Re: [R] Sweave, Bibtex, package references
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
[EMAIL PROTECTED]
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:[EMAIL PROTECTED]
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
[EMAIL PROTECTED]
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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
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
__
R-help@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.
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.
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
[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
__
R-help@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.
Re: [R] Sweave, Bibtex, package references
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
[EMAIL PROTECTED]
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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
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
__
R-help@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.
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.
__
R-help@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.
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
[EMAIL PROTECTED]
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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
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
__
R-help@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.
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.
__
R-help@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.
Re: [R] Sweave, Bibtex, package references
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
[EMAIL PROTECTED]
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:[EMAIL PROTECTED]
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
[EMAIL PROTECTED]
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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED]
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
__
R-help@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.
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.
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
