Docs overhaul

[dsweber2]

Checklist

Please:

• Make sure this PR is against "dev", not "main".
• Request a review from one of the current epipredict main reviewers:
  dajmcdon.
• Make sure to bump the version number in DESCRIPTION and NEWS.md.
  Always increment the patch version number (the third number), unless you are
  making a release PR from dev to main, in which case increment the minor
  version number (the second number).
• Describe changes made in NEWS.md, making sure breaking changes
  (backwards-incompatible changes to the documented interface) are noted.
  Collect the changes under the next release number (e.g. if you are on
  0.7.2, then write your changes under the 0.8 heading).
• Consider pinning the epiprocess version in the DESCRIPTION file if
  • You anticipate breaking changes in epiprocess soon
  • You want to co-develop features in epipredict and epiprocess

Change explanations for reviewer

Draft ready for review:

• Landing Page
• Getting Started
• Customized Forecasters
• Reference
  • Using the add/update/remove and adjust functions
  • Smooth Quantile regression
• preprocessing and models examples
• backtesting forecasters

Magic GitHub syntax to mark associated Issue(s) as resolved when this is merged into the default branch

• Resolves https://github.com/cmu-delphi/forecasting-team-meta/issues/26
• Resolves More clearly document symmetrize for residuals #264
• Resolves Switch vignettes to using standalone data #261
• Resolves Vignette illustrating FluSight Forecaster #256
• Resolves Clarify documentation for and sanity-check nafill_buffer usage #320
• Resolves Vignettes #232

[dajmcdon]

/preview-docs

[github-actions]

🚀 Deployed on https://67f5a1065c980a95c56b327c--epipredict.netlify.app

[dshemetov]

Our setup is generating docs in dev/, so the link is off, this works: https://6792d4953137ef0ce0547a4f--epipredict.netlify.app/dev/ Edit: this has been fixed

Also FYI: the bot edits its own comment for links. Each preview is a separate link and the links stick around for like 90 days. You can see the previous links in the comment edit history.

[dsweber2]

/preview-docs

[dsweber2]

So something weird is happening with the plot for flatline_forecaster, not really sure why. Going to dig into that next.

I added an option to replace the data for the autoplot so you can compare with new data instead

[dsweber2]

Draft of the getting started is ready, moving on to a draft of the "guts" page (name a placeholder), which is an overview of creating workflows by hand

[dsweber2]

So something weird is happening with the plot for flatline_forecaster, not really sure why. Going to dig into that next.

After some digging, I don't think there are any bugs, just some edge-case behavior that we may not want:

1. Thresholding and extrapolation don't interact well. In this case, the quantiles it fits are 0.05 and 0.95, and it correctly rounds the 5% quantile up to zero (b/c of the negative values it is actually negative w/out constraint). But, it also looks to plot the 2.5% and 97.5% quantiles, which extrapolate doesn't know should also be zero. This results in quantiles with negative values.
2. The other thing is that the interpolated quantiles change quite a bit after thresholding if there's not very many quantiles. For example, the median gets pushed up quite a bit, but the point prediction doesn't reflect that.

My take away: never fit just the 5% and 95% quantiles. At least do the 50%. That fixes most of the jank this uncovers.

[dsweber2]

/preview-docs

[dshemetov]

Including 0.5 into the user's selection sounds simple and reasonable to me. They can always filter out what they don't want.

[dsweber2]

/preview-docs

[dsweber2]

/preview-docs

@nmdefries this also updates the backtesting vignette; I'm dropping the Canadian example because it basically had no revisions.

[dsweber2]

/preview-docs

[dajmcdon]

My linewrapping preference is largely due to code review:

1. It starts being hard to read on the PR viewer;
2. More importantly, git flags the whole line as changed, so shorter lines means its easier to track the diff.

But the specifics don't matter to me so much.

[dsweber2]

\preview-docs

[dshemetov]

suggestion: make these visible in the code, so the vignette code can be reproduced by someone following along.