Repository navigation
Conversation
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
This fixes the fixed-effect covariance calculation for taxa with missing observations. In ANCOM-BC2, the default
pseudo = 0treats zero counts as missing on the log scale, so this can also affect count tables without anyNAs in the original data.Previously, missing contributions were replaced with
0.1, and the covariance used the full design rather than the observations actually fitted for each taxon. The fix uses those observations consistently and keepsNAuncertainty for non-estimable coefficients. The shared helper affects both ANCOM-BC and ANCOM-BC2; mixed-model code is unchanged.I checked the covariance against
sandwich::vcovHC(type = "HC0")and verified consistency under reference reversal and covariate rescaling. All existing tests pass after updating two expected values.Related to #338 and #339.