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5/8 Maintenance: one multiview branch, small fixes, dead code removed (results unchanged) - #130
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…emovals from a review Results are unchanged (regression harness identical to the previous commit). - An unknown multiViewMethod is an error naming the choices (it failed with "object 'result' not found"). - The merge, prevalidation and PCA branches of crossValidate were the same apart from the clinical filter; they are one branch. - CV loses its unused independent train/test path, which could not work (it refitted on NULL data). - train and predict align the samples of a list of tables by name, as prepareData does. - prepareDataFormals includes maxSimilarity, so train and runTest pass it to prepareData. - prepareData's maxSimilarity uses stats::cor; dcanr (one call) is dropped from Imports. - Unused mergeTrainInterface, fastCox (from CMA, built an undefined class) and simplifyResults removed. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4
This was referenced Oct 9, 2026
DarioS
marked this pull request as ready for review
October 28, 2026 02:05
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Summary
Maintenance from a read-only review: duplicated code merged, small bugs fixed, dead code and one dependency removed. Results are unchanged.
Why and what
crossValidatewere the same except for the clinical filter. They are now one branch, so a fix can't be missed in one of the three.multiViewMethod(e.g."Merge") is an error naming the choices. It used to fail with "object 'result' not found".CVloses an unused independent train/test path that could not work (it refitted onNULLdata).trainandpredictalign the samples of a list of tables by name, asprepareDatadoes. Tables in different sample orders were silently mismatched.maxSimilarityis passed throughtrainandrunTesttoprepareData.dcanrwas imported for onecor.pairscall, which equalsstats::cor(to 4e-16);stats::coris used anddcanrdropped.mergeTrainInterface(never called);fastCox(left over from CMA, built an undefined class);simplifyResults.Do results change?
No. The regression harness gives identical results to part 4.
Evidence
291 tests pass. Further maintenance ideas are listed in ProjectClassifyR
docs/MAINTAINABILITY.md:runTestandsamplesMetricMap;These need decisions and are not included here.
🤖 Generated with Claude Code
https://claude.ai/code/session_01TfsjwkbDbHkX4kJZNe4ER4