1-1 to 2001-1-1.
if example = c('1992-3-1','1994-1-1') and interval = 1095, note, 1095 = 365 * 3, so the
program treat this as 3 years.
Then you are supposed to get the ensemble consisting of following part:
1. 1992-3-1 to 1994-1-1 first one is the example, and it’s NOT start from 1990-3-1. 2. 1995-3-1 to
1997-1-1 second one starts from 1993, because "interval" is 3 years. 3. 1998-3-1 to 2000-1-1
getHisEnsem 33
because the last one "2000-3-1 to 2002-1-1", 2002 exceeds the original TS range, so it will not be
included.
Sometimes, there are leap years and months with 31 days included in some ensemble part, in which
case the length of the data will be different, e.g., 1999-1-1 to 1999-3-1 is 1 day less than 2000-1-1
to 2000-3-1. In this situation, the data will use example as a standard. If the example is 1999-1-1 to
1999-3-1, then the latter one will be changed to 2001-1-1 to 2000-2-29, which keeps the start Date
and change the end Date.
If the end date is so important that cannot be changed, try to solve this problem by resetting the
example period, to make the event included in the example.
Good set of example and interval can generate good ensemble.
buffer Sometimes the model needs to run for a few days to warm up, before the forecast. E.g., if a
forecast starts at ’1990-1-20’, for some model like MIKE NAM model, the run needs to be started
about 14 days. So the input timeseries should start from ’1990-1-6’.
Buffer is mainly used for the model hotstart. Sometimes the hot start file cannot contain all the
parameters needed, only some important parameters. In this case, the model needs to run for some
time, to make other parameters ready for the simulation.
name Assuming you have two ggplot outputs, you want to plot them together. In this situation, you
need a name column to differentiate one ggplot output from the other. You can assigne this name
by the argument directly, name has to be assigned if output = 'ggplot' is selected,
Value
A ensemble time series using historical data as forecast.
References
Examples
data(testdl)
a <- testdl[[1]]
# Choose example from "1994-2-4" to "1996-1-4"

b <- getHisEnsem(a, example = c('1994-2-4', '1996-1-4'))
# Default interval is one year, can be set to other values, check help for information.
# Take 7 months as interval

b <- getHisEnsem(a, example = c('1994-2-4', '1996-1-4'), interval = 210, plot = 'cum')
# Take 30 days as buffer
b <- getHisEnsem(a, example = c('1994-2-4', '1996-1-4'), interval = 210, buffer = 30)
34 getLMom
getLMom get L moment analysis of the input distribution
Description
get L moment analysis of the input distribution
Usage
getLMom(dis)
Arguments
dis A distribution, for hydrology usually a time series with only data column without
time.
Value
The mean, L-variation, L-skewness and L-kurtosis of the input distribution
References
• J. R. M. Hosking (2015). L-moments. R package, version 2.5. URL: https://CRAN.R-

project.org/package=lmom.
Examples
dis <- seq(1, 100)

getLMom(dis)

