[R] One pdf file with plots and text output

[Rainer M Krug]

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.