R help - Sep 2009 - Writing R Scripts and passing command line arguments

Hi Guys
I am Abhishek, primarily a bioinformatician.  I have recently started using
a lot of R thanks to some excellent packages available.

Lately I have felt the need to batch process few of the R scripts I have
been working with and strangely enough I am not able to find a good resource
on how to best do this. I did find few old threads on the archives but none
convinced me much. So here I am asking the same thing again hoping to get a
good solution.

1. What's the best way to pass command line arguments to R scripts ?
2. How to execute R scripts from command line ? When I use R CMD BATCH I see
no output on the screen
3. What does R --slave --vanilla do  ?

Thanks,
-Abhi

	[[alternative HTML version deleted]]

See ?commandArgs, the getopt package and ?Rscript

On Mon, Sep 7, 2009 at 1:47 PM, Abhishek Pratap<abhishek.vit at gmail.com>
wrote:
> Hi Guys
> I am Abhishek, primarily a bioinformatician. ?I have recently started using
> a lot of R thanks to some excellent packages available.
>
> Lately I have felt the need to batch process few of the R scripts I have
> been working with and strangely enough I am not able to find a good
resource
> on how to best do this. I did find few old threads on the archives but none
> convinced me much. So here I am asking the same thing again hoping to get a
> good solution.
>
> 1. What's the best way to pass command line arguments to R scripts ?
> 2. How to execute R scripts from command line ? When I use R CMD BATCH I
see
> no output on the screen
> 3. What does R --slave --vanilla do ??
>
> Thanks,
> -Abhi
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
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>

Abhishek Pratap wrote:
> 
> 
> 1. What's the best way to pass command line arguments to R scripts ?
> 
> 
As Gabor mentioned, the commandArgs function and the getopt package provide
some excellent starting points for this.



Abhishek Pratap wrote:
> 
> 
> 2. How to execute R scripts from command line ? When I use R CMD BATCH I
> see 
> no output on the screen 
> 
> 
I believe R CMD BATCH dumps all of it's output to a file ending in .Rout. If
you want more control over input and output to your script then Rscript is
the utility to use.


Abhishek Pratap wrote:
> 
> 
> 3. What does R --slave --vanilla do  ?
> 
> 
If I recall correctly, --vanilla makes it so that R does not waste time
trying to load a previously saved session and also makes it so that R does
not try to save history and environment variables when it exits. Vanilla
also disables the loading of options from profile files such as ~/.Rprofile.

I think --slave makes R shut up about it's self and run more quietly than it
normally does.

Hope that helps!

-Charlie

-----
Charlie Sharpsteen
Undergraduate
Environmental Resources Engineering
Humboldt State University
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