getMeanPreci 35
getMeanPreci Get mean rainfall data.
Description
Get mean rainfall data, e.g. mean annual rainfall, mean monthly rainfall and mean winter rainfall.
Usage
getMeanPreci(
inputTS,
method = NULL,
yearIndex = NULL,
monthIndex = NULL,
fullResults = FALSE,
omitNA = TRUE,
plot = FALSE,
...
)
Arguments
inputTS A time series with only data column (1 column).
method A string showing the method used to calculate mean value, e.g., "annual". more
information please refer to details.
yearIndex A NUMERIC ARRAY showing the year index of the time series.
monthIndex A NUMERIC ARRAY showing the month index of the time series.
fullResults A boolean showing whether the full results are shown, default is FALSE. If
FALSE, only mean value will be returned, if TRUE, the sequence of values will
be returned.
omitNA A boolean showing in the calculation, whether NA is omitted, default is FALSE.
plot A boolean showing whether the results will be plotted.
..., title,x,y showing the title and x and y axis of the plot, shoud be a string.
Details
There are following methods to be selected, "annual": annual rainfall of each year is plotted. "win-
ter", "spring", "autumn", "summer": seasonal rainfall of each year is plotted. Month(number 1 to
12): month rainfall of each year is plotted, e.g. march rainfall of each year. "meanMonthly": the
mean monthly rainfall of each month over the whole period.
Since "winter" is a crossing year, 12, 1, 2, 12 is in former year, and 1, 2 are in latter year. so winter
belongs to the latter year.
Value
The mean value of the input time series or the full results before calculating mean.
36 getNcdfVar
getMoment get moment analysis of the input distribution
Description
get moment analysis of the input distribution
Usage
getMoment(dis)
Arguments
dis A distribution, for hydrology usually a time series with only data column without
time.
Value
The mean, variation, skewness and kurtosis of the input distribution
References
• Lukasz Komsta and Frederick Novomestky (2015). moments: Moments, cumulants, skew-
ness, kurtosis and related tests. R package version 0.14. https://CRAN.R-project.org/package=moments
Examples
dis <- seq(1, 100)
getMoment(dis)
getNcdfVar Get variable name of the NetCDF file.
Description
Get variable name in the NetCDF file. After knowning the name, you can use loadNcdf to load the
target variable.
Usage
getNcdfVar(filePath)
getPreciBar 37
Arguments
filePath A path pointing to the netCDF file.
Value
The names of the varialbes in the file.
References
• David Pierce (2015). ncdf4: Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files. R package version 1.14.1. https://CRAN.R-project.org/package=ncdf4
Examples
getPreciBar get mean rainfall bar plot of the input dataset or time series.
Description
get mean rainfall bar plot of the input dataset or time series.
Usage
getPreciBar(
data,
method,
cell = "mean",
output = "data",
name = NULL,
plotRange = TRUE,
member = NULL,
omitNA = TRUE,
info = FALSE,
...
)

getPreciBar(
data,
38 getPreciBar
method,
cell = "mean",
output = "data",
name = NULL,
plotRange = TRUE,
member = NULL,
omitNA = TRUE,
info = FALSE,
...
)

getPreciBar(
data,
method,
cell = "mean",
output = "data",
name = NULL,
plotRange = TRUE,
member = NULL,
omitNA = TRUE,
info = FALSE,
...
)
Arguments
data A list containing different information, should be the result of reading netcdf file
using loadNcdf, or a time series, with first column the Date, second the value.
Time series can be an ENSEMBLE containning different members. Than the
mean value will be given and the range will be given.
method A string showing the calculating method of the input time series. More infor-
mation please refer to the details.
cell A vector containing the locaton of the cell, e.g. c(2, 3), default is "mean", rep-
resenting the spatially averaged value. Check details for more information.
output A string showing the type of the output, if output = 'ggplot', the returned
data can be used in ggplot and getPreciBar_comb(); if output = 'plot', the
returned data is the plot containing all layers’ information, and can be plot di-
rectly or used in grid.arrange; if not set, the data will be returned.
ferentiate different outputs in the later multiplot using getSpatialMap_comb.
plotRange A boolean showing whether the range will be plotted.
member A number showing which member is selected to get, if the dataset has a "mem-
ber" dimension. Default is NULL, if no member assigned, and there is a "mem-
ber" in dimensions, the mean value of the members will be taken.
omitNA A boolean showing whether the missing value is omitted.
getPreciBar 39
info A boolean showing whether the information of the map, e.g., max, mean ...,
default is FALSE.
Details
There are following methods to be selected, "annual": annual rainfall of each year is plotted. "win-
ter", "spring", "autumn", "summer": seasonal rainfall of each year is plotted. Month(number 1 to
12): month rainfall of each year is plotted, e.g. march rainfall of each year. "meanMonthly": the
mean monthly rainfall of each month over the whole period.
#Since "winter" is a crossing year, 12, 1, 2, 12 is in former year, and 1, 2 are in latter year. #so
winter belongs to the latter year.
cell representing the location of the cell, NOTE: this location means the index of the cell, IT IS
NOT THE LONGITUDE AND LATITUDE. e.g., cell = c(2,3), the program will take the 2nd
longitude and 3rd latitude, by the increasing order. Longitude comes first.
S4 method.
Value
The calculated mean value of the input time series and the plot of the result.
References
Examples
#gridData provided by package is the result of \code{loadNcdf()}
data(tgridData)
b1 <- getPreciBar(tgridData, method = 'annual')
b2 <- getPreciBar(tgridData, method = 'meanMonthly')
data(testdl)
TS <- testdl[[1]]
a <- getPreciBar(TS, method = 'spring')
# if info = T, the information will be given at the bottom.
a <- getPreciBar(TS, method = 'spring', info = TRUE)

