Make likelihood() work with <epichains_summary>, <epichains>, and <numeric> objects

[jamesmbaazam]

This PR closes #39.

• Please check if the PR fulfills these requirements

• I have read the CONTRIBUTING guidelines
• A new item has been added to NEWS.md
• Tests for the changes have been added (for bug fixes / features)
• Docs have been added / updated (for bug fixes / features)
• Checks have been run locally and pass

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

A feature

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

likelihood() works only with a numeric vector of chains.

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

An <epichains_tree> or <epichains_summary> object can be passed directly to likelihood() to estimate the likelihood of observing the chains.

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

Not applicable.

• Other information:

- Do we want to override the other relevant arguments (offspring_dist, stat_max, etc) with the attributes of an <epichains_tree> when passed, or should the user still supply them?

• Currently, if the data contains Inf and stat_max is Inf, it errors because R cannot generate an infinite sequence (See

  epichains/R/likelihood.R

  Line 104 in 5e6fd49

  calc_sizes <- seq_len(stat_max - 1)

  ).

@sbfnk, how can we surmount this issue?

Would it make sense to calculate the likelihood using only the finite values and in the case where individual = TRUE , return NA for the Inf values?

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.07%. Comparing base (a7faf3a) to head (8bb0e64).
Report is 119 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #213      +/-   ##
==========================================
+ Coverage   99.03%   99.07%   +0.03%     
==========================================
  Files           8        8              
  Lines         729      755      +26     
==========================================
+ Hits          722      748      +26     
  Misses          7        7              

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

[sbfnk]

Looks good! Just a minor comment.

[jamesmbaazam]

@sbfnk Currently, if the data contains Inf (more likely when an <epichains_summary> is passed) and stat_max is Inf, it errors because R cannot generate an infinite sequence (See

epichains/R/likelihood.R

Lines 103 to 104 in 5e6fd49

	if (any(stat_rep_vect == stat_max)) {
	calc_sizes <- seq_len(stat_max - 1)

)

Would it make sense to calculate the likelihood using only the finite values and in the case where individual = TRUE, return NA where the entry is Inf?

[sbfnk]

@sbfnk Currently, if the data contains Inf (more likely when an <epichains_summary> is passed) and stat_max is Inf, it errors because R cannot generate an infinite sequence (See

epichains/R/likelihood.R

Lines 103 to 104 in 5e6fd49

	if (any(stat_rep_vect == stat_max)) {
	calc_sizes <- seq_len(stat_max - 1)

)
Would it make sense to calculate the likelihood using only the finite values and in the case where individual = TRUE, return NA where the entry is Inf?

I don't think it would be correct to exclude some of the outbreaks from the likelihood.

We can only have data containing Inf with a finite stat_max in the simulation, right? So it doesn't really make a huge amount of sense to then calculate the likelihood with stat_max as Inf. Perhaps this should be added to the summary as attribute anyway? The likelihood function could then read it out and set stat_max to the "correct" value.

[jamesmbaazam]

@sbfnk Currently, if the data contains Inf (more likely when an <epichains_summary> is passed) and stat_max is Inf, it errors because R cannot generate an infinite sequence (See

epichains/R/likelihood.R

Lines 103 to 104 in 5e6fd49

	if (any(stat_rep_vect == stat_max)) {
	calc_sizes <- seq_len(stat_max - 1)

)
Would it make sense to calculate the likelihood using only the finite values and in the case where individual = TRUE, return NA where the entry is Inf?

I don't think it would be correct to exclude some of the outbreaks from the likelihood.

We can only have data containing Inf with a finite stat_max in the simulation, right? So it doesn't really make a huge amount of sense to then calculate the likelihood with stat_max as Inf.

Perhaps this should be added to the summary as attribute anyway?

This is already the case.

The likelihood function could then read it out and set stat_max to the "correct" value.

That makes sense. See change here 8a35bc7. Did you mean that?