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")
# }