Re: [Rd] R package BibTex entries: looking for a more general solution
On 12/19/2011 2:02 AM, Renaud Gaujoux wrote: Hi, I actually adapted and integrated this feature into Achim's -- nice -- function (posted on r-help). Romain included it a couple of weeks ago into the bibtex package as function write.bib, and submitted the update to CRAN, but some NOTEs in the check delayed its availability on CRAN. You can still install and try out the new version with: install.packages(bibtex, repos=http://R-Forge.R-project.org;) Keys for multiple citations are generated as pkgname%i, which might not be ideal, but works ok though. It might be better not number the first (main) citation. Romain, I think I will submit a patch for this. Hope this helps. Thanks, Renaud I now have a working function, Rpackages.bib() that is roughly equivalent to your write.bib() and other related material at http://euclid.psych.yorku.ca/SCS/Private/Rbibs/ Also, see the document http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpkg-test.pdf which reports some problems perl fixes for the generated bibentries. These might be incorporated into the functions to make the resulting bibtex files directly usable. Your bibtex package seems the most natural place for this. Also, write.bib() doesn't seem to work unless you pass a list of package names. write.bib() Error in is(entry, bibentry) : argument entry is missing, with no default write.bib(NULL) Error in write.bib(NULL) : Invalid argument `entry`: expected a bibentry object or a character vector of package names. best, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R package BibTex entries: looking for a more general solution
Indeed I broke the function when adding support for bibentry objects... By the way, let's give credits back to Ceasars: I am not the author of the bibtex package, Romain Francois is. I just contributed the write.bib function, mainly inspired by Achim's function. Romain, I will send a fix for this now. Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa On 19/12/2011 15:56, Michael Friendly wrote: On 12/19/2011 2:02 AM, Renaud Gaujoux wrote: Hi, I actually adapted and integrated this feature into Achim's -- nice -- function (posted on r-help). Romain included it a couple of weeks ago into the bibtex package as function write.bib, and submitted the update to CRAN, but some NOTEs in the check delayed its availability on CRAN. You can still install and try out the new version with: install.packages(bibtex, repos=http://R-Forge.R-project.org;) Keys for multiple citations are generated as pkgname%i, which might not be ideal, but works ok though. It might be better not number the first (main) citation. Romain, I think I will submit a patch for this. Hope this helps. Thanks, Renaud I now have a working function, Rpackages.bib() that is roughly equivalent to your write.bib() and other related material at http://euclid.psych.yorku.ca/SCS/Private/Rbibs/ Also, see the document http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpkg-test.pdf which reports some problems perl fixes for the generated bibentries. These might be incorporated into the functions to make the resulting bibtex files directly usable. Your bibtex package seems the most natural place for this. Also, write.bib() doesn't seem to work unless you pass a list of package names. write.bib() Error in is(entry, bibentry) : argument entry is missing, with no default write.bib(NULL) Error in write.bib(NULL) : Invalid argument `entry`: expected a bibentry object or a character vector of package names. best, -Michael __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R package BibTex entries: looking for a more general solution
Hi, I actually adapted and integrated this feature into Achim's -- nice -- function (posted on r-help). Romain included it a couple of weeks ago into the bibtex package as function write.bib, and submitted the update to CRAN, but some NOTEs in the check delayed its availability on CRAN. You can still install and try out the new version with: install.packages(bibtex, repos=http://R-Forge.R-project.org;) Keys for multiple citations are generated as pkgname%i, which might not be ideal, but works ok though. It might be better not number the first (main) citation. Romain, I think I will submit a patch for this. Hope this helps. Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R package BibTex entries: looking for a more general solution
Back in 2010 I raised this issue, and there was some discussion,
https://stat.ethz.ch/pipermail/r-devel/2010-November/058987.html
The goal, then, as now is to have a way to produce a bibtex-clean .bib
file (i.e., not requiring
manual editing except in unusual circumstances) reflecting installed
packages
for use in writing where one often needs/wants to cite all packages used
in a given article.
Achim wrote the function below which largely does this job, quite
nicely now that most
DESCRIPTION files now contain Authors@R fields. However, something
changed since
R 2.11.1 when I tried this last, so that the function no longer
generates keys for packages
which contain *more than one citation*.
I've tried debugging with browser(), but can't figure out how to make
the lines around FIXME
work. Can someone help?
