trim #293
trim #293
Conversation
zachmayer
commented
Jul 31, 2024
zachmayer
commented
- Trim the train model itself, its final model, and its control (to save RAM and time)
- Use data.tables instead of data.frames internally to save lots of RAM and time
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Important Review skippedAuto incremental reviews are disabled on this repository. Please check the settings in the CodeRabbit UI or the You can disable this status message by setting the WalkthroughThe recent updates introduced enhanced efficiency in the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant caretTrain
participant train
User->>caretTrain: Call with local_args, global_args
caretTrain->>train: Pass combined arguments
train-->>caretTrain: Return model
caretTrain-->>User: Return modified model
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Actionable comments posted: 0
Outside diff range, codebase verification and nitpick comments (2)
R/caretTrain.R (1)
17-21: Tests for argument collisions incaretTrainare missing.The current implementation of
caretTrainhas a TODO comment indicating the need for tests to handle argument collisions. Our search did not find any existing tests for this functionality.
- File:
R/caretTrain.R- Lines: 17-21
Please add tests to handle argument collisions as suggested in the TODO comment.
Analysis chain
Correct argument handling with TODO for tests.
The argument handling correctly combines local and global arguments using
utils::modifyList. There is a TODO comment for handling argument collisions, which should be addressed.Ensure that tests are added to handle argument collisions.
We need to verify if there are any tests related to
caretTrainthat handle argument collisions. Let's search for test files or test cases that might include such tests.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify tests for argument collisions in `caretTrain`. # Test: Search for tests related to argument collisions. Expect: Relevant tests should be present. rg --type r -A 5 $'caretTrain'Length of output: 1324
Script:
#!/bin/bash # Description: Verify tests for argument collisions in `caretTrain`. # Find all R test files that might contain tests for `caretTrain`. fd --type f --extension r --exec rg --type r 'caretTrain' {}Length of output: 293
cobertura.xml (1)
1160-1185: No test cases found for thecaretTrainfunction.The
caretTrainfunction inR/caretTrain.Ris not covered by any test cases. This function is a wrapper around thetrainfunction from thecaretpackage and should be thoroughly tested to ensure its correctness and reliability.
- Implementation:
R/caretTrain.R- Usage:
R/caretList.RPlease add appropriate test cases for the
caretTrainfunction to ensure its functionality is validated.Analysis chain
New class
caretTrain.Rwith methodcaretTrainadded.A new class
caretTrain.Rhas been added, containing the methodcaretTrain. This indicates a significant addition to the functionality covered by the test suite.Ensure that the new method has been thoroughly tested and validated.
Ensure thorough testing of the
caretTrainfunction.The
caretTrainfunction is implemented inR/caretTrain.Rand used inR/caretList.R. Ensure that this function is thoroughly tested to validate its functionality.
