[R] Sweave, Bibtex, package references

[ONKELINX, Thierry]

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 op 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 op 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 op 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 op r-project.org
[mailto:r-help-bounces op 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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> and any annex are purely those of the writer and may not be regarded
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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.