Improve transparency by warning when max_cohort_size triggers downsampling#930
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adilraza99 wants to merge 2 commits intomalariagen:masterfrom
Open
Improve transparency by warning when max_cohort_size triggers downsampling#930adilraza99 wants to merge 2 commits intomalariagen:masterfrom
adilraza99 wants to merge 2 commits intomalariagen:masterfrom
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When n_samples > max_cohort_size, the dataset is randomly downsampled without notification. This adds a UserWarning explaining the original and new sample counts, and how to disable downsampling. No change to logic, defaults, or returned data.
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Hi @jonbrenas This PR adds a UserWarning when All checks are passing. Would appreciate your review. |
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Hi @jonbrenas, Thanks again for your review and guidance. If you know of any important issues where additional help would be useful, I’d be happy to work on them. Appreciate your time! |
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Summary
This PR improves transparency when cohort downsampling occurs.
Currently, if
max_cohort_sizeis specified and the number of availablesamples exceeds this value, the cohort is silently downsampled. Because
no notification is emitted, users may incorrectly assume all available
samples were used, which can affect reproducibility and interpretation.
This change emits a
UserWarningwhen downsampling is triggered.Fixes #912