diff options
| -rw-r--r-- | R/hierarchical_kinetics.R | 21 | ||||
| -rw-r--r-- | man/hierarchical_kinetics.Rd | 20 |
2 files changed, 38 insertions, 3 deletions
diff --git a/R/hierarchical_kinetics.R b/R/hierarchical_kinetics.R index e545754a..ae60d43c 100644 --- a/R/hierarchical_kinetics.R +++ b/R/hierarchical_kinetics.R @@ -1,7 +1,24 @@ #' Hierarchical kinetics template #' #' R markdown format for setting up hierarchical kinetics based on a template -#' provided with the mkin package. +#' 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. +#' +#' 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"))'. #' #' @inheritParams rmarkdown::pdf_document #' @param ... Arguments to \code{rmarkdown::pdf_document} @@ -24,7 +41,7 @@ hierarchical_kinetics <- function(..., keep_tex = FALSE) { 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(cache = TRUE, comment = "", tidy = FALSE, echo = TRUE) knitr::opts_chunk$set(fig.align = "center", fig.pos = "H") options(knitr.kable.NA = "") diff --git a/man/hierarchical_kinetics.Rd b/man/hierarchical_kinetics.Rd index 2a8e211c..f965df1a 100644 --- a/man/hierarchical_kinetics.Rd +++ b/man/hierarchical_kinetics.Rd @@ -17,7 +17,25 @@ R Markdown output format to pass to } \description{ R markdown format for setting up hierarchical kinetics based on a template -provided with the mkin package. +provided with the mkin package. This format is based on \link[rmarkdown:pdf_document]{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. +} +\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{ |