You can see the result from this at
http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpackages-2.14.0.bib
The function is also at:
# Original code by Achim Zeileis, 16 Dec 2009, R-help
# Added: support header and preamble
Rpackages.bib - function(filename = paste(Rpackages-,getRversion(),
.bib, sep=),
header=TRUE, preamble=NULL, suppress.warnings=TRUE, verbose = TRUE)
{
## installed packages
pkgs - unique(installed.packages()[,1])
if (suppress.warnings) warn - options(warn=-1)
bibs - lapply(pkgs, function(x) try(toBibtex(citation(x
if (suppress.warnings) options(warn)
n.installed - length(bibs)
## omit failed citation calls
ok - !(sapply(bibs, class) == try-error)
pkgs - pkgs[ok]
bibs - bibs[ok]
n.converted - sum(ok)
## unify to list of Bibtex
bibs - lapply(bibs, function(x) if(inherits(x, Bibtex)) list(x)
else x)
## FIXME: add bibtex keys to each entry [the line below does not work!!]
pkgs - lapply(seq_along(pkgs), function(i) if(length(bibs[[i]]) 1)
paste(pkgs[i], 1:length(bibs[[i]]), sep = ) else pkgs[i])
pkgs - do.call(c, pkgs)
bibs - do.call(c, bibs)
for(i in seq_along(pkgs)) bibs[[i]][1] -
gsub({,, paste({, pkgs[i], ,, sep = ), bibs[[i]][1], fixed
= TRUE)
if(header) header - gsub(^, %, toLatex(sessionInfo()))
output - file(filename, a)
cat(header, preamble, sep='\n', file=output, append=TRUE)
## write everything to a single .bib file
writeLines(do.call(c, lapply(bibs, as.character)), con=output)
close(output)
if(verbose) cat(Converted, n.converted, of, n.installed,
package citations to BibTeX,
\nResults written to file, filename, \n)
## return Bibtex items invisibly
invisible(bibs)
}
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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Re: [Rd] R package BibTex entries: looking for a more general solution
Michael,
meanwhile the bibentry class that Kurt mentioned back in the discussion
in 2010 is fully implemented in R. Hence the code can be simplified when
working with the bibentry objects directly (instead of the Bibtex
objects derived from them).
I've quickly hacked some code to illustrate how the function needs to be
modified but I didn't have the time to integrate it into the function
(I'm currently traveling).
## query packages and their bibentries
pkgs - unique(installed.packages()[,1])
bibs - lapply(pkgs, function(x) try(citation(x)))
## exclude those with errors
ok - !(sapply(bibs, class) == try-error)
pkgs - pkgs[ok]
bibs - bibs[ok]
## number of bibentries per package
nref - sapply(bibs, length)
## merge all bibentries
bibs - do.call(c, bibs)
## add citation keys
bibkeys - lapply(1:length(nref), function(i)
if(nref[i] 1) paste(pkgs[i], 1:nref[i], sep = :) else pkgs[i])
bibs$key - as.list(unlist(bibkeys))
And then you just need to say toBibtex(bibs) or writeLines(toBibtex(bibs))
or something along those lines.
For more details on the new classes, see this recent working paper by Kurt
Duncan and myself: http://epub.wu.ac.at/3269/.
So much for today.
Best wishes,
Z
On Fri, 16 Dec 2011, Michael Friendly wrote:
Back in 2010 I raised this issue, and there was some discussion,
https://stat.ethz.ch/pipermail/r-devel/2010-November/058987.html
The goal, then, as now is to have a way to produce a bibtex-clean .bib file
(i.e., not requiring
manual editing except in unusual circumstances) reflecting installed
packages
for use in writing where one often needs/wants to cite all packages used in
a given article.
Achim wrote the function below which largely does this job, quite nicely
now that most
DESCRIPTION files now contain Authors@R fields. However, something changed
since
R 2.11.1 when I tried this last, so that the function no longer generates
keys for packages
which contain more than one citation.
I've tried debugging with browser(), but can't figure out how to make the
lines around FIXME
work. Can someone help?
You can see the result from this at
http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpackages-2.14.0.bib
The function is also at:
# Original code by Achim Zeileis, 16 Dec 2009, R-help
# Added: support header and preamble
Rpackages.bib - function(filename = paste(Rpackages-,getRversion(),
.bib, sep=),
header=TRUE, preamble=NULL, suppress.warnings=TRUE, verbose = TRUE)
{
## installed packages
pkgs - unique(installed.packages()[,1])
if (suppress.warnings) warn - options(warn=-1)
bibs - lapply(pkgs, function(x) try(toBibtex(citation(x
if (suppress.warnings) options(warn)
n.installed - length(bibs)
## omit failed citation calls
ok - !(sapply(bibs, class) == try-error)
pkgs - pkgs[ok]
bibs - bibs[ok]
n.converted - sum(ok)
## unify to list of Bibtex
bibs - lapply(bibs, function(x) if(inherits(x, Bibtex)) list(x) else x)
