Run an R-script from command line and store results in subdirectory

Question

I want to run an R-script from the command line (on a Linux machine) and store the results in a subdirectory of the working directory. It looks like that:

./myscript.r [param 1] [param 2] [param 3]

Given 3 binomial parameters there are 4 conditions in total. I want to store the results of each condition in a subdirectory of the working directory.

Is there an elegant way to do that or do I really need to copy my R-script to every subdirectory?

Monochord

Can't you take care of that in the R script itself whether via save, write.csv, etc.? You can create new directories from R using the system command. – Extortion

could you pass the parameters within the script and have it write to each directory? Something like a for loop for each parameter? – Marrero

If your R program writes to stdout, just pipe the output to a file specified relative to the current directory. – Pernickety

You should include a minimal representative example of your program to provide more context for your problem. – Ila

Answer 1

Purcell,try saving and running this script on your computer. Provide it a few different kinds and combinations of arguments.

#!/usr/bin/Rscript
args <- commandArgs(TRUE)
print(args)
class(args)

For instance, I ran ./test.R test=1 one=test.

Using this command in combination with paste0() statements should give you what you need to tailor your output locations based on the parameters provided.

Motherwort