How can I pass an array as argument to an R script command line run?

Question

I'm trying to pass an array of hundreds of elements as an argument of an R script via command line in Windows. Firstly, I'd like to declare my array in some way. I'm doing that in command line:

set my_array=c(0,1,2,3,4,5,6,7,8,9,...,700)

Then I want to run my script and get the array as argument.

Rscript my_script my_array

But when I try this an error message came up saying that 'the object my_array" could not be found. I know how to get the arguments in my script, using args <- commandArgs(TRUE). I just need to recognize my declared array as an argument - or declare it in the right way and pass it in the right way as an argument to my script.

Thanks!

Rafael Toledo · Accepted Answer · 2017-06-27 20:42:14Z

First, i am not sure if you should use set to declare any variable in terminal, but you can see more of this on man set page.

There are some ways i think you can try to pass an array to R script, it mainly depends on how you declare the my_array in terminal.

1 - "my_array" can be a string in bash:

$ my_array="c(0,1,2,3,4)"
$ Rscript my_script ${my_array}

And use the eval(parse(text=())) in R script to transform the argument as a vector to R environment.

args <- commandArgs(trailingOnly=TRUE) 
print(args)
# c(0,1,2,3,4,5,6,7,8,9)

args <- eval(parse(text=args[1]))
print(args)
# [1] 0 1 2 3 4 5 6 7 8 9

2 - "my_array" can be an array in bash:

$ my_array=(0,1,2,3,4)
$ Rscript my_script ${my_array[*]}

and in R the args is already your array, but of type character:

args <- commandArgs(trailingOnly=TRUE) 
print(args)
# [1] "0" "1" "2" "3" "4" "5"

Joy · Accepted Answer · 2017-06-27 20:27:07Z

I think I understand what you're trying to do here, let me know if I'm wrong.

I created an R script (called script.R) that contains the following:

args <- commandArgs(TRUE)
eval(parse(text=args[1]))
print(myarray)

I can then call the script like this (from my command line)

Rscript script.R myarray="c(1,3,4)"

As you can see, the argument gets passed (in your script you could do print(args) to see what gets passed and how), I use eval(parse(text=...))) to make it execute (create myarray in the script) and then I can do what I want with it (in my case, I printed it, but you could do analysis or other stuff). Does this help?

Thanks, Joy! But my problem is that I'll have to pass many arrays of hundreds of elements. So if I declare the arrays in the same command line, as in Rscript script.R myarray="c(1,3,4)" I could not declare everything I need.

albielin · Accepted Answer · 2018-04-04 19:32:34Z

1

If you have hundreds of values in the array, perhaps it'd more useful to write it to a text file and pass the file path as a parameter and have R read it in.

answered Apr 4, 2018 at 19:32

albielin

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