## FIXME: add bibtex keys to each entry [the line below does not work!!]
pkgs - lapply(seq_along(pkgs), function(i) if(length(bibs[[i]]) 1)
paste(pkgs[i], 1:length(bibs[[i]]), sep = ) else pkgs[i])
pkgs - do.call(c, pkgs)
bibs - do.call(c, bibs)
for(i in seq_along(pkgs)) bibs[[i]][1] -
gsub({,, paste({, pkgs[i], ,, sep = ), bibs[[i]][1], fixed =
TRUE)
if(header) header - gsub(^, %, toLatex(sessionInfo()))
output - file(filename, a)
cat(header, preamble, sep='\n', file=output, append=TRUE)
## write everything to a single .bib file
writeLines(do.call(c, lapply(bibs, as.character)), con=output)
close(output)
if(verbose) cat(Converted, n.converted, of, n.installed,
package citations to BibTeX,
\nResults written to file, filename, \n)
## return Bibtex items invisibly
invisible(bibs)
}
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R package BibTex entries: looking for a more general solution
I strongly support this proposal! I also find it inconvenient to cite
some R packages and really do not like edit the BibTeX entries
manually.
Regards,
Yihui
--
Yihui Xie xieyi...@gmail.com
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On Wed, Nov 3, 2010 at 8:44 AM, Michael Friendly frien...@yorku.ca wrote:
== Summary ==
* Problem: BibTeX entries extracted from R packages via citation() require
too much manual editing to be
of general use.
* Proposal: Date: fields should be made mandatory in package DESCRIPTION
files, perhaps
beginning with warnings from R CMD check
* Proposal: Package authors should be encouraged to use a (new)
Contributors: field in the DESCRIPTION file
rather than packing all information into the Author: field, which at present
cannot often be parsed by BibTeX.
* Files: All test files referred to here can be found at
http://euclid.psych.yorku.ca/SCS/Private/Rbibs/
== Details ==
Around 16 Dec. 2009, I queried R-help about automating the extraction of
citation()s from R packages. The stimulus
was that some journals, notably JSS, now require a reference and citation of
every R package mentioned,
and it is a pain to create these manually, no less maintain them for current
versions.
The result of that query was a function, Rpackage.bibs() by Achim Zeileis
that I have been using ever since.
Code in: http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpackages.bib.R
On one current system I get the following:
Rpackage.bibs(file=Rpackages-R.2.11.1.bib)
Converted 230 of 230 package citations to BibTex
Results written to file Rpackages-R.2.11.1.bib
Warning messages:
1: In citation(x) :
no date field in DESCRIPTION file of package 'codetools'
2: In citation(x) :
no date field in DESCRIPTION file of package 'gridBase'
3: In citation(x) : no date field in DESCRIPTION file of package 'iplots'
See:
http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpkg-test.pdf
for the result of processing this .bib file with latex/bibtex using the
jss.bst bibliography style
I'm writing to R-Devel because the DESCRIPTION and inst/CITATION files in R
packages provide the
basic data used in citation() and any methods based on this, and yet the
information in these files is
often insufficient to generate well-formed BibTeX entries for use in
vignettes and publications.
One easy case is illustrated above, where 3 packages have no Date: field so
the BibTeX gets no
year = {},
and references get printed as Murrell, P () for gridBase. (In my
original test under R 2.9.1, there where
~ 20 such warnings.) Thus, I propose that Date: be a required field in
DESCRIPTION files, and
R CMD check complain if this is not found.
The more difficult case has to do with the Author: field in the DESCRIPTION
file (when no CITATION file is present)
People can write whatever they want here, and the result looks sort of OK
when printed by citation(), but confuses
BibTeX mightly. One example:
citation(akima)
To cite package ‘akima’ in publications use:
Fortran code by H. Akima R port by Albrecht Gebhardt aspline function
by Thomas Petzoldt petzo...@rcs.urz.tu-dresden.de enhancements and
corrections by Martin Maechler (2009). akima: Interpolation of
irregularly spaced data. R package version 0.5-4.
http://CRAN.R-project.org/package=akima
A BibTeX entry for LaTeX users is
@Manual{,
title = {akima: Interpolation of irregularly spaced data},
author = {Fortran code by H. Akima R port by Albrecht Gebhardt aspline
function by Thomas Petzoldt petzo...@rcs.urz.tu-dresden.de enhancements
and corrections by Martin Maechler},
year = {2009},
note = {R package version 0.5-4},
url = {http://CRAN.R-project.org/package=akima},
}
ATTENTION: This citation information has been auto-generated from the
package DESCRIPTION file and may need manual editing, see
‘help(citation)’ .
