R help - Mar 2007 - Passing command line parameters to a script

Hi,
 Does any one know if it is possible to create an R script that can use
command line parameters. I can execute an R script from the command line,
but I  cannot figure out how to pass parameters to the script. The only
resources I have found seem somewhat involved or incomplete.

Any help is appreciated.
Akintayo

	[[alternative HTML version deleted]]

Does system("command -arguments") works for you?

Xiaohui

akintayo holder wrote:
> Hi,
>  Does any one know if it is possible to create an R script that can use
> command line parameters. I can execute an R script from the command line,
> but I  cannot figure out how to pass parameters to the script. The only
> resources I have found seem somewhat involved or incomplete.
>
> Any help is appreciated.
> Akintayo
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>

probably you're looking for ?commandArgs().


I hope it helps.

Best,
Dimitris

----
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
     http://www.student.kuleuven.be/~m0390867/dimitris.htm


----- Original Message ----- 
From: "akintayo holder" <blakdogg at gmail.com>
To: <r-help at stat.math.ethz.ch>
Sent: Tuesday, March 06, 2007 9:11 AM
Subject: [R] Passing command line parameters to a script

> Hi,
> Does any one know if it is possible to create an R script that can 
> use
> command line parameters. I can execute an R script from the command 
> line,
> but I  cannot figure out how to pass parameters to the script. The 
> only
> resources I have found seem somewhat involved or incomplete.
>
> Any help is appreciated.
> Akintayo
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

#!/bin/sh
echo 'a="${1}"; b="${2}";
source("myRcodeUsing_a_and_b.R"); ' | R
--vanilla --quiet

and you can run this from shell like:

./callR valueOfa valueOfb

Best, Oleg

akintayo holder wrote:
> Hi,
>  Does any one know if it is possible to create an R script that can use
> command line parameters. I can execute an R script from the command line,
> but I  cannot figure out how to pass parameters to the script. The only
> resources I have found seem somewhat involved or incomplete.
> 
> Any help is appreciated.
> Akintayo
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466