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Posted on September 19, 2015 by Nathalie in R bloggers | 0 Comments

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This post describes how to pass external arguments to R when calling a Rscript with a
command line. The case study presented here is very simple: a Rscript is called which
Most vie
needs, as an input, a �le name (a text �le containing data which are loaded into R to be
processed) and which can also accept an optional additional argument (an output �le PCA vs Autoe
name: if this argument is not provided, the program supplies one by default). Reduction
How to write
Note: The program just loads a text �le containing data, �lters out non numeric variables 5 Ways to Sub
and writes a text �le with remaining numeric variables only. PowerBI vs. R
Alternatives C
R style 10 Must-Know
relocate()
The most natural way to pass arguments from the command line is to use the function Date Formats
commandArgs . This function scans the arguments which have been supplied when the How to Remo
current R session was invoked. So creating a script named sillyScript.R which starts
with
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#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)

and running the following command line

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Rscript --vanilla sillyScript.R iris.txt out.txt

will create a string vector args which contains the entries iris.txt and out.txt .
Missing and default arguments can be handled this way:

# test if there is at least one argument: if not, return an error

if (length(args)==0) {
stop("At least one argument must be supplied (input file).n", call.=FALSE)
} else if (length(args)==1) {
# default output file
args[2] = "out.txt"
}

The simple use case described in the introduction thus gives

## program...
df = read.table(args[1], header=TRUE)
num_vars = which(sapply(df, class)=="numeric")
df_out = df[ ,num_vars]
write.table(df_out, file=args[2], row.names=FALSE)

Finally, the command lines

Rscript --vanilla sillyScript.R iris.txt out.txt

or

Rscript --vanilla sillyScript.R iris.txt

will both load the �le iris.txt , �lter out the non numeric variables and write the
resulting data in out.txt . Whereas running

Rscript --vanilla sillyScript.R

Error: At least one argument must be supplied (input file).

Execution halted

python style
One package allows to obtain the same result in a python-like style: the package
optparse. The package can be used to perform a similar task. Basically, the package

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contains the functions

make_option to declare options, their �ags, types, default values and help
messages;
OptionParser to read the arguments passed to the R script and parse_args to
parse them according to what has been declared thanks to make_option .

The functions are used as follows:

#!/usr/bin/env Rscript
Ocean B
library("optparse")

option_list = list( Ocean Ba

make_option(c("-f", "--file"), type="character", default=NULL,
help="dataset file name", metavar="character"),
make_option(c("-o", "--out"), type="character", default="out.txt",
help="output file name [default= %default]", metavar="character"
);

opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);

which produces a list opt that contains all the arguments sorted by order of
appearance in option_list and which can be called by their names as declared in this
object: opt$file and opt$out . Then, managing null arguments is performed as
follows:

if (is.null(opt$file)){
print_help(opt_parser)
stop("At least one argument must be supplied (input file).n", call.=FALSE)
}

in which the function print_help print the help page of the option list as declared in
the object option_list .

The remaining of the function is almost unchanged:

## program...
df = read.table(opt$file, header=TRUE)
num_vars = which(sapply(df, class)=="numeric")
df_out = df[ ,num_vars]
write.table(df_out, file=opt$out, row.names=FALSE)

If the entire script is saved in a �le called yasrs.R ,

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Rscript --vanilla yasrs.R

will give

Usage: testScript.R [options]

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-f CHARACTER, --file=CHARACTER
dataset file name
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-o CHARACTER, --out=CHARACTER R-bloggers, an
output file name [default= out.txt]

-h, --help
Show this help message and exit
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Error: At least one argument must be supplied (input file).
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Show this help message and exit Probability M
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Passing arguments to an R script from command lines |... https://www.r-bloggers.com/2015/09/passing-argument...

will both create the �le out.txt as described in the introduction of this post. R programme
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