[R] One pdf file with plots and text output

tom sgouros tomfool at as220.org
Wed Oct 17 14:55:20 CEST 2007


Latex has its own search path for packages like sweave.sty.  Run the
texconfig program and look at the configuration.  The TEXMF variable is
the one you're interested in.  Search your system for a file called
texmf.cnf, and edit that to change the TEXMF.  It sounds like the sweave
installation doesn't do that, or maybe it failed in your case.

 -tom


Romain Francois <rfrancois at mango-solutions.com> wrote:

> You can also specify the full path of the latex package, for me:
> 
> \usepackage{/usr/local/lib/R/share/texmf/Sweave}
> 
> Regards,
> 
> Romain
> 
> ONKELINX, Thierry wrote:
> > It works fine with me (on windows). But I've copied sweave.sty into my
> > workdirectory. See the Sweave FAQ
> > (http://www.ci.tuwien.ac.at/~leisch/Sweave/FAQ.html#x1-14000A.12)
> >
> >
> > ------------------------------------------------------------------------
> > ----
> > ir. Thierry Onkelinx
> > Instituut voor natuur- en bosonderzoek / Research Institute for Nature
> > and Forest
> > Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
> > methodology and quality assurance
> > Gaverstraat 4
> > 9500 Geraardsbergen
> > Belgium
> > tel. + 32 54/436 185
> > Thierry.Onkelinx at inbo.be
> > www.inbo.be 
> >
> > Do not put your faith in what statistics say until you have carefully
> > considered what they do not say.  ~William W. Watt
> > A statistical analysis, properly conducted, is a delicate dissection of
> > uncertainties, a surgery of suppositions. ~M.J.Moroney
> >
> >
> >
> >   
> >> -----Oorspronkelijk bericht-----
> >> Van: Rainer M Krug [mailto:Rainer+R-help at krugs.de] 
> >> Verzonden: woensdag 17 oktober 2007 14:17
> >> Aan: ONKELINX, Thierry
> >> CC: r-help
> >> Onderwerp: Re: [R] One pdf file with plots and text output
> >>
> >> I am getting somewhere - but running system("pdflatex 
> >> GrowthAll") fails, as it does not find sweave.sty. I already 
> >> linked the directory where it can be found 
> >> (/usr/lib/R/share/texmf/) into my personal texfm directory 
> >> (/texmf/tex/latex/R)\ and ran texhash (as root and as n ormal 
> >> user), but it still does not find it. If I enter the filename 
> >> manually, pdflatex works.
> >>
> >> Any ideas?
> >>
> >> Rainer
> >>
> >>
> >> ONKELINX, Thierry wrote:
> >>     
> >>> You create a source file ("GrowthAll.Rnw") that looks a bit 
> >>>       
> >> like this
> >>     
> >>> \documentclass[11pt]{report}
> >>> \usepackage{Sweave}
> >>> \SweaveOpts{echo = FALSE}
> >>> \begin{document}
> >>>
> >>> <<fig = T>>=
> >>> x.lm <- lm()
> >>> plot(x.lm)
> >>> @
> >>>
> >>> <<>>=
> >>> summary(x.lm)
> >>> @
> >>> \end{document}
> >>>
> >>>
> >>> Then run in R: 
> >>> Sweave("GrowthAll.Rnw")
> >>> system("pdflatex GrowthAll")
> >>>
> >>> Have a look at the Sweave manual. It contains some examples.
> >>>
> >>> HTH,
> >>>
> >>> Thierry
> >>>
> >>>
> >>>       
> >> ----------------------------------------------------------------------
> >>     
> >>> --
> >>> ----
> >>> ir. Thierry Onkelinx
> >>> Instituut voor natuur- en bosonderzoek / Research Institute 
> >>>       
> >> for Nature 
> >>     
> >>> and Forest Cel biometrie, methodologie en kwaliteitszorg / Section 
> >>> biometrics, methodology and quality assurance Gaverstraat 4 9500 
> >>> Geraardsbergen Belgium tel. + 32 54/436 185 
> >>>       
> >> Thierry.Onkelinx at inbo.be 
> >>     
> >>> www.inbo.be
> >>>
> >>> Do not put your faith in what statistics say until you have 
> >>>       
> >> carefully 
> >>     
> >>> considered what they do not say.  ~William W. Watt A statistical 
> >>> analysis, properly conducted, is a delicate dissection of 
> >>> uncertainties, a surgery of suppositions. ~M.J.Moroney
> >>>
> >>>
> >>>
> >>>       
> >>>> -----Oorspronkelijk bericht-----
> >>>> Van: Rainer M Krug [mailto:Rainer+R-help at krugs.de]
> >>>> Verzonden: woensdag 17 oktober 2007 11:28
> >>>> Aan: ONKELINX, Thierry
> >>>> CC: Prof Brian Ripley; r-help
> >>>> Onderwerp: Re: [R] One pdf file with plots and text output
> >>>>
> >>>> ONKELINX, Thierry wrote:
> >>>>         
> >>>>> I use Sweave for this kind of purposes.
> >>>>>           
> >>>> I was thinking about Sweave as well, but I don't 
> >>>>         
> >> understand how I can 
> >>     
> >>>> use it.
> >>>>
> >>>> Let's say I have a source file, which defines a function
> >>>>
> >>>> DoGrowthAll <- function()
> >>>>    {
> >>>>      pdf("GrowthAll.pdf", height=11, width=8, paper="a4")
> >>>>      sink("GrowthAll.txt")
> >>>>      try(
> >>>>          {
> >>>>            plot(x.lm)
