Hi, I am trying to run some R commands into my bash scripts and want to use shell variables in the R commands and store the output of R objects into shell variables for further usage in downstream analyses. So far I have managed the first, but how to get values out of R script? I am using "here documents" (as a starter, maybe something else is simpler or better; suggestions greatly appreciated). A basic random example: #!/bin/sh MYVAR=2 R --slave --quiet --no-save <<EEE x<-5 z<-x/$MYVAR zz<-x*$MYVAR EEE How get the values of z and zz into shell variables? Thanks D [[alternative HTML version deleted]]
This is not an R question. Use the print function in R and use backticks in
bash.
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"David A." <dasolexa at hotmail.com> wrote:
>
>Hi,
>
>I am trying to run some R commands into my bash scripts and want to use
>shell variables in the R commands and store the output of R objects
>into shell variables for further usage in downstream analyses. So far I
>have managed the first, but how to get values out of R script? I am
>using "here documents" (as a starter, maybe something else is
simpler
>or better; suggestions greatly appreciated).
>
>A basic random example:
>
>#!/bin/sh
>MYVAR=2
>R --slave --quiet --no-save <<EEE
>x<-5
>
>z<-x/$MYVAR
>zz<-x*$MYVAR
>EEE
>
>
>How get the values of z and zz into shell variables?
>
>
>Thanks
>
>D
>
> [[alternative HTML version deleted]]
>
>______________________________________________
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>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.
On 11/07/2011 05:17 PM, David A. wrote:> Hi, > > I am trying to run some R commands into my bash scripts and want to use shell variables in the R commands and store the output of R objects into shell variables for further usage in downstream analyses. So far I have managed the first, but how to get values out of R script? I am using "here documents" (as a starter, maybe something else is simpler or better; suggestions greatly appreciated). >hi, maybe this can be helpful: http://rwiki.sciviews.org/doku.php?id=tips:scriptingr I personally didn't manage to successfully write a 'fully functional' script, though, because of quoting troubles and so on. best regards, -- Matteo Giani