R/citation.R

In knitr: A General-Purpose Package for Dynamic Report Generation in R

#' Generate BibTeX bibliography databases for R packages
#'
#' This function uses \code{utils::\link{citation}()} and
#' \code{utils::\link{toBibtex}()} to create bib entries for R packages and
#' write them in a file. It can facilitate the auto-generation of bibliography
#' databases for R packages, and it is easy to regenerate all the citations
#' after updating R packages.
#'
#' For a package, the keyword \samp{R-pkgname} is used for its bib item, where
#' \samp{pkgname} is the name of the package. Citation entries specified in the
#' \file{CITATION} file of the package are also included. The main purpose of
#' this function is to automate the generation of the package citation
#' information because it often changes (e.g. author, year, package version,
#' ...).
#'
#' There are at least two different uses for the URL in a reference list.  You
#' might want to tell users where to go for more information; in that case, use
#' the default \code{packageURL = TRUE}, and the first URL listed in the
#' \file{DESCRIPTION} file will be used. Be careful:  some authors don't put the
#' most relevant URL first. Alternatively, you might want to identify exactly
#' which version of the package was used in the document.  If it was installed
#' from CRAN or some other repositories, the version number identifies it, and
#' \code{packageURL = FALSE} will use the repository URL (as used by
#' \code{utils::\link{citation}()}).
#'
#' @param x Package names. Packages which are not installed are ignored.
#' @param file The (\file{.bib}) file to write. By default, or if \code{NULL},
#'   output is written to the R console.
#' @param tweak Whether to fix some known problems in the citations, especially
#'   non-standard format of author names.
#' @param width Width of lines in bibliography entries. If \code{NULL}, lines
#'   will not be wrapped.
#' @param prefix Prefix string for keys in BibTeX entries; by default, it is
#'   \samp{R-} unless \code{\link{option}('knitr.bib.prefix')} has been set to
#'   another string.
#' @param lib.loc A vector of path names of R libraries.
#' @param packageURL Use the \code{URL} field from the \file{DESCRIPTION} file.
#'   See Details below.
#' @return A list containing the citations. Citations are also written to the
#'   \code{file} as a side effect.
#' @note Some packages on CRAN do not have standard bib entries, which was once
#'   reported by Michael Friendly at
#'   \url{https://stat.ethz.ch/pipermail/r-devel/2010-November/058977.html}. I
#'   find this a real pain, and there are no easy solutions except contacting
#'   package authors to modify their DESCRIPTION files. Anyway, the argument
#'   \code{tweak} has provided ugly hacks to deal with packages which are known
#'   to be non-standard in terms of the format of citations; \code{tweak = TRUE}
#'   is by no means intended to hide or modify the original citation
#'   information. It is just due to the loose requirements on package authors
#'   for the DESCRIPTION file. On one hand, I apologize if it really mangles the
#'   information about certain packages; on the other, I strongly recommend
#'   package authors to consider the \samp{Authors@@R} field (see the manual
#'   \emph{Writing R Extensions}) to make it easier for other people to cite R
#'   packages. See \code{knitr:::.tweak.bib} for details of tweaks. Also note
#'   this is subject to future changes since R packages are being updated. If
#'   you want to contribute more tweaks, please edit the file
#'   \file{inst/misc/tweak_bib.csv} in the source package.
#' @export
#' @author Yihui Xie and Michael Friendly
#' @examplesIf interactive()
#' write_bib(c('RGtk2', 'gWidgets'), file = 'R-GUI-pkgs.bib')
#' unlink('R-GUI-pkgs.bib')
#'
#' write_bib(c('animation', 'rgl', 'knitr', 'ggplot2'))
#' write_bib(c('base', 'parallel', 'MASS'))  # base and parallel are identical
#' write_bib('cluster', prefix = '')  # a empty prefix
#' write_bib('digest', prefix = 'R-pkg-')  # a new prefix
#' write_bib('digest', tweak = FALSE)  # original version
#'
#' # what tweak=TRUE does
#' str(knitr:::.tweak.bib)
write_bib = function(
