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 Street Web: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
