Issue #481: Update pkgdown structure

[nikosbosse]

Description

This PR closes #481 by reorganising the pgkdown function categories, broadly following the structure outlined in the paper.

In addition, there are some minor fixes like

• fixing the doi rendering in the DESCRIPTION
• fixing the CRAN downloads badge

Checklist

• My PR is based on a package issue and I have explicitly linked it.
• I have included the target issue or issues in the PR title as follows: issue-number: PR title
• I have tested my changes locally.
• I have added or updated unit tests where necessary.
• I have updated the documentation if required.
• I have built the package locally and run rebuilt docs using roxygen2.
• My code follows the established coding standards and I have run lintr::lint_package() to check for style issues introduced by my changes.
• I have added a news item linked to this PR.
• I have reviewed CI checks for this PR and addressed them as far as I am able.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.84%. Comparing base (4fee240) to head (25c59e9).
Report is 46 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #886      +/-   ##
==========================================
+ Coverage   95.47%   98.84%   +3.37%     
==========================================
  Files          21       21              
  Lines        1568     1556      -12     
==========================================
+ Hits         1497     1538      +41     
+ Misses         71       18      -53     

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[nikosbosse]

I'm going to go ahead and merge this as there isn't really any substantial code change here and I want to make progress with #837.

I mean apologies.

Also I'd still be interested whether you think the pkgdown categories broadly make sense.