From 886c9ef013124aa954d960c655b349b5340ff154 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 19 Dec 2022 12:31:56 +0100
Subject: Rename template folder, create format

Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used
as a document format in the template. In this way, the template file can
be freed from some R code and yaml options that the average user does
not have to be aware of.
---
 R/hierarchical_kinetics.R | 39 +++++++++++++++++++++++++++++++++++++++
 R/parplot.R               |  2 +-
 2 files changed, 40 insertions(+), 1 deletion(-)
 create mode 100644 R/hierarchical_kinetics.R

(limited to 'R')

diff --git a/R/hierarchical_kinetics.R b/R/hierarchical_kinetics.R
new file mode 100644
index 00000000..f7ffb333
--- /dev/null
+++ b/R/hierarchical_kinetics.R
@@ -0,0 +1,39 @@
+#' 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("New 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$set(echo = FALSE, cache = TRUE, comment = "", tidy = FALSE)
+  knitr::opts_chunk$set(fig.align = "center", fig.pos = "H")
+  options(knitr.kable.NA = "")
+
+  fmt <- rmarkdown::pdf_document(...,
+    keep_tex = keep_tex,
+    toc = TRUE,
+    includes = rmarkdown::includes(in_header = "header.tex"),
+    extra_dependencies = c("float", "listing", "framed")
+  )
+
+  return(fmt)
+}
diff --git a/R/parplot.R b/R/parplot.R
index e9c18947..3da4b51a 100644
--- a/R/parplot.R
+++ b/R/parplot.R
@@ -23,7 +23,7 @@
 #' of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478.
 #' doi: 10.1186/s12859-021-04373-4.
 #' @seealso [multistart]
-#' @importFrom stats median
+#' @importFrom stats median quantile
 #' @export
 parplot <- function(object, ...) {
   UseMethod("parplot")
-- 
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