initial multiclass support

[zachmayer]

Initial working version of multiclass ensembling. Work to be done:

• predict.caretList return a matrix of probs, not a vector for the positive class.
• predict.caretStack return a matrix of probs, not a vector for the positive class.
• Internally, makePredObsMatrix just uses positive class probs. Make it use ALL class probs so we can do proper ensembling.
• Fix the test to do a train/test split and make a confusion matrix

[coveralls]

Coverage increased (+32.5%) to 96.934% when pulling dd523fa on multiclass into 27a4555 on master.

[dmpe]

@zachmayer still would like to see this being merged :) someday

[zachmayer]

Closing in favor of #260

[zachmayer]

rebase here: #279

[coderabbitai]

Walkthrough

The update encompasses several enhancements and fixes, including adjusting the order of Makefile targets to ensure operations run in a cleaner, more organized manner. Documentation within the R scripts has been corrected to accurately reference functions from the caret package. Additionally, functionality for multiclass problems has been streamlined, with associated tests improved and new ones added to ensure robust performance.

Changes

File(s) / Group	Summary
Makefile	Adjusted target order, added coverage target, updated .PHONY list.
R/caretEnsemble.R, R/caretList.R, man/caretList.Rd, man/metrics.Rd, man/predict.caretStack.Rd, man/varImp.caretEnsemble.Rd	Updated doc comments to reference caret package functions correctly.
R/helpers_functions.R, tests/testthat/test-helper_functions.R, tests/testthat/test-multiclass.R	Updated handling and tests for multiclass problems, including removing deprecated error check.
R/caretStack.R	Clarified documentation to reference predict.train from caret.

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[coderabbitai]

Actionable comments posted: 1

Review details

Configuration used: .coderabbit.yaml
Review profile: CHILL

Commits

Files that changed from the base of the PR and between 63602eb and b8ec20c.

Files selected for processing (12)

• Makefile (2 hunks)
• R/caretEnsemble.R (2 hunks)
• R/caretList.R (1 hunks)
• R/caretStack.R (1 hunks)
• R/helper_functions.R (2 hunks)
• cobertura.xml (15 hunks)
• man/caretList.Rd (2 hunks)
• man/metrics.Rd (1 hunks)
• man/predict.caretStack.Rd (1 hunks)
• man/varImp.caretEnsemble.Rd (1 hunks)
• tests/testthat/test-helper_functions.R (1 hunks)
• tests/testthat/test-multiclass.R (1 hunks)

Files not summarized due to errors (1)

• cobertura.xml: Error: Message exceeds token limit

Files skipped from review due to trivial changes (6)

• R/caretEnsemble.R
• man/caretList.Rd
• man/metrics.Rd
• man/predict.caretStack.Rd
• man/varImp.caretEnsemble.Rd
• tests/testthat/test-multiclass.R

Additional comments not posted (9)

Makefile (2)

3-3: LGTM! Addition of the coverage target.

The addition of the coverage target is correctly implemented and follows the existing conventions in the Makefile.

Also applies to: 58-58

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6-6: LGTM! Update to the all target.

Including clean and coverage in the all target is a good practice to ensure a clean build and generate coverage reports.

R/caretStack.R (1)

46-47: LGTM! Update to documentation references for predict.train.

The documentation now correctly references the caret package, ensuring accuracy.

tests/testthat/test-helper_functions.R (1)

32-32: LGTM! Removal of expect_error check.

The function check_caretList_model_types is called directly, indicating improved handling or validation. Ensure that test coverage is sufficient to verify this change.

R/helper_functions.R (1)

Line range hint 195-195:
LGTM! Removal of multiclass check.

The function check_caretList_model_types no longer checks for multiclass problems, aligning with the PR objectives of adding multiclass support. Ensure that multiclass handling is verified.

R/caretList.R (2)

160-161: Approve documentation updates.

The updates to the documentation comments correctly reference the train and trainControl functions from the caret package.

Also applies to: 165-165

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Line range hint 168-219:
Verify caretList function for multiclass support.

Ensure that the caretList function correctly handles multiclass ensembling as per the new requirements. Specifically, verify that it can process and return models for multiclass problems.

cobertura.xml (2)

3-3: Verify the accuracy of the coverage data.

Ensure that the coverage data, including lines covered, lines valid, branches covered, and branches valid, is accurate and reflects the current state of the codebase.

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3-3: Timestamp update.

The timestamp has been updated to reflect the current date and time.