[R] reading in results from system(). There must be an easier way...

[Michael A. Gilchrist]

Wow, that's elegant and simple.  It's also faster than my approach.

NB, you don't need to use close(), read.delim() closes the pipe when its done 
reading.

Thank you all for your suggestions, they really helped me with this problem 
and understand R just a bit better.

Sincerely,

Mike
-----------------------------------------------------
Department of Ecology & Evolutionary Biology
569 Dabney Hall
University of Tennessee
Knoxville, TN 37996-1610

phone:(865) 974-6453
fax:  (865) 974-6042

web: http://eeb.bio.utk.edu/gilchrist.asp
-----------------------------------------------------


On Fri, 12 Sep 2008, Prof Brian Ripley wrote:

> Why not use
>
> con <- pipe(COMMAND)
> foo <- read.delim(con, colClasses="numeric")
> close(con)
>
> ?  See the 'R Data Input/Output Manual'.
>
> On Fri, 12 Sep 2008, Michael A. Gilchrist wrote:
>
>> Hello,
>> 
>> I am currently using R to run an external program and then read the results 
>> the external program sends to the stdout which are tsv data.
>> 
>> When R reads the results in it converts it to to a list of strings which I 
>> then have to maniuplate with a whole slew of commands (which, figuring out 
>> how to do was a reall challenge for a newbie like myself)--see below.
>> 
>> Here's the code I'm using.  COMMAND runs the external program.
>>
>>    rawInput= system(COMMAND,intern=TRUE);##read in tsv values
>>    rawInput = strsplit(rawInput, split="\t");##split elements w/in the list
>> 					      ##of character strings by "\t"
>>    rawInput = unlist(rawInput); ##unlist, making it one long vector
>>    mode(rawInput)="double"; ##convert from strings to double
>>    finalInput = data.frame(t(matrix(rawInput, nrow=6))); ##convert
>> 
>> Because I will be doing this 100,000 of times as part of an optimization 
>> problem, I am interested in learning a more efficient way of doing this 
>> conversion.
>> 
>> Any suggestions would be appreciated.
>> 
>> 
>> Thanks in advance.
>> 
>> Mike
>> 
>> 
>> -----------------------------------------------------
>> Department of Ecology & Evolutionary Biology
>> 569 Dabney Hall
>> University of Tennessee
>> Knoxville, TN 37996-1610
>> 
>> phone:(865) 974-6453
>> fax:  (865) 974-6042
>> 
>> web: http://eeb.bio.utk.edu/gilchrist.asp
>> 
>
> -- 
> 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
>