Add a mixed model section to the milo tutorial - #71
Merged
Conversation
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Covers the Milo mixed model added in scverse/pertpy#1069, modelling
Siteas a random intercept rather than as a fixed effect.The notebook was executed end to end against that branch, so the new cells carry their outputs and every other output is refreshed from the same run. On this dataset the mixed model fits 4307 neighbourhoods: 6 have a group without any cells and are reported as NaN, 21 of the remaining 4301 do not converge, and the site variance runs between 0.02 and 0.66.
Merge after scverse/pertpy#1069, since
(1 | variable)designs do not exist on pertpy main yet.