Yes, the ATTENTION note does say that manual editing may be necessary, but I
think a worthy goal would be
to try to reduce the need for this.
One simple way to do that would be to support an extra Contributions: field
in the DESCRIPTION file,
so that Authors: can be more cleanly separated for the purpose of creating
well-structured BibTeX.
Perhaps others have better ideas.
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street Web:http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
__
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Re: [Rd] R package BibTex entries: looking for a more general solution
Michael Friendly writes:
Thanks for the suggestions. In fact, we are currently working on this
issue. A lot of improvements have already been done, see ?person and
?bibentry for R 2.12.0 or later, especially the details and examples
sections. Some more work still needs to be done, though. We will write a
primer that introduces the new features when all of them are available.
Best
-k
== Summary ==
* Problem: BibTeX entries extracted from R packages via citation()
require too much manual editing to be
of general use.
* Proposal: Date: fields should be made mandatory in package DESCRIPTION
files, perhaps
beginning with warnings from R CMD check
* Proposal: Package authors should be encouraged to use a (new)
Contributors: field in the DESCRIPTION file
rather than packing all information into the Author: field, which at
present cannot often be parsed by BibTeX.
* Files: All test files referred to here can be found at
http://euclid.psych.yorku.ca/SCS/Private/Rbibs/
== Details ==
Around 16 Dec. 2009, I queried R-help about automating the extraction of
citation()s from R packages. The stimulus
was that some journals, notably JSS, now require a reference and
citation of every R package mentioned,
and it is a pain to create these manually, no less maintain them for
current versions.
The result of that query was a function, Rpackage.bibs() by Achim
Zeileis that I have been using ever since.
Code in: http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpackages.bib.R
On one current system I get the following:
Rpackage.bibs(file=Rpackages-R.2.11.1.bib)
Converted 230 of 230 package citations to BibTex
Results written to file Rpackages-R.2.11.1.bib
Warning messages:
1: In citation(x) :
no date field in DESCRIPTION file of package 'codetools'
2: In citation(x) :
no date field in DESCRIPTION file of package 'gridBase'
3: In citation(x) : no date field in DESCRIPTION file of package 'iplots'
See:
http://euclid.psych.yorku.ca/SCS/Private/Rbibs/Rpkg-test.pdf
for the result of processing this .bib file with latex/bibtex using the
jss.bst bibliography style
I'm writing to R-Devel because the DESCRIPTION and inst/CITATION files
in R packages provide the
basic data used in citation() and any methods based on this, and yet the
information in these files is
often insufficient to generate well-formed BibTeX entries for use in
vignettes and publications.
One easy case is illustrated above, where 3 packages have no Date: field
so the BibTeX gets no
year = {},
and references get printed as Murrell, P () for gridBase. (In my
original test under R 2.9.1, there where
~ 20 such warnings.) Thus, I propose that Date: be a required field in
DESCRIPTION files, and
R CMD check complain if this is not found.
The more difficult case has to do with the Author: field in the
DESCRIPTION file (when no CITATION file is present)
People can write whatever they want here, and the result looks sort of
OK when printed by citation(), but confuses
BibTeX mightly. One example:
citation(akima)
To cite package ‘akima’ in publications use:
Fortran code by H. Akima R port by Albrecht Gebhardt aspline function
by Thomas Petzoldt petzo...@rcs.urz.tu-dresden.de enhancements and
corrections by Martin Maechler (2009). akima: Interpolation of
irregularly spaced data. R package version 0.5-4.
http://CRAN.R-project.org/package=akima
A BibTeX entry for LaTeX users is
@Manual{,
title = {akima: Interpolation of irregularly spaced data},
author = {Fortran code by H. Akima R port by Albrecht Gebhardt aspline
function by Thomas Petzoldt petzo...@rcs.urz.tu-dresden.de
enhancements and corrections by Martin Maechler},
year = {2009},
note = {R package version 0.5-4},
url = {http://CRAN.R-project.org/package=akima},
}
ATTENTION: This citation information has been auto-generated from the
package DESCRIPTION file and may need manual editing, see
‘help(citation)’ .
Yes, the ATTENTION note does say that manual editing may be necessary,
but I think a worthy goal would be
to try to reduce the need for this.
One simple way to do that would be to support an extra Contributions:
field in the DESCRIPTION file,
so that Authors: can be more cleanly separated for the purpose of
creating well-structured BibTeX.
Perhaps others have better ideas.
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb:http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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