Build Comprehensive TMB documentation Overview Files Description *.Rmd Human generated documentation. Auto-converted to *.md. Doxyfile Controls the doxygen specific documentation. mainpage.Rmd Controls the doxygen mainpage. Add a new vignette by dumping a .Rmd file in this folder. Vignettes show up under 'related pages' in doxygen. Requirements Command line tools sudo apt-get install doxygen pandoc pandoc-citeproc graphviz librsvg2-dev R packages install.packages(c("knitr", "bookdown", "rsvg")) Export options Command Output description Output location make dox Reduced doxygen (easier to read) html/index.html make dox-full Full doxygen html/index.html make gitbook Gitbook _book/Tutorial.html make inject_links Insert doxygen links in previous _book/Tutorial.html make pdf-book Pdf book _book/_main.pdf make refman Full reference manual latex/refman.pdf