Sync main with dev, epiprocess 0.9.0

[dshemetov]

Checklist

Please:

• [x] Make sure this PR is against "dev", not "main".
• [x] Request a review from one of the current epipredict main reviewers: dajmcdon.
• [x] 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).
• [x] 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).
• [x] 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

This is mostly so we can get our main documentation page updated. It's currently 10 versions behind!

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

• Resolves #{issue number}

[dajmcdon]

Agreed that this is way behind. Before we do this, I'd like to resolve

• [x] #377
• [x] #379
• [x] #383