40 getPreciBar_comb
getPreciBar_comb Combine bars together
Description
Combine bars together
Usage
getPreciBar_comb(
...,
list = NULL,
nrow = 1,
x = "",
y = "",
title = "",
output = FALSE
)
Arguments
... different barplots generated by getPreciBar(,output = 'ggplot'), refer to
details.
list If input is a list containing different ggplot data, use llist = inputlist. NOTE:
yOU HAVE TO PUT A list = , before your list.
Details
..., representing different ouput generated by getPreciBar(,output = 'ggplot'), they have to be
of the same type, e.g., 1. Jan precipitation of different years, Feb precipitation of different years,
and... They are both monthly precipitation, and they share x axis.
2. Mean monthly precipitation of different dataset. e.g., long term mean monthly precipitation and
short term mean monthly precipitation. They are both mean monthly precipitation.
Value
A combined barplot.
References
getSpatialMap 41
Examples
data(tgridData)# the result of \code{\link{loadNcdf}}

#output type of getPreciBar() has to be 'ggplot'.
b1 <- getPreciBar(tgridData, method = 2, output = 'ggplot', name = 'b1')
b2 <- getPreciBar(tgridData, method = 3, output = 'ggplot', name = 'b2')
getPreciBar_comb(b1, b2)
getSpatialMap Get spatial map of the input dataset.
Description
Get spatial map of the input dataset.
Usage
getSpatialMap(dataset, method = NULL, member = "mean", ...)
Arguments
dataset A list containing different information, should be the result of reading netcdf file
using loadNcdf.
method A string showing different calculating method for the map. More information
please refer to details.
member A number showing which member is selected to get, if the dataset has a "mem-
ber" dimension. Default is NULL, if no member assigned, and there is a "mem-
ber" in dimensions, the mean value of the members will be taken.
... several arguments including x, y, title, catchment, point, output, name, info,
scale, color, type in ?getSpatialMap_mat for details.
Details
There are following methods to be selected, "meanAnnual": annual rainfall of each year is plot-
ted. "winter", "spring", "autumn", "summer": MEAN seasonal rainfall of each year is plotted.
Month(number 1 to 12): MEAN month rainfall of each year is plotted, e.g. MEAN march rainfall
of each year. "mean", "max", "min": mean daily, maximum daily, minimum daily precipitation.
Value
A matrix representing the raster map is returned, and the map is plotted.
42 getSpatialMap_comb
Examples
## Not run:
#gridData provided in the package is the result of \code {loadNcdf}
data(tgridData)
getSpatialMap(tgridData, method = 'meanAnnual')
getSpatialMap(tgridData, method = 'winter')
getSpatialMap(tgridData, method = 'winter', catchment = testCat)
file <- system.file("extdata", "point.txt", package = "hyfo")

point <- read.table(file, header = TRUE, sep = ',' )
getSpatialMap(tgridData, method = 'winter', catchment = testCat, point = point)
## End(Not run)
# More examples can be found in the user manual on http://yuanchao-xu.github.io/hyfo/
getSpatialMap_comb Combine maps together
Description
Combine maps together
Usage
getSpatialMap_comb(
...,
list = NULL,
nrow = 1,
x = "",
y = "",
title = "",
output = FALSE
)
Arguments
... different maps generated by getSpatialMap(,output = 'ggplot'), see de-
tails.
list If input is a list containing different ggplot data, use list = inputlist.
getSpatialMap_comb 43

