#' PeerJ journal format.
#'
#' Format for creating submissions to The PeerJ.
#'
#' @inheritParams rmarkdown::pdf_document
#' @param ... Additional arguments to \code{base_format}
#' @param base_format The function to use for the base format of the article.
#'   By default, this is \code{rmarkdown::pdf_document}, but to use bookdown's
#'   cross-referencing feature, this can be set to \code{bookdown::pdf_document2}
#'
#' @return R Markdown output format to pass to
#'   \code{\link[rmarkdown:render]{render}}
#'
#' @details This was adapted from the
#' \href{https://www.overleaf.com/latex/templates/latex-template-for-peerj-journal-and-pre-print-submissions/ptdwfrqxqzbn}{PeerJ Overleaf Template}.
#'
#' @note If you use \code{rmarkdown::pdf_document()}, all internal references
#' (i.e. tables and figures) must use \code{\\ref\{\}} whereas with
#' \code{bookdown::pdf_document2()}, you can additionally use \code{\\@@ref()}.
#'
#' @examples
#'
#' \dontrun{
#' library(rmarkdown)
#' draft("MyArticle.Rmd", template = "peerj_article", package = "rticles")
#' }
#'
#' @export
peerj_article <- function(..., keep_tex = TRUE, citation_package = "none",
                          base_format = rmarkdown::pdf_document) {
  if (inherits(base_format, "character")){
    FMT <- eval(parse(text = base_format))
  } else {
    FMT <- match.fun(base_format)
  }
  out <- FMT(...,
             citation_package = citation_package,
             keep_tex = keep_tex,
             template = find_resource("peerj_article", "template.tex"))
}