R command line arguments in scripts

Purpose

Here it is shown how to use Rscript and pass arguments to an R script.

Prerequisites

It is assumed that the reader is familiar with the use of R as well as R scripting, and is familiar wth the linux bash shell.

Using Rscript and command line arguments

When performing computation on the cluster using R, it is necessary to run those scripts from the command line, rather than interactively using R’s graphical user interface. Consider the following R function that is defined in, e.g., ‘logistic.R’:

logistic <- function(r, x) {    r*x*(1.0 - x)
}

From R’s GUI interface, you typically use this from the console as follows:

> source(\"logistic.R\")
> logistic(3.2, 0.5)

It is trivial to write an R script ‘logistic-wrapper.R’ that can be run from the command line, and that takes to arguments, the first being ‘r’, the second ‘x’.

args <- commandArgs(TRUE)
r <- as.double(args[1])
x <- as.double(args[2])

source(\"logistic.R\")

logistic(r, x)

The first line of this script stores all arguments passed to the script in the array ‘args. The second (third) line converts the first (second) element of that array from a string to a double precision number using the function ‘as.double’, and stores it into r (x).

Now from the linux command line, one can run the script above for r = 3.2 and x = 0.5 as follows:

$ Rscript logistic-wrapper.R 3.2 0.5

Note that you should have loaded the appropriate R module, e.g.,

$ module load R

Suppose now that the script needs to be extended to iterate the logistic map ‘n’ times, where the latter value is passed as the third argument to the script.

args <- commandArgs(TRUE)
r <- as.double(args[1])
x <- as.double(args[2])
n <- as.integer(args[3])

source(\"logistic.R\")

for (i in 1:n) x <- logistic(r, x)
print(x)

Note that since the the third argument represents the number of iterations, it should be interpreted as an integer value, and hence be converted appropriately using the function ‘as.integer’.

The script is now invoked from the linux command line with three parameters as follows:

$ Rscript cl.R 3.2 0. 5 100

Note that if you pass an argument that is to be interpreted as a string in your R program, no conversion is needed, e.g.,

name <- args[4]

Here it is assumed that the ‘name’ is passed as the fourth command line argument.