vignettes/render_vignettes.R

In lvclark/polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

# Script to render vignettes for source package.
# Not to be included in package build.
library(rmarkdown)

render("polyRADtutorial.Rmd") # html_vignette
render("isolocus_sorting.Rmd")

# markdown version viewable on GitHub
render("polyRADtutorial.Rmd", 
       output_format = github_document(toc = TRUE, html_preview = FALSE))
render("isolocus_sorting.Rmd", 
       output_format = github_document(toc = TRUE, html_preview = FALSE))

cleanEqns <- function(file){
  mylines <- readLines(file)
  mylines <- gsub("$\\\\frac{ploidy - 1}{ploidy}$", "(ploidy - 1)/ploidy", fixed = TRUE,
                  mylines)
  mylines <- gsub("\\(\\frac{ploidy - 1}{ploidy}\\)", "(ploidy - 1)/ploidy", fixed = TRUE,
                  mylines)
  mylines <- gsub("\\(H_{ind}/H_E\\)", "*H*<sub>*i**n**d*</sub>/*H*<sub>*E*</sub>",
                  fixed = TRUE, mylines)
  writeLines(mylines, con = file)
}

cleanEqns("polyRADtutorial.md")
cleanEqns("isolocus_sorting.md")