On 12/16/2009 08:32 AM, Achim Zeileis wrote:
On Tue, 15 Dec 2009, Michael Friendly wrote:
Achim and others:
Achim's solution could be directly usable if it also added a BibTeX key,
perhaps just the name of the package to the '@Manual{,' initial line
of each. I wrapped the previous suggestions in a function, and played
around with the components, but can't quite see how to account for the
failed citation calls. Can anyone take the next step?
I had also thought about this after sending my previous solution, so
here is an update Michael's version of the function (renamed to the name
of the default file). Apart from some smaller touch-ups this has the
following changes:
- Instead of taking the unique() bibs, I now use the unique() pkgs.
(In principle, packages with the same name could be installed in
different libraries, potentially containing different citations.
But I thought it would be overkill to check for that.)
- Citation keys are simply "pkgname" if there is only a single
BibTeX item, and "pkgname1" to "pkgnameN" if there are N BibTeX
items.
(This does not assure that citation keys are unique, though. If
there is a package "foo" with 2 citation entries and another package
"foo2" with only a single entry, these could be confused. A workaround
would be to use "pkgname1" instead of "pkgname" as the citation key
even if there is a single citation only. But I thought that would
be less intuitive.)
Rpackages.bib <- function(file = "Rpackages.bib", verbose = TRUE)
{
## installed packages
pkgs <- unique(installed.packages()[,1])
bibs <- lapply(pkgs, function(x) try(toBibtex(citation(x))))
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)
## add bibtex keys to each entry
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)
## write everything to a single .bib file
writeLines(do.call("c", lapply(bibs, as.character)), file)
if(verbose) cat("Converted", n.converted, "of", n.installed,
"package citations to BibTeX",
"\nResults written to file", file, "\n")
## return Bibtex items invisibly
invisible(bibs)
}
Best,
Z
And you can read it back into R with package bibtex:
> require( bibtex )
> entries <- read.bib( "Rpackages.bib" )
but then although the key is read, it is not displayed, because of
utils:::toBibtex.citation:
> entries[[1]]
A BibTeX entry for LaTeX users is
@Manual{,
title = {ant: Version of ant specific to R},
author = {Romain Francois},
year = {2009},
note = {R package version 0.0-10},
}
> str( entries[[1]] )
List of 4
$ title : chr "ant: Version of ant specific to R"
$ author:List of 1
..$ :List of 2
.. ..$ name : Named chr [1:3] "Romain" "" "Francois"
.. .. ..- attr(*, "names")= chr [1:3] "first" "middle" "last"
.. ..$ email: NULL
.. ..- attr(*, "class")= chr "person"
..- attr(*, "class")= chr "personList"
$ year : chr "2009"
$ note : chr "R package version 0.0-10"
- attr(*, "class")= chr "citation"
- attr(*, "srcref")=Class 'srcref' atomic [1:6] 1 1 6 1 1 1
.. ..- attr(*, "srcfile")=Class 'srcfile' <environment: 0x8ed067c>
- attr(*, "entry")= chr "Manual"
- attr(*, "key")= chr "ant
Should I submit some patch to allow printing of the key when there is a
key attribute. Maybe the key could also be used for character based
indexing of citationList objects.
Romain
--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/HlX9 : new package : bibtex
|- http://tr.im/Gq7i : ohloh
`- http://tr.im/FtUu : new package : highlight
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