Details
For getSpatialMap_comb, the maps to be compared should be with same size and resolution, in
other words, they should be fully overlapped by each other.
If they have different resolutions, use interpGridData{ecomsUDG.Raccess} to interpolate.
Value
A combined map.
References
Examples
## Not run:
data(tgridData)# the result of \code{\link{loadNcdf}}
#The output should be 'ggplot'
a1 <- getSpatialMap(tgridData, method = 'summer', output = 'ggplot', name = 'a1')
a2 <- getSpatialMap(tgridData, method = 'winter', output = 'ggplot', name = 'a2')
a3 <- getSpatialMap(tgridData, method = 'mean', output = 'ggplot', name = 'a3')
a4 <- getSpatialMap(tgridData, method = 'max', output = 'ggplot', name = 'a4')
getSpatialMap_comb(a1, a2)
# or you can put them into a list.

getSpatialMap_comb(list = list(a1, a2), nrow = 2)
## End(Not run)

44 getSpatialMap_mat
getSpatialMap_mat Replot raster matrix
Description
replot the matrix output from getSpatialMap, when output = 'data' or output is default value.
Usage
getSpatialMap_mat(
matrix,
title_d = NULL,
catchment = NULL,
point = NULL,
output = "data",
name = NULL,
info = FALSE,
scale = "identity",
color = NULL,
...
)
Arguments
matrix A matrix raster, should be the result of getSpatialMap(), output should be
default or ’data’
title_d A string showing the title of the plot, defaut is NULL.
catchment A catchment file geting from shp2cat() in the package, if a catchment is avail-
able for background.
point A dataframe, showing other information, e.g., location of the gauging stations.
The the data.frame should be with columes "name, lon, lat, z, value".
output A string showing the type of the output, if output = 'ggplot', the returned
data can be used in ggplot and getSpatialMap_comb(); if output = 'plot',
the returned data is the plot containing all layers’ information, and can be plot
directly or used in grid.arrange; if not set, the raster matrix data will be returned.
ferentiate different outputs in the later multiplot using getSpatialMap_comb.
info A boolean showing whether the information of the map, e.g., max, mean ...,
default is FALSE.
scale A string showing the plot scale, ’identity’ or ’sqrt’.
color Most of time you don’t have to set this, but if you are not satisfied with the de-
fault color, you can set your own palette here. e.g., color = c('red','blue'),
then the value from lowest to highest, will have the color from red to blue. More
info about color, please check ?palette().
default is about precipitation.
getSpatialMap_mat 45
Value
A matrix representing the raster map is returned, and the map is plotted.
References
• Hadley Wickham (2011). The Split-Apply-Combine Strategy for Data Analysis. Journal of
Statistical Software, 40(1), 1-29. URL http://www.jstatsoft.org/v40/i01/.
• Original S code by Richard A. Becker and Allan R. Wilks. R version by Ray Brownrigg.
Enhancements by Thomas P Minka <tpminka at media.mit.edu> (2015). maps: Draw Geo-
graphical Maps. R package version 2.3-11. https://CRAN.R-project.org/package=maps
• Roger Bivand and Nicholas Lewin-Koh (2015). maptools: Tools for Reading and Handling
Spatial Objects. R package version 0.8-36. https://CRAN.R-project.org/package=maptools
• Roger Bivand and Colin Rundel (2015). rgeos: Interface to Geometry Engine - Open Source
(GEOS). R package version 0.3-11. https://CRAN.R-project.org/package=rgeos
Examples
## Not run:
data(tgridData)# the result of \code{loadNcdf}
#the output type of has to be default or 'data'.
a1 <- getSpatialMap(tgridData, method = 'mean')
a2 <- getSpatialMap(tgridData, method = 'max')
a3 <- getSpatialMap(tgridData, method = 'winter')
a4 <- getSpatialMap(tgridData, method = 'summer')
#For example, if we want to investigate the difference between mean value and max.
a5 <- a2 - a1
getSpatialMap_mat(a4)
#Or to investigate the difference between winter value and summer value.
a6 <- a3 - a4
getSpatialMap_mat(a6)
## End(Not run)

