Hierarchical kinetics template — hierarchical

+ +

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.

+ +

Usage

hierarchical_kinetics(..., keep_tex = FALSE)

+ +

Arguments

+ + +

...: Arguments to rmarkdown::pdf_document
keep_tex: Keep the intermediate tex file used in the conversion to PDF. +Note that this argument does not control whether to keep the auxiliary +files (e.g., .aux) generated by LaTeX when compiling .tex to +.pdf. To keep these files, you may set options(tinytex.clean = +FALSE).

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")
+# }
+
+