Multiple issues: make `offspring_dist` accept a function

sbfnk commented 9 months ago

Please check if the PR fulfills these requirements
[X] I have read the CONTRIBUTING guidelines
[X] A new item has been added to NEWS.md
[X] Tests for the changes have been added (for bug fixes / features)
[X] Docs have been added / updated (for bug fixes / features)
What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)

This PR changes the offspring_dist argument of likelihood and simulate_chains to expect a function instead of a character string.

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

Yes. No version has been released yet so not going through a deprecation cycle.

Other information:

Doing this necessitated two further changes:

remove the construct_offspring_ll_name function and instead integrate the code into likelihood; because of the way the function name is extracted from the offspring_dist argument (using substitute) this can't be passed on to lower level functions; as this function was only used in this one instance I think we can live with the loss
add an rgborel function; this is a difference from previous behaviour, where the ll function name could be informed from the string passed and now it needs a function with that name; the function itself is not actually called when estimating the likelihood if the corresponding ll function exists so this could, in principle, be an empty dummy function; however, for documentation/clarity purposes it is probably a good idea to have this function anyway

Closes #25 Closes #167

codecov-commenter commented 9 months ago

Codecov Report

Attention: 3 lines in your changes are missing coverage. Please review.

Comparison is base (d3e8d85) 99.45% compared to head (6bf6e90) 98.90%.

:exclamation: Current head 6bf6e90 differs from pull request most recent head e2df869. Consider uploading reports for the commit e2df869 to get more accurate results

Files	Patch %	Lines
R/borel.r	78.57%	3 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #188 +/- ## ========================================== - Coverage 99.45% 98.90% -0.55% ========================================== Files 8 8 Lines 546 548 +2 ========================================== - Hits 543 542 -1 - Misses 3 6 +3 ```

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sbfnk commented 9 months ago

Might need updating in line with #190