Reorganize S4 code and documentation

[hsloot]

Related issues

None

Checklist

• [x] R CMD CHECK successful
• [x] tests included
• [x] documentation included or updated
• [x] commit messages follow commit guidelines

Optional, but recommended:

• [x] code passes lintr::lint_package() without errors

Description

Proposed changes:

• Re-organize S4 code
• Adapt documentation if required

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 95.85%. Comparing base (6e3272a) to head (f7bf5d6).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #117 +/- ## ========================================== + Coverage 95.78% 95.85% +0.07% ========================================== Files 46 55 +9 Lines 1399 1399 ========================================== + Hits 1340 1341 +1 + Misses 59 58 -1 ```

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