Knit a directory of files from the command line

knit_dir.R

#!/usr/bin/env Rscript

# to run from command line:
## chmod +x knit_dir.R
## ./knit_dir.R <dir-name>

# from https://stackoverflow.com/a/49950761
# to avoid conflicts between packages
# breaking things
clean_search <- function() {
  defaults <- c(".GlobalEnv",
                paste0("package:", getOption("defaultPackages")),
                "Autoloads",
                "package:base")
  currentList <- search()
  deletes <- setdiff(currentList, defaults)
  for (entry in deletes)
    detach(entry, character.only = TRUE)
}

# function to knit directory
knit_dir <- function(dir) {
  # create the full path
  full_dir <- normalizePath(dir)
  
  # list the Rmd files with full names
  files <-
    list.files(full_dir, pattern = '*.Rmd$', full.names = TRUE)
  
  # render the files using all output formats in the YAML
  purrr::map(files, function(file) {
    # clean search list to avoid conflicts
    clean_search()
    
    # render the file using all
    # output formats in a new env
    rmarkdown::render(file,
                      output_format = "all",
                      envir = new.env())
  })
}

# pull out the first command line argument
dir <- commandArgs(trailingOnly = TRUE)[1]

# run the function
knit_dir(dir)

Have added the cleanSearch() function from https://stackoverflow.com/a/49950761 to fix conflicts between packages