Using Roxygen2 to document functions in an R package (CC293)

Including documentation for the functions in your R package is critical to helping end users use your package. Documenting your code can easily be done using Roxygen2. In this Code Club, Pat uses Roxygen2 syntax to help document the functions in his phylotypr R package. Along the way, he refactors the code to improve the documentation and shows some tricks to improving the utility of the documentation. Documenting code isn't the most fun part of package development, but it's really important! This episode is part of an ongoing effort to develop an R package that implements the naive Bayesian classifier.

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You can find my blog post for this episode at https://www.riffomonas.org/code_club/....

Check out the GitHub repository at the:
* Beginning of the episode: https://github.com/riffomonas/phyloty...
* End of the episode: https://github.com/riffomonas/phyloty...

#rstats #readr #vroom #data.table #read.delim #rdp #16S #classification #classifier #microbialecology #microbiome

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0:00 Introduction
3:24 Separating functions into different files
7:44 Basics of documenting functions
11:18 Using markdown in documentation
18:33 Inheriting documentation for parameters from other functions
25:31 Formatting multi-paragraph text
28:00 Inserting a "Note" section
29:04 Adding hyper links to documentation
33:25 Inserting a "References" section
36:52 Re-using references across functions
38:26 Checking that package builds correctly