From 9ae42bd20bc2543a94cf1581ba9820c2f9e3afbd Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 20 Apr 2023 19:53:28 +0200 Subject: Fix and rebuild documentation, see NEWS I had to fix the two pathway vignettes, as they did not work with the released version any more. So they and the multistart vignette which got some small fixes as well were rebuilt. Complete rebuild of the online docs with the released version. The documentation of the 'hierarchial_kinetics' format had to be fixed as well. --- docs/reference/hierarchical_kinetics.html | 197 ++++++++++++++++++++++++++++++ 1 file changed, 197 insertions(+) create mode 100644 docs/reference/hierarchical_kinetics.html (limited to 'docs/reference/hierarchical_kinetics.html') diff --git a/docs/reference/hierarchical_kinetics.html b/docs/reference/hierarchical_kinetics.html new file mode 100644 index 00000000..98764bf0 --- /dev/null +++ b/docs/reference/hierarchical_kinetics.html @@ -0,0 +1,197 @@ + +Hierarchical kinetics template — hierarchical_kinetics • mkin + + +
+
+ + + +
+
+
+

Hierarchical kinetics template

+ Source: R/hierarchical_kinetics.R + +
+ +
+

R markdown format for setting up hierarchical kinetics based on a template +provided with the mkin package. This format is based on rmarkdown::pdf_document. +Chunk options are adapted. Echoing R code from code chunks and caching are +turned on per default. character for prepending output from code chunks is +set to the empty string, code tidying is off, figure alignment defaults to +centering, and positioning of figures is set to "H", which means that +figures will not move around in the document, but stay where the user +includes them.

+
+ +
+ 
hierarchical_kinetics(..., keep_tex = FALSE)
+
+ +
+

Arguments

+
...
+

Arguments to rmarkdown::pdf_document

+ + +
keep_tex
+

Keep the intermediate tex file used in the conversion to PDF

+ +
+
+

Value

+ + +

R Markdown output format to pass to +render

+ + +
+
+

Details

+

The latter feature (positioning the figures with "H") depends on the LaTeX +package 'float'. In addition, the LaTeX package 'listing' is used in the +template for showing model fit summaries in the Appendix. This means that +the LaTeX packages 'float' and 'listing' need to be installed in the TeX +distribution used.

+

On Windows, the easiest way to achieve this (if no TeX distribution +is present before) is to install the 'tinytex' R package, to run +'tinytex::install_tinytex()' to get the basic tiny Tex distribution, +and then to run 'tinytex::tlmgr_install(c("float", "listing"))'.

+
+ +
+

Examples

+ 

+# \dontrun{
+library(rmarkdown)
+# The following is now commented out after the relase of v1.2.3 for the generation
+# of online docs, as the command creates a directory and opens an editor
+#draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin")
+# }
+
+
+
+
+ +
+ + +
+ + + + + + + + -- cgit v1.2.1