> >>>>            summary(xlm)
> >>>>            .
> >>>>            .
> >>>>            .
> >>>>          }
> >>>>          )
> >>>>      sink()
> >>>>      dev.off()
> >>>>      system("xpdf ./GrowthAll.pdf", wait=FALSE)
> >>>>    }
> >>>>
> >>>> Now how can I use Sweave to create this report?
> >>>>
> >>>> Rainer
> >>>>
> >>>>         
> >>>>> HTH,
> >>>>>
> >>>>> Thierry
> >>>>>
> >>>>>
> >>>>>           
> >> ---------------------------------------------------------------------
> >>     
> >>>> -
> >>>>         
> >>>>> --
> >>>>> ----
> >>>>> ir. Thierry Onkelinx
> >>>>> Instituut voor natuur- en bosonderzoek / Research Institute
> >>>>>           
> >>>> for Nature
> >>>>         
> >>>>> and Forest Cel biometrie, methodologie en kwaliteitszorg 
> >>>>>           
> >> / Section 
> >>     
> >>>>> biometrics, methodology and quality assurance Gaverstraat 4 9500 
> >>>>> Geraardsbergen Belgium tel. + 32 54/436 185
> >>>>>           
> >>>> Thierry.Onkelinx at inbo.be
> >>>>         
> >>>>> www.inbo.be
> >>>>>
> >>>>> Do not put your faith in what statistics say until you have
> >>>>>           
> >>>> carefully
> >>>>         
> >>>>> considered what they do not say.  ~William W. Watt A statistical 
> >>>>> analysis, properly conducted, is a delicate dissection of 
> >>>>> uncertainties, a surgery of suppositions. ~M.J.Moroney
> >>>>>
> >>>>>
> >>>>>
> >>>>>           
> >>>>>> -----Oorspronkelijk bericht-----
> >>>>>> Van: r-help-bounces at r-project.org
> >>>>>> [mailto:r-help-bounces at r-project.org] Namens Rainer M Krug
> >>>>>> Verzonden: woensdag 17 oktober 2007 11:02
> >>>>>> Aan: Prof Brian Ripley
> >>>>>> CC: r-help
> >>>>>> Onderwerp: Re: [R] One pdf file with plots and text output
> >>>>>>
> >>>>>> Prof Brian Ripley wrote:
> >>>>>>             
> >>>>>>> On Wed, 17 Oct 2007, Rainer M Krug wrote:
> >>>>>>>
> >>>>>>>               
> >>>>>>>> Hi
> >>>>>>>>
> >>>>>>>> I create one pdf file with plots via pdf() and one text
> >>>>>>>>                 
> >>>> file with
> >>>>         
> >>>>>>>> text via sink() that works very nice. But I would prefer
> >>>>>>>>                 
> >>>>>> to have one
> >>>>>>             
> >>>>>>>> pdf file with plots and the text which I store in the
> >>>>>>>>                 
> >>>>>> te=xt file via sink(). I.e.
> >>>>>>             
> >>>>>>>> x.lm<-lm(...)
> >>>>>>>> pdf()
> >>>>>>>> plot(x.lm)
> >>>>>>>> NOW THE TEXT OF summary(xlm) IN THE PDF FILE
> >>>>>>>> dev.off()
> >>>>>>>>
> >>>>>>>> Is this possible or is there a different format which I
> >>>>>>>>                 
> >>>> could use?
> >>>>         
> >>>>>>> You can easily post-process the files to obtain a single
> >>>>>>>               
> >>>>>> file.  Going
> >>>>>>             
> >>>>>>> from text to pdf involves many arbitrary choices, but a 
> >>>>>>>               
> >> good text 
> >>     
> >>>>>>> processor will help you make those and incorporate pdf 
> >>>>>>>               
> >> figures: I 
> >>     
> >>>>>>> would use pdflatex, but there are many other tools to 
> >>>>>>>               
> >> do the job.
> >>     
> >>>>>> Thanks for pointing out the post-processing route (I have done 
> >>>>>> similar script based pdf creations via pdflatex before),
> >>>>>>             
> >>>> but I would
> >>>>         
> >>>>>> like to have something only for me to make it easier to read the 
> >>>>>> results.
> >>>>>> It does not need to be nicely layouted - just the text in
> >>>>>>             
> >>>> the pdf in
> >>>>         
> >>>>>> whatever font would be fine.
> >>>>>>
> >>>>>> ______________________________________________
> >>>>>> R-help at r-project.org mailing list
> >>>>>> 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.
> >>     
> >>>>> ______________________________________________
> >>>>> R-help at r-project.org mailing list
> >>>>> 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.
> >>>>>           
> >>> ______________________________________________
> >>> R-help at r-project.org mailing list
> >>> 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.
> >>>       
> >>     
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > 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.
> >
> >   
> 
> 
> -- 
> Mango Solutions
> data analysis that delivers
> 
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> 
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
> 


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 ------------------------
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 http://sgouros.com  
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