46 loadNcdf
list2Dataframe Convert a list to a dataframe.
Description
Convert a list of different time series to a dataframe. Usually the list is the output of extractPeriod
NOTE: Since it’s dataframe, so the dataframes in the input datalist should have the same date, if
not, please use extractPeriod to process.
Usage
list2Dataframe(datalist)
Arguments
datalist A list containing different time series, each sub list has to have the same length.
Value
The converted dataframe
Examples
# open file attached in the package.
file <- system.file("extdata", "testdl.txt", package = "hyfo")
datalist <- dget(file) # read list file.
datalist_new <- extractPeriod(datalist, commonPeriod = TRUE)
dataframe <- list2Dataframe(datalist_new)
loadNcdf Load NetCDF file
Description
Load NetCDF file
Usage
loadNcdf(filePath, varname, tz = "GMT", ...)
monthlyPreci 47
Arguments
filePath A path pointing to the NetCDF file, version3.
varname A character representing the variable name, you can use getNcdfVar to get the
basic information about the variables and select the target.
tz A string representing the time zone, default is GMT, if you know what time zone
is you can assign it in the argument. If tz = '', current time zone will be taken.
... Several arguments including Year, month, lon, lat type in ?downscaleNcdf for
details.You can load while downscale, and also first load than use downscaleNcdf
to downscale.
Value
A list object from hyfo containing the information to be used in the analysis, or biascorrection.
References
Examples
# you can directly add your downscale information to the argument.

nc1 <- loadNcdf(filePath, varname, year = 2006, lon = c(-2, -0.5), lat = c(43.2, 43.7))
nc2 <- loadNcdf(filePath, varname, year = 2005, month = 3:8, lon = c(-2, -0.5),
lat = c(43.2, 43.7))
# More examples can be found in the user manual on http://yuanchao-xu.github.io/hyfo/
monthlyPreci Get monthly rainfall
Description
Get monthly rainfall
48 plotTS
Usage
monthlyPreci(TS, year, mon)
Arguments
TS A rainfall time series.
year A list showing the year index of the time series.
mon A list showing the mon index of the time series.
Value
the monthly rainfall matrix of the rainfall time series.
plotTS plot time series, with marks on missing value.
Description
plot time series, with marks on missing value.
Usage
plotTS(
...,
type = "line",
output = "data",
plot = "norm",
name = NULL,
showNA = TRUE,
x = NULL,
y = NULL,
title = NULL,
list = NULL
)
Arguments
... input time series.
type A string representing the type of the time series, e.g. ’line’ or ’bar’.
the data that can be directly plotted by ggplot2 will be returned, which is easier
for you to make series plots afterwards.
plot representing the plot type, there are two types, "norm" and "cum", "norm" gives
an normal plot, and "cum" gives a cumulative plot. Default is "norm".
plotTS 49
ferentiate different outputs in the later multiplot using plotTS_comb.
showNA A boolean representing whether the NA values should be marked, default is
TRUE.
x label for x axis.
y label for y axis.
title plot title.
list If your input is a list of time series, then use list = your time sereis list
Details
If your input has more than one time series, the program will only plot the common period of
different time series.
Value
A plot of the input time series.
References
Examples
plotTS(testdl[[1]])
plotTS(testdl[[1]], x = 'xxx', y = 'yyy', title = 'aaa')
# If input is a datalist
plotTS(list = testdl)
# Or if you want to input time series one by one

# If plot = 'cum' then cumulative curve will be plotted.
plotTS(testdl[[1]], testdl[[2]], plot = 'cum')
# You can also directly plot multicolumn dataframe

dataframe <- list2Dataframe(extractPeriod(testdl, commonPeriod = TRUE))
plotTS(dataframe, plot = 'cum')
# Sometimes you may want to process the dataframe and compare with the original one
dataframe1 <- dataframe
dataframe1[, 2:4] <- dataframe1[, 2:4] + 3
plotTS(dataframe, dataframe1, plot = 'cum')
# But note, if your input is a multi column dataframe, it's better to plot one using plotTS,
# and compare them using plotTS_comb. If all data are in one plot, there might be too messy.

