Fix OffsetReal.calculateLogP() double-subtracting offset#73
Merged
Conversation
calculateLogP() passed param.get() - offset.get() to logDensity(), but logDensity(x) itself subtracts offset, so the underlying distribution was evaluated at param - 2*offset. Also adds testCalculateLogPOfOffsetReal covering Exp and Normal.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Fixes #72.
Summary
OffsetReal.calculateLogP()evaluated the underlying distribution atparam - 2 * offsetinstead ofparam - offset, because both the override and thelogDensity(x)it called subtracted the offset.param.get()directly tologDensity(), matching the convention used bydensity(x)andcalcLogP(value)in the same class.testCalculateLogPOfOffsetRealcovering Exp and Normal cases (the existingMeanOfParametricDistributionTestonly exercisedgetMean()).No production callers of
OffsetReal.calculateLogP()exist in beast3 today, so no MCMC results were affected. Downstream consumers (LPhyBeast) need this fixed before they can useOffsetRealas a prior.Test plan
mvn test -Dtest=MeanOfParametricDistributionTest— all 7 tests pass on the new branchmvn test -Dtest='*Distribution*Test,*Prior*Test'— all 36 tests in beast-base pass