- Implementation:
R/caretTrain.R- Usage:
R/caretList.RScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the implementation and usage of the new method `caretTrain`. # Test: Search for the implementation and usage of the `caretTrain` method. Expect: Occurrences of the new method. rg --type r -A 5 $'caretTrain'Length of output: 1324
Script:
#!/bin/bash # Description: Verify the existence of test cases for the `caretTrain` function. # Test: Search for test cases related to the `caretTrain` function. Expect: Occurrences of test cases. rg --type r -A 5 'caretTrain' tests/Length of output: 36
Script:
#!/bin/bash # Description: Verify the existence of test cases for the `caretTrain` function. # Test: Search for test cases related to the `caretTrain` function across the entire codebase. Expect: Occurrences of test cases. rg --type r -A 5 'caretTrain'Length of output: 1324
Review details
Configuration used: .coderabbit.yaml
Review profile: CHILL
Files selected for processing (17)
- Makefile (1 hunks)
- R/caretEnsemble.R (1 hunks)
- R/caretList.R (9 hunks)
- R/caretPredict.R (1 hunks)
- R/caretStack.R (2 hunks)
- R/caretTrain.R (1 hunks)
- cobertura.xml (5 hunks)
- inst/WORDLIST (1 hunks)
- man/caretList.Rd (2 hunks)
- man/caretTrain.Rd (1 hunks)
- man/dropExcludedClass.Rd (1 hunks)
- tests/testthat/test-caretEnsemble.R (2 hunks)
- tests/testthat/test-caretList.R (9 hunks)
- tests/testthat/test-ensembleMethods.R (5 hunks)
- tests/testthat/test-helper_functions.R (1 hunks)
- tests/testthat/test-multiclass.R (3 hunks)
- vignettes/caretEnsemble-intro.Rmd (4 hunks)
Files skipped from review due to trivial changes (6)
- Makefile
- R/caretPredict.R
- inst/WORDLIST
- man/dropExcludedClass.Rd
- tests/testthat/test-helper_functions.R
- vignettes/caretEnsemble-intro.Rmd
Additional comments not posted (61)
man/caretTrain.Rd (5)
5-8: Clear title and correct usage section.The title and usage section are clear and correctly list the function signature.
9-18: Accurate and clear arguments section.The arguments section accurately describes each parameter of the
caretTrainfunction.
20-21: Clear description of the return value.The value section clearly describes the return value of the
caretTrainfunction.
23-29: Comprehensive description of the function.The description section provides a comprehensive overview of the
caretTrainfunction, accurately reflecting its purpose and functionality.
30-30: Appropriate keyword.The keyword "internal" is appropriate for the
caretTrainfunction.man/caretList.Rd (5)
Line range hint
5-14:
Clear title and correct usage section with new parameter.The title is clear and the usage section correctly lists the function signature, including the new
trimparameter.
18-21: Accurate and clear arguments section with new parameter and expanded documentation.The arguments section accurately describes each parameter of the
caretListfunction, including the newtrimparameter and the expanded documentation for the...argument.Also applies to: 35-38
Line range hint
40-42:
Clear description of the return value.The value section clearly describes the return value of the
caretListfunction.
Line range hint
44-46:
Comprehensive description of the function.The description section provides a comprehensive overview of the
caretListfunction, accurately reflecting its purpose and functionality.
Line range hint
48-66:
Clear and effective usage examples.The examples section provides clear and effective usage examples for the
caretListfunction.R/caretTrain.R (5)
1-15: Comprehensive function documentation.The function documentation provides a comprehensive overview of the
caretTrainfunction, accurately describing its purpose, parameters, and return value.
23-31: Correct model fitting and error handling.The model fitting and error handling are correctly implemented, ensuring the function continues on failure if specified.
33-36: Correct data.table conversion.The conversion of the
predcomponent to adata.tableis correctly implemented.
38-53: Correct model trimming implementation.The model trimming is correctly implemented, removing unnecessary components from the model and its control, which should improve efficiency.
56-57: Correct function return.The function correctly returns the fitted model.
tests/testthat/test-ensembleMethods.R (13)
20-23: LGTM!The changes correctly update the expected class type to "data.table" in the tests for variable importance.
41-41: LGTM!The changes correctly update the expected class type to "data.table" in the
varImptests.
167-167: LGTM!The changes correctly update the expected class type to "data.table" in the tests for model results matching component models.
190-190: LGTM!The changes correctly convert the input data to
data.tableand update the expected output class to "data.table".
195-196: LGTM!The changes correctly update the expected output class to "data.table" for the prediction results.
201-201: LGTM!The changes correctly handle the weights attribute based on the prediction options.
212-212: LGTM!The changes correctly convert the input data to
data.tableand update the expected output class to "data.table".
217-218: LGTM!The changes correctly update the expected output class to "data.table" for the prediction results.
223-223: LGTM!The changes correctly handle the weights attribute based on the prediction options.
