How to create a vignette for an R package (CC297)

Vignettes are powerful tools for helping users learn how to use your R package. In this episode, Pat shows how to use the tools from the {usethis} R package to build a vignette to introduce users to the {phylotypr} R package. This episode is part of an ongoing effort to develop an R package that implements the naive Bayesian classifier for classifying 16S rRNA gene sequences.

The link to the mothur wiki for the RDP reference files: https://mothur.org/wiki/rdp_reference...
Other reference files can be accessed here: https://mothur.org/wiki/taxonomy_outl...


If you want to get a physical copy of R Packages: https://amzn.to/43pMR8L
If you want a free, online version of R packages: https://r-pkgs.org/

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/mothur/trainset19/...

#rstats #usethis #devtools #rdp #16S #classification #classifier #microbialecology #microbiome

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0:00 Introduction
1:58 Refactoring package's data objects
10:44 Updating documentation for data objects
19:24 Update preliminary vignette with trainset9
20:53 Creating true package vignette with use_vignette()
26:05 Writing and rendering vignette Rmd file
32:20 Filing issues in GitHub file tracker
33:33 Inspecting vignette in built package