R/cite_packages.r

In karldw/kdw.junk: Miscellaneous Functions Karl Found Useful

.cite_one <- function(pkg, ...) {
  cite <- utils::toBibtex(utils::citation(pkg, ...))
  if (identical(pkg, "base")) {
    pkg <- "r_core"
  }

  # Handle cases where authors list multiple citations (only pick the first)
  cite_lines <- paste(cite)
  empty_lines <- which(cite_lines == "")
  bracket_lines <- which(cite_lines == "}")  # lone bracket on a line
  if (length(empty_lines) + 1 != length(bracket_lines)) {
    stop("Multi-citation detection failed for ", pkg)
  }
  if (length(empty_lines) > 0) {
    if (! all((empty_lines - 1) %in% bracket_lines)) {
      stop("Multi-citation detection failed for ", pkg)
    }
    # Take only the first cite by taking all the lines up until the first
    # empty line (which we just confirmed is after a closing bracket)
    cite <- cite[seq_len(bracket_lines[1])]
    class(cite) <- "Bibtex"
  }
  cite[1] <- .tidy_gsub(cite[1], "(@[a-zA-Z]+{),", paste0("\\1", pkg, ","))

  # Also adjust to the biblatex "@software" and set a version
  # cite[1] <- gsub("@Manual{", "@software{", cite[1], fixed = TRUE)
  version_row <- which(names(cite) == "note")
  cite[version_row] <- cite[version_row] |>
    .tidy_gsub("R package version ", "", fixed = TRUE)
  names(cite)[version_row] <- "version"
  # Make CRAN lower case
  if ("url" %in% names(cite)) {
    cite["url"] <- .tidy_gsub(cite["url"], "CRAN.R", "cran.r", fixed = TRUE)
  }
  # Convert quotes to forms that work with latex
  if ("title" %in% names(cite)) {
    cite["title"] <- cite["title"] |>
      .tidy_gsub(" '", " `", fixed = TRUE) |>
      .tidy_gsub("` ", "' ", fixed = TRUE) |>
      .tidy_gsub("`}", "'}", fixed = TRUE)
  }
  return(cite)
}

#' Cite currently attached pacakges
#'
#' @param outfile Write results to a file. The default, NULL, doesn't write a file.
#' @param include Extra packages to include, beyond those that have been
#'  attached (ones that you've called `library()` for.)
#'  The default, "base", includes a citation for R itself.
#' @return A list of citations, invisibly
#'
#' Note that some packages provide multiple citations. This function will pick only the
#' first one they provided.
#'
#' @examples
#' cite_attached_packages()
#' @export
cite_attached_packages <- function(outfile = NULL, include = "base") {
  prev_enc <- getOption("encoding")
  on.exit(options(encoding = prev_enc), add = TRUE)
  options(encoding = "utf8")
  # Don't auto-include RevoUtilsMath (can still be manually included with the include param)
  # If no packages have been attached, otherPkgs will be NULL, which is fine.
  pkg_names <- setdiff(names(utils::sessionInfo()$otherPkgs), "RevoUtilsMath")

  include <- include[! is.na(include)]
  pkg_names <- c(pkg_names, include)
  cites <- lapply(pkg_names, .cite_one)
  if (!is.null(outfile)) {
    cites_text <- paste(lapply(cites, paste, collapse = "\n"), collapse = "\n\n")
    writeLines(cites_text, outfile, useBytes = TRUE)
  }
  invisible(cites)
}