Rscript example

[statquant2]

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[Petr Savicky]

On Thu, Mar 01, 2012 at 11:53:00AM -0800, statquant2 wrote:

> Hi there,
> I am trying to find an example how to use Rscript
> Let's suppose I want to pass 3 arguments (I don't want [options] and -e
> [expressions] as described in help)
>
> *on the command line
> myRscript.R -arg1=value1 -arg2=value2 -arg3=value3
>
> *In the script
> #! /path/to/Rscript
> args = commandArgs(TRUE);
>
> >From what I see args is just a string, do I do things correctly ?

Hi.

Extending your example with print(args), i obtained

  ./myRscript.R -arg1=value1 -arg2=value2 -arg3=value3
  [1] "-arg1=value1" "-arg2=value2" "-arg3=value3"

If you can use a fixed order of the arguments, then you
need not use the "-arg[i]=" parts. The arguments are
strings on the command line, so they are also passed
to R as strings, but you can convert them inside the
script. For example, with the above script, i get

  ./myRscript.R 23 45 78
  [1] "23" "45" "78"

However, if the script contains

   args <- as.numeric(args)

, then i get

  ./myRscript.R 23 45 78
  [1] 23 45 78

which is a numeric vector.

If you want to keep the "arg[i]=" structure, you can have in
the script

  x <- strsplit(args, "=")
  print(x)

and a call produces

  ./myRscript.R -arg1=value1 -arg2=value2 -arg3=value3
  [[1]]
  [1] "-arg1"  "value1"
 
  [[2]]
  [1] "-arg2"  "value2"
 
  [[3]]
  [1] "-arg3"  "value3"

The list "x" may then be further analyzed.

Hope this helps.

Petr Savicky.

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[statquant2]

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[Petr Savicky]

On Thu, Mar 01, 2012 at 11:18:33PM -0800, statquant2 wrote:
> Hey Petr,
> ok I was thinking that R would handle the split by itself.
> I guess using eval we can even make arg1=val1 being executed by R.

Hi.

For executing the assignments, try myRscript.R containing

  args <- commandArgs(TRUE);
  argmat <- sapply(strsplit(args, "="), identity)
 
  for (i in seq.int(length=ncol(argmat))) {
      assign(argmat[1, i], argmat[2, i])
  }

  # available variables
  print(ls())

  # print variables arg1, arg2, arg3
  print(arg1)
  print(arg2)
  print(arg3)

Then the command line

  ./myRscript.R arg1=aa arg2=22 arg3=cc

yields

  [1] "argmat" "args"   "arg1"   "arg2"   "arg3"   "i"    
  [1] "aa"
  [1] "22"
  [1] "cc"

Another option for setting some variables before executing an R script
is to have two scripts, a shell script and an R script, containing

shell script "callR.sh"

  #!/bin/bash
 
  <PATH_TO_R>/bin/R --vanilla << EEE
  args <- c("$2","$3","$4","$5")
  source("$1")
  EEE

a trivial R script "tst.R"

  print(args)

Then,

  ./callR.sh tst.R aa 22 cc

leads to

  ...
  ...
  Type 'demo()' for some demos, 'help()' for on-line help, or
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
 
  > args <- c("aa","22","cc","")
  > source("tst.R")
  [1] "aa" "22" "cc" ""  
  >

Hope this helps.

Petr Savicky.

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