  x = .packages(), file = '', tweak = TRUE, width = NULL,
  prefix = getOption('knitr.bib.prefix', 'R-'), lib.loc = NULL,
  packageURL = TRUE
) {
  system.file = function(...) base::system.file(..., lib.loc = lib.loc)
  citation = function(...) utils::citation(..., lib.loc = lib.loc)
  x = x[nzchar(x)] # remove possible empty string
  idx = mapply(system.file, package = x) == ''
  if (any(idx)) {
    warning('package(s) ', paste(x[idx], collapse = ', '), ' not found')
    x = x[!idx]
  }
  # no need to write bib for packages in base R other than `base` itself
  x = setdiff(x, setdiff(xfun::base_pkgs(), 'base'))
  x = sort(x)
  bib = sapply(x, function(pkg) {
    cite = citation(pkg, auto = if (pkg != 'base') {
      meta = packageDescription(pkg, lib.loc = lib.loc)
      # don't use the citation() URL if the package has provided its own URL
      if (is.null(meta$URL)) return(meta)
      if (packageURL) meta$Repository = meta$RemoteType = NULL
      # the package may have provided multiple URLs, in which case we use the
      # first. We also work around a bug in citation() up to R 4.3.1. The grep
      # pattern here is problematic, but it's what citation() was using.
      if (getRversion() < '4.3.2' && grepl('[, ]', meta$URL))
        meta$URL = sub('[, ].*', '', meta$URL)
      # always remove URLs after the first one
      meta$URL = sub(',? .*', '', meta$URL)
      meta
    })
    if (tweak) {
      # e.g. gpairs has "gpairs: " in the title
      cite$title = gsub(sprintf('^(%s: )(\\1)', pkg), '\\1', cite$title)
      # e.g. KernSmooth has & in the title
      cite$title = gsub(' & ', ' \\\\& ', cite$title)
    }
    entry = toBibtex(cite)
    entry[1] = sub('\\{,$', sprintf('{%s%s,', prefix, pkg), entry[1])
    entry
  }, simplify = FALSE)
  if (tweak) {
    for (i in intersect(names(.tweak.bib), x)) {
      message('tweaking ', i)
      bib[[i]] = merge_list(bib[[i]], .tweak.bib[[i]])
    }
    bib = lapply(bib, function(b) {
      b['author'] = sub('Duncan Temple Lang', 'Duncan {Temple Lang}', b['author'])
      # remove the ugly single quotes required by CRAN policy
      b['title'] = gsub("(^|\\W)'([^']+)'(\\W|$)", '\\1\\2\\3', b['title'])
      # keep the first URL if multiple are provided
      if (!is.na(b['note'])) b['note'] = gsub(
        '(^.*?https?://.*?),\\s+https?://.*?(},\\s*)$', '\\1\\2', b['note']
      )
      if (!('year' %in% names(b))) b['year'] = .this.year
      b
    })
  }
  # also read citation entries from the CITATION file if provided
  bib2 = lapply(x, function(pkg) {
    if (pkg == 'base') return()
    if (system.file('CITATION', package = pkg) == '') return()
    cites = citation(pkg, auto = FALSE)
    cites = Filter(x = cites, function(cite) {
      # exclude entries identical to citation(pkg, auto = TRUE)
      !isTRUE(grepl('R package version', cite$note))
    })
    s = make_unique(unlist(lapply(cites, function(cite) {
      if (is.null(cite$year)) format(Sys.Date(), '%Y') else cite$year
    })))
    mapply(cites, s, FUN = function(cite, suffix) {
      # the entry is likely to be the same as citation(pkg, auto = TRUE)
      if (isTRUE(grepl('R package version', cite$note))) return()
      entry = toBibtex(cite)
      entry[1] = sub('\\{,$', sprintf('{%s%s,', pkg, suffix), entry[1])
      entry
    }, SIMPLIFY = FALSE)
  })
  bib = c(bib, unlist(bib2, recursive = FALSE))
  bib = lapply(bib, function(b) {
    idx = which(names(b) == '')
    if (!is.null(width)) b[-idx] = str_wrap(b[-idx], width, 2, 4)
    structure(c(b[idx[1L]], b[-idx], b[idx[2L]], ''), class = 'Bibtex')
  })
  if (!is.null(file) && length(x)) write_utf8(unlist(bib), file)
  invisible(bib)
}

.this.year = sprintf('  year = {%s},', format(Sys.Date(), '%Y'))

#' @include utils.R

# hack non-standard author fields
.tweak.bib = local({
  x = read.csv(inst_dir('misc/tweak_bib.csv'), stringsAsFactors = FALSE)
  if (Sys.getlocale('LC_COLLATE') == 'en_US.UTF-8') {
    x = x[order(xtfrm(x$package)), , drop = FALSE]  # reorder entries by package names
    try_silent(write.csv(x, inst_dir('misc/tweak_bib.csv'), row.names = FALSE))
  }
  setNames(
    lapply(x$author, function(a) c(author = sprintf('  author = {%s},', a))),
    x$package
  )
})