Convert duplicated code into helper functions

[jamesmbaazam]

• Please check if the PR fulfils these requirements

• I have read the CONTRIBUTING guidelines
• The commit message follows our guidelines
• Tests for the changes have been added (for bug fixes / features)
• Docs have been added / updated (for bug fixes / features)

• What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)

• It refactors simulate_chains(), simulate_summary(), and likelihood() to remove duplicated code by converting them into internal helper functions follows:

  • Simulation related operations have been modularised into .init_susc_pop(), .sample_possible_offspring(), and
    .get_susceptible_offspring().
  • Input checking is now remitted to 3 functions, .check_sim_args(), which checks the shared arguments of the simulate_* () functions, and 2 smaller functions, .check_statistic_args() which checks stat_max and statistic together in multiple functions, and .check_time_args(), which checks the time-related arguments: generation_time, t0, and tf.

• Tests and documentation, where necessary, have been added.

• What is the current behaviour? (You can also link to an open issue here)

This is a refactoring exercise and leads to no user-facing behaviour change.

• What is the new behaviour (if this is a feature change)?

  This is a refactoring exercise and leads to no user-facing behaviour change.

• Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)

No.

• Other information:

• This PR closes Code duplication as a result of splitting chain_sim() #44.

[sbfnk]

Great stuff. Also

> cyclocomp::cyclocomp(simulate_chains )
[1] 15

so can switch the lintr on again.

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (d22fd51) 98.90% compared to head (56c0a74) 98.94%.

❗ Current head 56c0a74 differs from pull request most recent head 32ccc24. Consider uploading reports for the commit 32ccc24 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #199      +/-   ##
==========================================
+ Coverage   98.90%   98.94%   +0.04%     
==========================================
  Files           8        8              
  Lines         550      571      +21     
==========================================
+ Hits          544      565      +21     
  Misses          6        6              

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[sbfnk]

All good. Just one last comment.