Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Addresses #2426
Blocking #2468
This relaxes two restrictions on
CoalescentLikelihood
that proved inconvenient in #2426:coal_times
andleaf_times
are no longer required to lie in[0, duration]
. Previously theCoalescentTimes*
distributions allowed times outside of[0,duration]
, butCoalescentLikelihood
required values in[0,duration]
. And it turns out real data showscoal_times
before the start of simulation.CoalescentLikelihood
no longer requires sortedcoal_times
. This made sense for theCoalescentTimes*
distributions for normalization, but is not needed for the likelihood.Tested
coal_times
in an SEIR smoke test