[R] Sweave, Bibtex, package references

[Paolo Sonego]

Dear Thierry,

Thank you very much!
As usual, I should have RTFM :-[

Kind Regards,
Paolo

ONKELINX, Thierry ha scritto:
> Paolo,
>
> Try using \nocite{*}. That will cite every entry in your bibliography.
>
> 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 a inbo.be 
> www.inbo.be 
>
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to
> say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of
> data.
> ~ John Tukey
>
> -----Oorspronkelijk bericht-----
> Van: Paolo Sonego [mailto:paolo.sonego a gmail.com] 
> Verzonden: dinsdag 28 oktober 2008 18:08
> Aan: ONKELINX, Thierry
> CC: R-List Help - use this to post
> Onderwerp: Re: [R] Sweave, Bibtex, package references
>
> Dear Thierry,
>
> Thank you very much for you very useful advice!
> I managed to solve my specific problem with this code:
>
> <<echo=FALSE>>=
> package <- grep("^package:", search(), value = TRUE)
> keep <- sapply(package, function(x) x == "package:base" || 
> !is.null(attr(as.environment(x), "path")))
> package <- sub("^package:", "", package[keep])
> pkgDesc <- lapply(package, packageDescription)
> basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) && 
> x$Priority == "base")
> otherPkgs <- package[!basePkgs]
> cite.by.name <- function(x){
>      res <- toBibtex(citation(x))
>      if (is.list(res)) res <- res[[1]]
>      res[1] <- sub("{",paste("{",x,sep=''),res[1],fixed=TRUE)
>      res
> }
> # suppressWarnings(cite.by.name("annotate"))
> tmp <- sapply( otherPkgs, function(x) try( cite.by.name(x) ) )
> for (i in 1:length(tmp)){
>     capture.output(tmp[[i]], file= "Rpackages.bib", append=T)
> }
> @
>
>
> It does work, more or less, but still I need to write manually one by 
> one  \nocite{otherPkgs[[1]]} \nocite{otherPkgs[[2]]} etc.
> in order to pop up the references in the Bibliography section
> \bibliographystyle{abbrv}
> \bibliography{Rpackages}
>
>
> Any idea how to automate this procedure?
>
> Best Regards,
> Paolo
>
> ONKELINX, Thierry ha scritto:
>   
>> Dear Paolo,
>>
>> Have a look at this thread:
>>
>>     
> http://www.nabble.com/Automating-citations-in-Sweave-td20128175.html#a20
>   
>> 128175
>>
>> 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 a inbo.be 
>> www.inbo.be 
>>
>> To call in the statistician after the experiment is done may be no
>>     
> more
>   
>> than asking him to perform a post-mortem examination: he may be able
>>     
> to
>   
>> say what the experiment died of.
>> ~ Sir Ronald Aylmer Fisher
>>
>> The plural of anecdote is not data.
>> ~ Roger Brinner
>>
>> The combination of some data and an aching desire for an answer does
>>     
> not
>   
>> ensure that a reasonable answer can be extracted from a given body of
>> data.
>> ~ John Tukey
>>
>> -----Oorspronkelijk bericht-----
>> Van: r-help-bounces a r-project.org
>>     
> [mailto:r-help-bounces a r-project.org]
>   
>> Namens Paolo Sonego
>> Verzonden: dinsdag 28 oktober 2008 12:41
>> Aan: R-List Help - use this to post
>> Onderwerp: [R] Sweave, Bibtex, package references
>>
>> Dear all,
>> I'm a big fan and happy user of the Sweave package for routine
>> reporting.
>>  From inside a .Rnw script, I'd like to produce the references in
>>     
> bibtex
>   
>> format for each package loaded in the environment, write them in a
>>     
> .bib 
>   
>> file  and load them back from the
>> \bibliography{bibliography} statement.
>> Is this feasible?
>> Any help would be greatly appreciated!
>> Thanks in advance,
>> Paolo
>>
>> ______________________________________________
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>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
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> schrijver weer 
>   
>> en binden het INBO onder geen enkel beding, zolang dit bericht niet
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> bevestigd is
>   
>> door een geldig ondertekend document. The views expressed in  this
>>     
> message 
>   
>> and any annex are purely those of the writer and may not be regarded
>>     
> as stating 
>   
>> an official position of INBO, as long as the message is not confirmed
>>     
> by a duly 
>   
>> signed document.
>>   
>>     
>
>
> Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer 
> en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
> door een geldig ondertekend document. The views expressed in  this message 
> and any annex are purely those of the writer and may not be regarded as stating 
> an official position of INBO, as long as the message is not confirmed by a duly 
> signed document.
>