Make non-user facing functions internal

[jamesmbaazam]

In this PR, I make a few changes:

• The simulation and analytical likelihood functions are made internal functions (and unexported) to resolve Unexport functions not directly called by users #131.
• The S3 constructors are also made internal to resolve Add examples to exported class constructors #160, removing the need to provide examples. Users are not expected to interact with the S3 functionality except for the print, summary, and aggregate methods.
• All internal functions are renamed to follow the dot-prefix naming style.
• A few documentation changes are also introduced. For example, where there was previously a "seealso" link to another function that has now been made internal, that tag is removed (See f5bec77 and 95637b4).

Other notes:

• likelihood() is refactored slightly so that the NAMESPACE search is done with a dot prefix function.
• The pkgdown Reference has been updated accordingly.
• No tests are expected to fail, so none are updated.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.80%. Comparing base (07f6087) to head (ae324cd).
Report is 6 commits behind head on main.

❗ Current head ae324cd differs from pull request most recent head e3b6104. Consider uploading reports for the commit e3b6104 to get more accurate results

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #225   +/-   ##
=======================================
  Coverage   98.80%   98.80%           
=======================================
  Files           8        8           
  Lines         584      587    +3     
=======================================
+ Hits          577      580    +3     
  Misses          7        7           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.