[Bioc-devel] converting old Rnw vignettes to Rmd + BiocStyle

Levi Waldron |w@|dron@re@e@rch @end|ng |rom gm@||@com
Fri Jan 14 16:51:51 CET 2022

Bioconductor has many (>800) Rnw PDF vignettes that would be more
user-friendly if converted to using Rmd+BiocStyle. I've identified a couple
students who are willing to work on this, and have started a Trello board
to organize the work:
https://trello.com/b/nJHqzR1j/bioconductor-vignettes-rnw-rmd-project. I
have a couple questions for bioc-devel:

1. I've only started moving vignettes from pre-triage to "core team
maintained", "community-contributed low priority" (less downloaded
packages), and "community-contributed high priority" (highly downloaded
packages). Please use comments on Trello to note any packages you'd like to
see added to the lower or high-priority list, including your own. If you
want to do a bunch of triage, I can add you to the Trello board. Before
starting work on any community-contributed package, we will contact the
maintainer to confirm whether they will accept a pull request that updates
their vignette.
2. Anyone have experience with the many Rnw -> Rmd converters that a Google
search turns up? I see Mike Love and Laurent Gatto are responsible for one
of them (https://gist.github.com/lgatto/d9d0e3afcc0a4417e5084e5ca46a4d9e),
would you still recommend it? I expect there to be some manual cleanup in
addition to adding BiocStyle markup, but the less the better.
3. If you or anyone you know wants to help out, let me know, I'll be
organizing a little group to work on this together.



Levi Waldron

Associate Professor

Department of Epidemiology and Biostatistics

CUNY Graduate School of Public Health and Health Policy

Institute for Implementation Science in Population Health

55 W 125th St, New York NY 10035


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