R help - Dec 2004 - Paths for Shell Scripts called from R

Hello list,

I suspect this is more a linux question than an R question, but I'll
describe my situation in case
anyone here knows of an elegant solution.

I'm using Sweave and R to create thousands of customized reports. Within an
R  loop, I have R create
a table.tex file using the CAT function which, for each iteration, creates a
unique table.tex file in
a subdirectory of the directory from which the master file is sourced. I have
written a shell script called
latexall that pdflatexs all the files in a given directory. I want to call
latexall from within R using the SYSTEM command after I've created all my
table.tex files. Later, the .pdfs of these tables are read into the
document using the includegraphics command (The reason I'm creating tables
this way is for
two reasons: 1. xtable and latextable are limited, especially when one is
producing complicated tables
with \multicolumn headings and \raisebox commands that make the tables look
nice; and 2. I've found
that precompiling tables and then inputing them into a .tex file using the
\includegraphics command
takes much of the headache out of table production in LaTeX. In particular,
tables that are too wide are
easily dealt with by changing the scale factor. Float placement also seems
easier to me when using
\includegraphics)

My bash shell script uses a standard for loop to loop over all the .tex file in
a directory

for f in *.tex

The problem that I'm having is that I can't seem to direct latexall to
the correct subdirectory without placing
latexall in the subdirectory with all the table.tex files and hard coding that
subdirectory into the the shell
script before using the SYSTEM command to call latexall.

for f in /home/directory/subdirectory/tables/*.tex  

Does anyone have an idea of how I can pass the appropriate path to my shell
script from within R?

I hope this makes sense. 

Any help greatly appreciated.

Damian

Damian Betebenner
Educational Research, Measurement & Evaluation
Lynch School of Education
Boston College
Chestnut Hill, MA 02467

(617) 552 4491

Damian Betebenner writes:
> Hello list,
> 
> I suspect this is more a linux question than an R question, but I'll
describe my situation in case
> anyone here knows of an elegant solution.
> 
...
> My bash shell script uses a standard for loop to loop over all the .tex
file in a directory
> 
> for f in *.tex
> 
> The problem that I'm having is that I can't seem to direct latexall
to the correct subdirectory without placing
> latexall in the subdirectory with all the table.tex files and hard coding
that subdirectory into the the shell
> script before using the SYSTEM command to call latexall.
> 
> for f in /home/directory/subdirectory/tables/*.tex  
> 
> Does anyone have an idea of how I can pass the appropriate path to my shell
script from within R?
> 
        You could use the $* argument in your bash script, and then pass
the argument via system(), on the call to the script. Suppose you have

$ cat pdflatexall.sh 
#!/bin/bash

for i in $1/*.tex; do
        echo pdflatex $i;
done

        In R you could call by using:

        system('pdflatexall.sh /tmp')

        Works fine here:

$ touch /tmp/bla1.tex /tmp/bla2.tex
$ R
> system('pdflatexall.sh /tmp')
pdflatex /tmp/bla1.tex
pdflatex /tmp/bla2.tex




--
Fernando Henrique Ferraz P. da Rosa
http://www.ime.usp.br/~feferraz

Damian Betebenner <damian.betebenner at bc.edu> writes:
> Does anyone have an idea of how I can pass the appropriate path to
> my shell script from within R?
Anything wrong with just setting the PATH variable? E.g.
>
Sys.putenv(PATH=paste(Sys.getenv("PATH"),"/home/bs/pd/scripts",sep=":"))
> system("SalesRank")
Sun Dec 12 00:10:55 CET 2004
29605


-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
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