In the Unix script, is there any way to run R files but with arguments in the Unix script?
I know that to run R files in that system, you will need to type "R -f "file" but what codes do you need in R so that you will need to type this instead on Unix:
"R -f "file" arg1 arg2"
Here is an example. Save this code in test.R:
#!/usr/bin/env Rscript
# make this script executable by doing 'chmod +x test.R'
help = cat(
"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Help text here
Arguments in this order:
1) firstarg
2) secondarg
3) thirdarg
4) fourtharg
./test.R firstarg secondarg thirdarg fourtharg
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
\n\n")
# Read options from command line
args = commandArgs(trailingOnly = TRUE)
if(is.element("--help", args) | is.element("-h", args) | is.element("-help", args) | is.element("--h", args)){
cat(help,sep="\n")
stop("\nHelp requested.")
}
print(args)
Do chmod +x test.R
Then invoke it using ./test.R a b c d. It should print: [1] "a" "b" "c" "d".
You can access each of the args by doing args[1] to get to a and args[4] to get to d.
The suggestion to use Rscript does seem useful but possibly not what is being asked. One can also start R from the command line with an input file that gets sourced. The R interpreter can access the commandArgs in that mode as well. This is a minimal "ptest.R" file in my user directory that is also my default working directory:
ca <- commandArgs()
print(ca)
From a Unix command line I can do:
$ r -f ~/ptest.r --args "test of args"
And R opens, displays the usual startup messages and announces packages loaded by .Rprofile and then:
> ca <- commandArgs()
> print(ca)
[1] "/Library/Frameworks/R.framework/Resources/bin/exec/R"
[2] "-f"
[3] "/Users/davidwinsemius/ptest.r"
[4] "--args"
[5] "test of args"
>
>
And then quits.
