Generate a BibTeX file of all installed packages

Rpackages_bib.R

#' Generate a BibTeX file of all installed packages
#' 
#' This function finds all packages installed in your R library and calls
#' `citation()` for each, collecting the BibTeX entries and writing these to
#' a file. It handles situations where there are multiple citations for a package.
#'
#' @param filename  Name of the .bib file to write to. 
#' @param header    Include a header giving `sessionInfo()` ?
#' @param preamble  Preamble for the BibTeX file
#' @param prefix    String to prefix the in the bibtex key
#' @param suppress.warnings Whether to suppress warnings
#' @param verbose
#'
#' @author Achim Zeileis, Michael Friendly 
#' @seealso [knitr::write_bib()] 
#'
#' @return   Invisibly returns the bibtex entries
#' @export
#'
#' @examples
#' Rpackages_bib()
#' Rpackages_bib(prefix="R-")    # match what knitr::write_bib() does
#' 
#' 

# Original code by Achim Zeileis, 16 Dec 2009, R-help
# Revised code for R 2.14.0 by Achim Zeleis, 16 Dec 2011, R-devel
# Added: support for header and preamble

## TODO:
#   - fix page numbers from (\d+)-(\d+) to $1--$2
#   - fix title MiXed CaSe words to {MiXed} {CaSe}
## Temp fix: use perl
#% Fixups:
#% 	title MiXed CaSe words modified to {MiXed} {CaSe} by:
#% 		perl -pi~ -e "m|title| && s|\s(\w+[A-Z]+\w*)(\b)| {$1}$2|g" Rpackages-2.14.0.bib 
#%   [This still does not handle strings like "S", "R", "(Voroni)", etc.]
#%	page numbers modified from dd-dd to dd--dd by
#%		perl -pi~ -e "m|pages| && s|(\d+)-(\d+)|$1--$2|" Rpackages-2.14.0.bib


 
Rpackages_bib <- function(filename = paste0("Rpackages-",getRversion(), ".bib"), 
		header=TRUE, 
		preamble=NULL, 
		prefix = NULL,
		suppress.warnings=TRUE, 
		verbose = TRUE)
{
  ## query packages and their bibentries
  pkgs <- unique(installed.packages()[,1])
  if (suppress.warnings) {
  	warn <- options(warn=-1)
  	on.exit(options(warn))
  }
  bibs <- lapply(pkgs, function(x) try(citation(x)))
  n.installed <- length(bibs)

  ## exclude those with errors
  ok <- !(sapply(bibs, class) == "try-error")
  pkgs <- pkgs[ok]
  bibs <- bibs[ok]
  n.converted <- sum(ok)

  ## number of bibentries per package
  nref <- sapply(bibs, length)
  ncit <- sum(nref)

  ## merge all bibentries
  bibs <- do.call("c", bibs)

  ## add citation keys; need to number those where there's more than one
  bibkeys <- lapply(1:length(nref), function(i)
    if(nref[i] > 1) paste0(prefix, pkgs[i], 1:nref[i], sep = "-") 
    else paste0(prefix, pkgs[i]))
  bibs$key <- as.list(unlist(bibkeys))

	# make page numbers proper: fix from (\d+)-(\d+) to $1--$2
	# this doesn't quite work-- it screws up the structure of the bibs object 
#  for (i in 1:length(bibs)) {
#    if(!is.null(bibs[[i]]$pages)) {
#    	bibs[[i]]$pages <-  sub('(\\d+)-(\\d+)', '\\1--\\2', bibs[[i]]$pages) 
#    	}
#    } 
	
	if(header) { 
		header <- gsub("^", "%", toLatex(sessionInfo()))
		header <- c(paste("%BibTeX file:", filename, "written", Sys.Date(), "by Rpackages.bib()\n"),
							header) 
	}
	unlink(filename)
	output <- file(filename, "a")
	cat(header, preamble, sep='\n', file=output, append=TRUE)
	writeLines(toBibtex(bibs), con=output)
  close(output)
  if(verbose) cat("Converted", n.converted, "citations in", n.installed,
    "packages to BibTeX, containing", ncit, "entries.",
    "\nResults written to file", filename, "\n")

  ## return Bibtex items invisibly
  invisible(bibs)
}