Update cheatsheet links

[jashapiro]

The training modules we have in the module-cheatsheets directory often point to documentation on http://rdocumentation.org, which seems to be either decaying or defunct. The most recent versions of packages described there are often out of date, including base R, which is only a max version of 3.6.2.

While this should not affect most of the content we are referring to, there are changes with R 4.0 that may come up, so we may want to update those links.

I also noticed that there were some links that no longer work (if they did before). These include the links to scran and scater, which point to versions past the ones that rdocumentation.org supports.

One idea is to switch over to https://rdrr.io, which seems to have more recent documentation. However, the documentation there is not versioned, so we would just be pointing people to whatever the latest (or at least fairly current) version of a particular function was. This may not be terrible, given that the links won't have to change in the future, but it is a little disappointing that you can't look up previous versions if the need arises.

[jaclyn-taroni]

This was slotted for this sprint, so wanted to give this a little "bump." It would be good to have this in progress before we meet next Tuesday.

[sjspielman]

Welp, @jaclyn-taroni this accidentally fell prey to my exploration of "why wont github notify me when I self-assign." Back on it now 💯

[sjspielman]

I think https://rdrr.io/ makes sense for this. One way to deal with versioning is to have a big caveat at the top of each cheatsheet, inside the existing blockquotes. For example, change:

The hyperlinks found in each piece of code will take you to the documentation for further information on the usage of each command.

to:

The hyperlinks found in each piece of code will take you to the documentation for further information on the usage of each command. Please be aware that the documentation will generally provide information about the given function's most current version, which will usually (but not always!) match what you have installed on your machine.

[sjspielman]

Will our RStudio server setup match the most up-to-date packages? For example, if we are using older versions of tidyverse packages, the documentation is potentially misleading. If our server is on older versions, we'll need something besides rdrr for tidyverse specifically. I don't expect anything in base R/utils to differ between versions 3-4, as long as we aren't doing |>.

Edit: This might be my brain on PBTA-mode with the older rocker.

[jashapiro]

We are not using the most up-to-date, because we freeze with renv, but we are on R 4 now, and the versions are pretty new.

Current version info (TMI):
https://github.com/AlexsLemonade/training-modules/blob/master/renv.lock

(Yes, you are thinking of PBTA... we are trying to keep this more current!)

[sjspielman]

@jashapiro Any strong feelings for/against using tidyverse.org domain links for the tidyverse packages? For those functions, I think it will be more helpful for users because all of tidyverse is integrated there, and it's easier to hop around to vignettes and other functions. I don't see those links changing anytime soon.

[jashapiro]

@jashapiro Any strong feelings for/against using tidyverse.org domain links for the tidyverse packages? For those functions, I think it will be more helpful for users because all of tidyverse is integrated there, and it's easier to hop around to vignettes and other functions. I don't see those links changing anytime soon.

I think those should be fine. I wish they allowed version-specific links, but since we have to abandon that anyway...

[jashapiro]

closed by #521

[jashapiro]

Oops, not closed. The following cheatsheets still need updates to match the changes in #521

• RNA-seq-cheatsheet.md
• pathway-analysis-cheatsheet.md
• machine-learning-cheatsheet.md

[jaclyn-taroni]

Should we file a separate issue for the remaining cheatsheets? We don't necessarily need those to be fixed before this training (as they are not immediately relevant). I know we link to them somewhere in the course website, but all links to the course website are "governed" by the release tag and we've already cut the release.

[jashapiro]

Yes, a separate issue would probably be better.

[jaclyn-taroni]

Filed #528 - closing this!