How to Pass Command Line Arguments to R CMD BATCH and Rscript

1. Use the commandArgs() Function to Retrieve Arguments in R
2. Use the R CMD BATCH Command to Redirect Output in R
3. Create the Script and Run the Command in R
4. Pass Command Line Arguments to R CMD BATCH Command in R
5. Pass Command Line Arguments to Rscript in R

When using the command line to run an R script file, we may want to pass arguments and save the output in a file. This article demonstrates these techniques using the R CMD BATCH command and the Rscript front-end.

We will start with some details common to both methods.

Use the commandArgs() Function to Retrieve Arguments in R

Arguments passed on the command line should be retrieved using the commandArgs() function. We will use it with the argument trailingOnly=TRUE.

The function returns a character vector.

Use the R CMD BATCH Command to Redirect Output in R

The R CMD BATCH command redirects the output to a .Rout file. The file contains the input commands, the result and error messages.

With the Rscript front-end, we have to redirect the output using the appropriate command for the shell/terminal. For several terminals, it is > filename.

We can redirect the input using options(echo=TRUE) at the beginning of the file. Error messages are not redirected.

We have to be careful when redirecting output to a file. The file will get created if it does not exist but will get overwritten otherwise.

Create the Script and Run the Command in R

To see how each method works, do the following.

Pass Command Line Arguments to R CMD BATCH Command in R

The syntax is below.

R CMD BATCH options "--args userargument1 userargument2" script_filename.R

Arguments cannot contain spaces. The exact quoting will depend on the shell in use.

The --vanilla option combines several R options.

Example code for the R file:

# Create 5 values in a sequence.
x = seq(from=0, to=20, by=5)
print(x)

# Get the arguments as a character vector.
myargs = commandArgs(trailingOnly=TRUE)
myargs

# The first argument is the text for hobby.
hobby = myargs[1]
hobby

# The second argument is the number of years of practice.
years = as.numeric(myargs[2])
years

The command:

R CMD BATCH --vanilla "--args Golf 8" script_filename.R

An output file of the same name as the input file, with the .Rout extension, gets created in the input file’s same directory.

Pass Command Line Arguments to Rscript in R

Rscript is a scripting front-end for R.

Arguments may contain spaces. Such arguments need to be in quotes.

The syntax is below.

Rscript script_filename.R 'user argument 1' userargument2 > rscript_output_file_name.txt

Example code for the R file:

# To print the command and its result in the output.
options(echo=TRUE)

# five random values from the standard normal distribution
x = rnorm(5)
print(x)

# Get the arguments as a character vector.
myargs = commandArgs(trailingOnly=TRUE)
myargs

# The first argument is the text for hobby.
hobby = myargs[1]
hobby

# The second argument is the number of years of practice.
years = as.numeric(myargs[2])
years

The command:

Rscript script_filename.R 'Playing Guitar' 3 > rscript_output_file_name.txt

The output file gets created. It has the input and output but not error messages.

References and Help

See Appendix B, Invoking R, of the manual: An Introduction to R.

Also, refer to R’s documentation of the commandArgs() function and the Rscript tool.