50 plotTS_comb
plotTS_comb Combine time seires plot together
Description
Combine time seires plot together
Usage
plotTS_comb(
...,
nrow = 1,
type = "line",
list = NULL,
x = "Date",
y = "",
title = "",
output = FALSE
)
Arguments
... different time series plots generated by plotTS(,output = 'ggplot'), refer to
details.
type A string showing ’line’ or ’bar’.
list If input is a list containing different ggplot data, use llist = inputlist.
output A boolean, if chosen TRUE, the output will be given. NOTE: yOU HAVE TO
PUT A list = , before your list.
Details
..., representing different ouput file generated by plotTS(,output = 'ggplot'),name = yourname,
different names must be assigned when generating different output.
e.g. a1, a2, a3 are different files generated by plotTS(,output = 'ggplot'),name = yourname,
you can set plotTS(a1,a2,a3) or plotTS(list = list(a1,a2,a3))
Value
A combined time series plot.
resample 51
References
Examples
a1 <- plotTS(testdl[[1]], output = 'ggplot', name = 1)
a2 <- plotTS(testdl[[2]], output = 'ggplot', name = 2)
plotTS_comb(a1, a2)
plotTS_comb(list = list(a1, a2), y = 'y axis', nrow = 2)
resample Resample your time series or ncdf files.
Description
Resameple your time series or ncdf files, more info pleae see details.
Usage
resample(data, method)


Arguments
data a hyfo grid data or a time series, with first column date, and second column
value. The date column should follow the format in as.Date, i.e. seperate with
"-" or "/". Check details for more information.
method A string showing whether you want to change a daily data to monthly data or
monthly data to daily data.e.g. "mon2day" and "day2mon".
Details
Note, when you want to change daily data to monthly data, a new date column will be generated,
usually the date column will be the middle date of each month, 15th, or 16th. However, if your
time series doesn’t start from the beginning of a month or ends to the end of a month, e.g. from
1999-3-14 to 2008-2-2, the first and last generated date could be wrong. Not only the date, but also
the data, because you are not calculating based on a intact month.
S4 method.
52 shp2cat
Value
converted time series.
References
Examples
# Daily to monthly
data(testdl)
TS <- testdl[[2]] # Get daily data
str(TS)
TS_new <- resample(TS, method = 'day2mon')
# Monthly to daily
TS <- data.frame(Date = seq(as.Date('1999-9-15'), length = 30, by = '1 month'),
runif(30, 3, 10))
TS_new <- resample(TS, method = 'mon2day')
#' # First load ncdf file.

nc_new <- resample(nc, 'day2mon')
shp2cat Get a catchment object from selected shape file.
Description
Get a catchment object from selected shape file.
Usage
shp2cat(filePath)
Arguments
filePath A string representing the path of the shape file.
Details
This function is based on the package rgdal and sp, and the output comes from the package sp
testCat 53
Value
A catchment object can be used in getSpatialMap().
References
• Roger Bivand, Tim Keitt and Barry Rowlingson (2015). rgdal: Bindings for the Geospatial
Data Abstraction Library. R package version 1.0-4. https://CRAN.R-project.org/package=rgdal
Examples
#open internal file

file <- system.file("extdata", "testCat.shp", package = "hyfo")
catchment <- shp2cat(file)
testCat testCat
Description
testCat
Usage
testCat
Format
A catchment file generated by library rgdal.
class Formal class ’SpatialPolygonsDataFrame’ [package "sp"] with 5 slots ...

