compile_ling: Compile the stock assessment document(s) for a given species

In iantaylor-NOAA/Lingcod_2021: Estimate the Status of Lingcod off the US West Coast in 2021

Compile the stock assessment document(s) for a given species

Description

Compile the stock assessment document(s) for a given species where the number of documents depends on the number of directories that you pass to dir. Typically, this happens in the directory called doc that stores a single directory for each stock. bookdown::render_book will be called inside on each directory in dir.

Usage

compile_ling(dir = "North", wipe = FALSE, ...)

Arguments

dir	A terribly named parameter that specifies which pdf you want to build. For lingcod, this is just "North" or "South". Also for just lingcod, we can use get_groups(info_groups) to get a vector of all the groups we have, which results in both documents being built.
wipe	A logical values specifying if you want to remove all cached objects. For lingcod, this will remove plots, custom_plots, and cached markdown files and will lead to the document taking approximately an hour to build.
...	Arguments you want to pass to bookdown::render_book.

Details

status: This function is currently in beta testing, which means that it

• might be helpful,

• could contain bugs,

• will more than likely have non-descript error and warning messages. Please post an issue or email the author of this function. Thank you for helping test it out, and we hope the pain is worth the gain!

index.Rmd When specifying a directory to bookdown::render_book, the file index.Rmd is normally used as the master file for rendering the book and all other files are brought in as chapters in alphabetical order. Here, in the sa4ss package we use ⁠00a.Rmd⁠ as the indexing file and all other .Rmd files are sourced in alphabetical order. The renaming is done automatically for you in the call to draft and just mentioned here for completeness.

Author(s)

Kelli F. Johnson and undergoing testing by Kelli F. Johnson

See Also

See compile_internal for the non-vectorized version of what happens inside each directory.

Other compile: compile_changebookname(), compile_internal()

Examples

## Not run: 
# An example for lingcod in 2021.
compile_ling(dir = file.path(get_groups(info_groups)))

## End(Not run)

iantaylor-NOAA/Lingcod_2021 documentation built on Oct. 30, 2024, 6:42 p.m.