Updates to vignettes and pkgdown

[joshwlambert]

This PR addresses:

• Add sections to pkgdown reference index #139
• link-citations: true in vignettes #140
• Convert references file from Bibtex to CSL-JSON #143

Update vignettes:

• now using CSL-JSON to handle bibliography
• link citations

Improved pkgdown site:

• Add custom function reference to group functions
• Add custom article reference to group and navbar header to vignettes
• Turn on code folding in vignettes (default show code, except for plotting chunks)

Removed functions from reference:

• create_prob_dist() (exported -> unexported)
• check_optim_conv() (unexported in manual -> unexported not in manual)

[joshwlambert]

Ideally, ends_with() or matches() would be used for the <epidist> and <vb_epidist> methods in the pkgdown reference. However, the distributions functions are methods of these classes and they are separated under their own header in the pkgdown reference. For this reason only <epiparam> uses ends_with() to group class methods.

[Bisaloo]

Ideally, ends_with() or matches() would be used for the and <vb_epidist> methods in the pkgdown reference. However, the distributions functions are methods of these classes and they are separated under their own header in the pkgdown reference. For this reason only uses ends_with() to group class methods.

You can create complex selection combinations in pkgdown index. E.g., ends_with("\\.epidist) and not tagged with with a specific keyword.

For example:

epiverse-trace/linelist@372d288#diff-4696b5e124c0b2a7e0ef4617c2e5be11de4ea153568c38fe79ee4925a8cb6b2e

[joshwlambert]

@Bisaloo Thanks for the tip, I didn't realise this was possible. Updates applied in a1cf03d

[jamesmbaazam]

This PR is very insightful.