Re^3: Passing parameters to R script

[Anonymous Monk]

That works fine, but there's a slightly neater way to do it; if you provide a TRUE value to the commandArgs function, it ignores any commandline parameters before (and including) --args.
So with Args <- commandArgs(TRUE), Args[1] is "100", and is the only element of the vector.

It's also possible to use a simpler syntax to call the script on the command line, which implicitly assumes that any arguments are given after the script name:
Rscript test.R 100

Cheers,
Julio

[Anonymous Monk]

In Bash shell

# a=1
# b=10
# Rscript -e "args<-commandArgs(TRUE);x=args[1]:args[2];x;mean(x);sd(x
+)" $a $b
 [1]  1  2  3  4  5  6  7  8  9 10
[1] 5.5
[1] 3.027650

So you can control variables on the command line R script and you can feed these variables into R itself using commandArgs(TRUE), and manipulate the variables as args1 and args2. So if I imagine if you are doing a system call in perl, you can also construct a similar Rscript on the command line, and get the output accordingly, which you can manipulate further within perl (or any other script).

[Anonymous Monk]

Here is simple function to parse unix way of parsing argument from R.

#
#
# EXAMPLE:
# R --test=mydata.csv
#> getopt('test')
#[1] "mydata.csv"

# getting numeric argument
# R --N=123
#> getopt('N',numeric=T)
#[1] 123
#

getopt <- function(argname, numeric = F)
  {
    args <- commandArgs()  
    argexp = sprintf('^--%s=',argname)
    idx <- regexpr(argexp, args);

    ret <- NA
    
    if ( any(idx > 0) )
    { # found matching argument  
    found <- args[idx > 0]
    value <- strsplit(found,"=")
    ret <- unlist(value)[2]
    }

    if ( numeric )
    ret <- as.numeric(ret)

    ret
  }

cheers, c.okugami