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 #131.
• The S3 constructors are also made internal to resolve #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 f5bec77c637fc9423f32b3ba66617e58e27f30b8 and 95637b40fd29264d49542e3ce04b478093873b73).

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 :white_check_mark:

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

:exclamation: 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

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

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