Version 2 Documentation Updates

[jwildfire]

I'm working on updates to the documentation for v2 and would like to use this discussion thread for feedback.

So far, I've rewritten the introductory "Shiny User Guide" vignette. If you've got time to give it a read and provide feedback that would be great. Feel free to edit the wiki page directly with any simple changes or to provide more general feedback as a response on this discussion thread.

I'll post responses here as more updates are available for review.

Thanks!

attn: @xni7 @samussiah @elimillera @JimBuchanan @mli1

[JimBuchanan]

Hi Jeremy, This is nicely done. Just one observation: This tab is created using the filter functionality included in the {datamods} pacakge<https://github.com/dreamRs/datamods#filter>. Package is misspelled. One question as an aside…the previous initialization code had an addition for loading larger datasets [safetyGraphicsApp(maxFileSize=100)]. Is there still a file limit that needs a line like this? I do have a very large SAS file of AE data and was wondering if I’m going to choke the app.

[jwildfire]

Thanks, Jim. I fixed the typo.

Good point about the file size. You could load it via safetyGraphicsApp(), but It would definitely be an issue in safetyGraphicsInit(). I just filed #613 to deal add that maxFileSize option there.

[xni7]

Vignette looks great, @jwildfire ! Just one comment: it would great to cross-reference various key vignettes, such as the data security one, which is related to deployment and backend data, advanced charting guide for developers etc. Pkgdown site is a nature place to put all relevant articles together. I think it would be really nice to update that prior to the R/Pharma workshop

[jwildfire]

Making some progress. Quick updates on the 4 vignettes from the call today:

• Overview vignette - Pretty much done. Thanks to @xni7 and @JimBuchanan for the reviews.
• Chart Vignette - Updated up to the Appendices. @elimillera @samussiah @xni7 @rescalan to review as time allows.
• Cookbook Vignette - Needs some tweaks using the most recent build, but should be pretty easy to update. @jwildfire to work on that after Chart Vignette
• Technical Vignette - Still just an outline. @xni7 to work on updates. We discussed just turning this in to a FAQ for the V2 release.

[jwildfire]

@xni7 I just did a quick reformat to the technical vignette to make it a FAQ.

@samussiah I added a Q/A about the rsconnect that included the code from earlier. Please Update with any other questions/feedback after you try to deploy internally.

[xni7]

not sure what the up arrow means on the left...

[jwildfire]

I think it's an upvote button ... though, it's not entirely clear we need both upvotes and the emoji replies ...

[jwildfire]

@xni7 @elimillera @samussiah @bzkrouse @rescalan - OK, I think I'm pretty much done with updates in the charts vignette. Thoughts/comments/edits very welcome!

[xni7]

Thanks @jwildfire, looks very nice! A couple of minor comments

• it may be better to archive those old vignettes from V1 to avoid confusion
• some advanced topics might be needed:
  • after adding hello_world chart, which is transient, how to make it persistent other than re-running the code, e.g. put into a pkg
  • how to connect other pkgs to {safetyGraphics}. e.g. if someone wrote a QTgraphics pkg. perhaps this would be a vignette for {safetyCharts} that can be linked to? e.g. how to develop a custom pkg similar to {safetyCharts}, or contribution guide to {safetyCharts}?

[jwildfire]

Thanks @xni7. I updated the sidebar in the wiki to hide the old pages. Also renamed files a bit to match the formatting in the package, so old links might not work. Click "wiki" in the navbar and using the sidebar should work though.

I like the advanced issues, but might hold off until after v2, unless someone else has time to add them.