Merge branch 'main' into custom_lsoda_call

1 files changed, 40 insertions, 0 deletions

diff --git a/R/hierarchical_kinetics.R b/R/hierarchical_kinetics.R
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+#' Hierarchical kinetics template
+#'
+#' R markdown format for setting up hierarchical kinetics based on a template
+#' provided with the mkin package.
+#'
+#' @inheritParams rmarkdown::pdf_document
+#' @param ... Arguments to \code{rmarkdown::pdf_document}
+#'
+#' @return R Markdown output format to pass to
+#'   \code{\link[rmarkdown:render]{render}}
+#'
+#' @examples
+#'
+#' \dontrun{
+#' library(rmarkdown)
+#' draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin")
+#' }
+#'
+#' @export
+hierarchical_kinetics <- function(..., keep_tex = FALSE) {
+
+  if (getRversion() < "4.1.0")
+    stop("You need R with version > 4.1.0 to compile this document")
+
+  if (!requireNamespace("knitr")) stop("Please install the knitr package to use this template")
+  if (!requireNamespace("rmarkdown")) stop("Please install the rmarkdown package to use this template")
+  knitr::opts_chunk$set(echo = FALSE, cache = TRUE, comment = "", tidy = FALSE, echo = TRUE)
+  knitr::opts_chunk$set(fig.align = "center", fig.pos = "H")
+  options(knitr.kable.NA = "")
+
+  fmt <- rmarkdown::pdf_document(...,
+    keep_tex = keep_tex,
+    toc = TRUE,
+    toc_depth = 3,
+    includes = rmarkdown::includes(in_header = "header.tex"),
+    extra_dependencies = c("float", "listing", "framed")
+  )
+
+  return(fmt)
+}