RE: [R] invoking R scripts from a linux shell ?
Ciao Enrico,
I think you can skip to use a shell as you described.
There are some ways to include R script in a perl script.
I included below two examples I wrote for better understand.
## prova1.pl ###
#!/usr/local/bin/perl
open (FILE, test.txt);
print FILE a,b,c,d,e\n1,2,3,4,5;
close FILE;
### Start R code
open (R_FH, |/usr/local/bin/R --no-save --slave) or die $!;
print R_FH qq{
data-read.csv(test.txt)
datamean-mean(as.numeric(as.character(data[1,])), na.rm=TRUE)
write(datamean, file=out.txt)
quit(save='no',status=0)
};
close R_FH;
# end R
open(FILE, out.txt);
while (FILE){
$mean= $_;
}
close FILE;
print Mean= .$mean;
or
prova2.pl ##
#!/usr/local/bin/perl
open (FILE, test.txt);
print FILE a,b,c,d,e\n1,2,3,4,5;
close FILE;
### Start R code
system(/usr/local/bin/R -q --vanilla rscript.r debug.out);
# end R
open(FILE, out.txt);
while (FILE){
$mean= $_;
}
close FILE;
print Mean= .$mean;
... in this way you can call the perl script only.
Regards,
Vittorio
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Enrico Curiotto
Sent: Friday, January 16, 2004 12:02 AM
To: [EMAIL PROTECTED]
Subject: [R] invoking R scripts from a linux shell ?
Hello,
I have written perl programs that extract data from a
text file, process them, and create other text files,
which I'd like to apply some statistics too (for
example with R).
I'd like to do it all in once , with a single script.
I'm not familiar with R, I'd like to know if this task
could be accomplished by creating a linux shells that
launches the perl scripts and then R functions that
maybe pass back some results to the system like in
this schema:
S --- Perl
H -
E --- R functions
L -
L
Is it possible ?
Where can I get information to do that? (to call R
from a shell, in background)
Are other better way to do that?
Thank you very much!
Enrico.
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Re: [R] invoking R scripts from a linux shell ?
Hi Enrico, As seen by other posts, there are many ways to accomplish this sort of thing. For simple tasks I've often found it easiest to call R from my script (in my case Python). I've not used BATCH mode and instead call R like this: R --slave --no-save script.R A common setup for me is to have a functions.R file with routines I want to use and then to generate a small R script from within Python that sources functions.R and calls the functions with the proper variables as determined by the script. HTH, + seth __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] invoking R scripts from a linux shell ?
Hello, I have written perl programs that extract data from a text file, process them, and create other text files, which I'd like to apply some statistics too (for example with R). I'd like to do it all in once , with a single script. I'm not familiar with R, I'd like to know if this task could be accomplished by creating a linux shells that launches the perl scripts and then R functions that maybe pass back some results to the system like in this schema: S --- Perl H - E --- R functions L - L Is it possible ? Where can I get information to do that? (to call R from a shell, in background) Are other better way to do that? Thank you very much! Enrico. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] invoking R scripts from a linux shell ?
-Original Message-
From: Enrico Curiotto [mailto:[EMAIL PROTECTED]
Hello,
I have written perl programs that extract data from a
text file, process them, and create other text files,
which I'd like to apply some statistics too (for
example with R).
I'd like to do it all in once , with a single script.
I'm not familiar with R, I'd like to know if this task
could be accomplished by creating a linux shells that
launches the perl scripts and then R functions that
maybe pass back some results to the system like in
this schema:
S --- Perl
H -
E --- R functions
L -
L
You can run R scripts in batch mode and direct output to file. That would be by far
the simplest. Or, you could explore RSOAP to run R as a web service which allows
creation of R sessions which persist (i.e. the binary data objects stay around)
between requests from another application (which could include a Perl script using
Perl's soap libraries). A third option is the Rserve system which allows connection
to R sessions using TCP/IP from other software applications.
See the R helpfile on the BATCH command (?BATCH) and/or
http:ess.r-project.org/Zope/projects/RSOAP/ and/or
http://stats.math.uni-augsburg.de/Rserve/
HTH,
-Eric
Is it possible ?
Where can I get information to do that? (to call R
from a shell, in background)
Are other better way to do that?
Thank you very much!
Enrico.
__
[EMAIL PROTECTED] mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
This email message, including any attachments, is for the so...{{dropped}}
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Re: [R] invoking R scripts from a linux shell ?
On Thu, 15 Jan 2004, Enrico Curiotto wrote: Hello, I have written perl programs that extract data from a text file, process them, and create other text files, which I'd like to apply some statistics too (for example with R). I'd like to do it all in once , with a single script. I'm not familiar with R, I'd like to know if this task could be accomplished by creating a linux shells that launches the perl scripts and then R functions that maybe pass back some results to the system like in this schema: You could call R in BATCH mode from the perl script using one of the system interface operators, e.g., system, or use the 'Shell' module. I have also bumped (but didn't try yet) into R-Perl interface called RSPerl which might be much more than you what you need. I think it is under the Omega link in the R website. If not google for RSPerl. 'R --help' will give you pointers to running R in BATCH mode. Itay -- [EMAIL PROTECTED] Fred Hutchinson Cancer Research Center __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
