[R] Creating bibtex file of all installed packages?

[Achim Zeileis]

On Wed, 16 Dec 2009, Romain Francois wrote:

> 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.

Maybe not at the moment. Kurt and I have been working on some revisions of 
the "citation" code which hopefully get incorporated into R-devel early 
next year. I'll try to keep this issue in mind.
Z

> 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
>
>
>