Running R Scripts from the Command Line

Sometimes we want to be able to execute R scripts from the command line. The basic way to do this is (in Powershell) via:

Rscript.exe my_script.R

in some cases, we might be able to omit the exe extension and just run:

Rscript my_script.R

Parameterized Scripts

A more flexible approach involves passing values from the command line script to the R script. To process command line input in R, we want the commandArgs() function:

args <- commandArgs(trailingOnly = TRUE)
 
for (i in seq_len(length(args))) {
	print(args[i])
}

The above will take all of the command line args and print them out. The trailingOnly argument tells R to only process the arguments after the name of the executable (Rscript.exe) and the file name (my_script.R). So if we ran the code:

Rscript.exe my_script.R "hello"

it would only print "hello"

To facilitate this from the shell side, we want to define our inputs as variables, then pass these to the Rscript command. Here’s how this looks in Powershell:

$var1 = 2024
$var2 = "hello"
 
Rscript.exe my_script.R $var1 $var2

One thing to note is that $var1 in this example will be coerced to a string. If we want to treat it as a numeric variable, we’d need to coerce it to numeric in R.