[R] "Pipelining" programs in R

Prof Brian Ripley ripley at stats.ox.ac.uk
Fri May 19 08:03:55 CEST 2006

You can use system() or pipe() and friends.  This is covered in Section 
5.1 of `Writing R Extensions'.

Perhaps the simplest way is to something like

tmp <- tempfile()
zz <- file(tmp, "w")
# write the input script to zz, e.g. via cat
res <- system(paste("myprog <", tmp), intern = TRUE)

and then parse the output from the character vector 'res'.

If you have a Unix-like OS and understand pipes, fifos and sockets you can 
also use those: see ?pipe.  (With a higher degree of understanding you can 
use some of these on Windows NT.)

It would have been very helpful to have known your OS, a piece of 
information the posting guide asked for.  (Since you talk about 'open'ing 
an executable, I surmise you are not familiar with traditional OSes which 
'run' programs.)

On Thu, 18 May 2006, Dan Rabosky wrote:

> Hello...
> I would like to use R for 'pipelining' data among several programs.  I'm
> wondering how I can use R to call another program, feed that program a set
> of parameters, and retrieve the output.
> E.g., I have an executable that, when opened, prompts the user to enter a
> set of parameters.  The program then executes & prompts the user for the
> name of an output file.  I need to run this program on a large batch of
> parameters, such that it would clearly be desirable to automate the
> process.  Is there a straightforward way to do this?  I can't find any
> online documentation addressing this topic, but perhaps I've not been
> looking in the right place.
> In pseudocode, supposing I have a large array of parameters in R:
> For each set of parameters
>         -Open Program.
>         -Enter Parameters.
>         -Cause program to execute (typically done by simply entering " \n
> " after manually entering parameters).
>         -Enter name of output file.
>         -Close program.
> Any advice will be greatly appreciated!
> Thanks,
> Dan Rabosky
> Dan Rabosky
> Department of Ecology and Evolutionary Biology
> 237 Corson Hall
> Cornell University
> Ithaca, NY14853-2701 USA
> web: http://www.birds.cornell.edu/evb/Graduates_Dan.htm
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Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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