54 tgridData
testdl testdl
Description
A list containing different precipitation time series.
Usage
testdl
Format
A list consists of 3 different lists.
AAA AAA, a dataframe containing a date column and a value column.
BBB BBB, a dataframe containing a date column and a value column.
CCC CCC, a dataframe containing a date column and a value column. ...
Source
http://meteo.navarra.es/estaciones/mapadeestaciones.cfm http://www4.gipuzkoa.net/oohh/web/esp/02.asp
References
• http://meteo.navarra.es/estaciones/mapadeestaciones.cfm
• #’ http://www4.gipuzkoa.net/oohh/web/esp/02.asp
tgridData tgridData
Description
A list containing different information getting from grid data file, e.g., netcdf file.
Usage
tgridData
Format
A list containing different information.
Variables variable information.
Data Data.
xyCoords longitude and latitude of the data.
Dates Date information. ...
writeNcdf 55
Source
http://www.meteo.unican.es/datasets/spain02
References
• Herrera, S., Ancell, R., Gutierrez, J. M., Pons, M. R., Frias, M. D., & Fernandez, J. (2012).
Development and analysis of a 50-year high-resolution daily gridded precipitation dataset over
Spain (Spain02). International Journal of Climatology (http://www.meteo.unican.es/datasets/spain02),
10.1002/joc.2256.
writeNcdf Write to NetCDF file using hyfo list file
Description
Write to NetCDF file using hyfo list file
Usage
writeNcdf(
gridData,
filePath,
missingValue = 1e+20,
tz = "GMT",
units = NULL,
version = 3
)
Arguments
gridData A hyfo list file from loadNcdf
filePath A path of the new NetCDF file, should end with ".nc"
missingValue A number representing the missing value in the NetCDF file, default is 1e20 #’
@param tz A string representing the time zone, default is GMT, if you know
what time zone is you can assign it in the argument. If tz = '', current time
zone will be taken.
tz time zone, default is "GMT"
units A string showing in which unit you are putting in the NetCDF file, it can be
seconds or days and so on. If not specified, the function will pick up the possible
largest time units from c('weeks','days','hours','mins','secs')
version ncdf file versions, default is 3, if 4 is chosen, output file will be foreced to version
4.
Value
An NetCDF version 3 file.
56 writeNcdf
References
Examples
# Then write to your work directory
# writeNcdf(nc, 'test.nc')

Index
∗Topic datasets getBiasFactor, 4, 24

testCat, 53 getBiasFactor,data.frame,data.frame-method
testdl, 54 (getBiasFactor), 24
tgridData, 54 getBiasFactor,list,list-method
(getBiasFactor), 24
applyBiasFactor, 3, 26 getEnsem_comb, 28
applyBiasFactor,data.frame,biasFactor-method getFrcEnsem, 29
(applyBiasFactor), 3 getHisEnsem, 31
applyBiasFactor,list,biasFactor.hyfo-method getLMom, 34
(applyBiasFactor), 3 getMeanPreci, 35
getMoment, 36
biasCorrect, 3, 4, 6, 25, 26 getNcdfVar, 36
biasCorrect,data.frame,data.frame,data.frame-method
getPreciBar, 37
(biasCorrect), 6 getPreciBar,data.frame-method
biasCorrect,list,list,list-method (getPreciBar), 37
(biasCorrect), 6 getPreciBar,list-method (getPreciBar),
biasFactor-class, 11 37
biasFactor.hyfo-class, 12 getPreciBar_comb, 40
getSpatialMap, 41
checkBind, 12
getSpatialMap_comb, 42
collectData, 13
getSpatialMap_mat, 44
collectData_csv_anarbe, 13
collectData_excel_anarbe, 14 list2Dataframe, 46
collectData_txt_anarbe, 15 loadNcdf, 17, 30, 38, 46, 55
coord2cell, 16
monthlyPreci, 47
downscaleNcdf, 17
plotTS, 48
extractPeriod, 18 plotTS_comb, 50
extractPeriod,data.frame-method
(extractPeriod), 18 resample, 51
extractPeriod,list-method resample,data.frame-method (resample),
(extractPeriod), 18 51
resample,list-method (resample), 51
fillGap, 20
shp2cat, 52
getAnnual, 22 testCat, 53
getAnnual,data.frame-method testdl, 54
(getAnnual), 22 tgridData, 54
getAnnual,list-method (getAnnual), 22
getAnnual_dataframe, 23 writeNcdf, 55
57

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Package ‘hyfo’

applyBiasFactor Apply bias factor to different forecasts for multi/operational/real time

## S4 method for signature 'data.frame,biasFactor'

## S4 method for signature 'list,biasFactor.hyfo'

######## hyfo grid file biascorrection

# If your input is obtained by \code{loadNcdf}, you can also directly biascorrect

# First load ncdf file.

biasFactor <- getBiasFactor(nc, tgridData)

biasFactor <- getBiasFactor(nc, tgridData, method = 'eqm', extrapolate = 'constant',

biasFactor <- getBiasFactor(nc, tgridData, method = 'gqm', preci = TRUE)

######## Time series biascorrection

# common period has to be extracted in order to better train the forecast.

datalist <- extractPeriod(testdl, startDate = '1994-1-1', endDate = '1995-10-1')

frc <- datalist[[1]]

# default method is scaling

biasFactor <- getBiasFactor(hindcast, obs, preci = TRUE)

# You can use other methods to biascorrect, e.g. delta method.

biasFactor <- getBiasFactor(hindcast, obs, method = 'gqm', preci = TRUE)

plotTS(obs, frc, frc_new, frc_new1, frc_new2, frc_new3, frc_new4, plot = 'cum')

# You can also give name to this input list.

# More examples can be found in the user manual on https://yuanchao-xu.github.io/hyfo/

biasCorrect Biascorrect the input timeseries or hyfo dataset

## S4 method for signature 'data.frame,data.frame,data.frame'

## S4 method for signature 'list,list,list'

######## hyfo grid file biascorrection

# If your input is obtained by \code{loadNcdf}, you can also directly biascorrect

# First load ncdf file.

######## Time series biascorrection

# common period has to be extracted in order to better train the forecast.

datalist <- extractPeriod(testdl, startDate = '1994-1-1', endDate = '1995-10-1')

frc <- datalist[[1]]

# default method is scaling, with 'multi' scaleType

frc_new1 <- biasCorrect(frc, hindcast, obs, preci = TRUE)

# You can use other scaling methods to biascorrect.

plotTS(obs, frc, frc_new, frc_new1, frc_new2, frc_new3, frc_new4, plot = 'cum')

# You can also give name to this input list.

# More examples can be found in the user manual on https://yuanchao-xu.github.io/hyfo/

biasFactor-class An S4 class, representing the biasFactor of single time series biasCor-

biasFactor.hyfo-class An S4 class, representing the biasFactor of hyfo file.

checkBind Check data for bind function.

collectData Collect data from different csv files.

#use internal data as an example.

a <- collectData(folder, fileType = 'csv', range = c(10, 20, 1,2))

# More examples can be found in the user manual on https://yuanchao-xu.github.io/hyfo/

#use internal data as an example.

# More examples can be found in the user manual on https://yuanchao-xu.github.io/hyfo/

#use internal data as an example.

# More examples can be found in the user manual on https://yuanchao-xu.github.io/hyfo/

coord2cell Change lon lat coordinates to cell coordinates

Change lon lat coordinates to cell coordinates

coord2cell(coord, lon, lat)

coord input lon lat coordinate

downscaleNcdf Downscale NetCDF file

nc <- loadNcdf(filePath, varname)

# Then write to your work directory

# More examples can be found in the user manual on https://yuanchao-xu.github.io/hyfo/

extractPeriod Extract period from list or dataframe.

## S4 method for signature 'data.frame'

## S4 method for signature 'list'