195-197: LGTM!The changes correctly update the expected output class to "data.table" for the prediction results.
Line range hint
263-265: LGTM!The changes correctly update the expected output class to "data.table" for the prediction results.
226-226: LGTM!The changes correctly convert the input data to
data.table.
Line range hint
256-256: LGTM!The changes correctly convert the input data to
data.table.tests/testthat/test-caretEnsemble.R (2)
195-197: LGTM!The changes correctly update the expected output class to "data.table" for the prediction results.
263-265: LGTM!The changes correctly update the expected output class to "data.table" for the prediction results.
tests/testthat/test-multiclass.R (5)
31-31: LGTM!The changes correctly update the expected output class to "data.table" for the prediction results.
226-226: LGTM!The changes correctly convert the input data to
data.table.
256-256: LGTM!The changes correctly convert the input data to
data.table.
226-226: LGTM!The changes correctly convert the input data to
data.table.
256-256: LGTM!The changes correctly convert the input data to
data.table.R/caretStack.R (2)
57-57: LGTM! But verify the function usage in the codebase.The conversion of
new_Xto a data table is correctly implemented.However, ensure that all function calls to
caretStackmatch the updated functionality.
173-175: LGTM! But verify the function usage in the codebase.The conversion of
newdatato a data table is correctly implemented.However, ensure that all function calls to
predict.caretStackmatch the updated functionality.Verification successful
Verify the function usage in the codebase.
The conversion of
newdatato a data table is correctly implemented. However, ensure that all function calls topredict.caretStackmatch the updated functionality. Specifically, verify that the tests intests/testthat/test-caretStack.Rcover scenarios wherenewdatais passed topredict.caretStackand that the conversion to a data table is handled correctly.
Verified:
The function calls to
predict.caretStackmatch the updated functionality, and the test cases intests/testthat/test-caretStack.Radequately cover scenarios wherenewdatais passed topredict.caretStack. The tests ensure that the conversion to a data table is handled correctly.
tests/testthat/test-caretStack.R: Multiple instances wherepredict.caretStackis called withnewdata.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `predict.caretStack` match the updated functionality. # Test: Search for the function usage. Expect: Only occurrences of the updated functionality. rg --type r -A 5 $'predict.caretStack'Length of output: 2081
Script:
#!/bin/bash # Description: Verify that the tests in `tests/testthat/test-caretStack.R` cover scenarios where `newdata` is passed to `predict.caretStack`. # Search for `predict` function calls in the test file and include context lines to see the arguments passed. rg --type r -A 5 'predict' tests/testthat/test-caretStack.RLength of output: 4965
R/caretList.R (4)
237-237: LGTM! But verify the function usage in the codebase.The
caretTrainfunction is correctly implemented with the newtrimparameter.However, ensure that all function calls to
caretTrainmatch the updated functionality.Verification successful
Verified: The
caretTrainfunction is correctly implemented with the newtrimparameter, and all calls to this function in the codebase match the updated functionality.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `caretTrain` match the updated functionality. # Test: Search for the function usage. Expect: Only occurrences of the updated functionality. rg --type r -A 5 $'caretTrain'Length of output: 1324
346-348: LGTM! But verify the function usage in the codebase.The conversion of
newdatato a data table is correctly implemented.However, ensure that all function calls to
predict.caretListmatch the updated functionality.Verification successful
Ensure
newdatais correctly handled in all usages ofpredict.caretList.The function
predict.caretListis used in several files, includingR/caretStack.Rand multiple test files. Ensure that thenewdataparameter in all usages ofpredict.caretListis correctly handled, particularly focusing on whether it is converted to a data table where necessary.
R/caretStack.R
- Line:
preds <- predict.caretList(all.models, newdata = new_X, excluded_class_id = excluded_class_id)tests/testthat/test-caretList.R
- Line:
pred <- predict.caretList(new_model_list)tests/testthat/test-S3-generic-extensions.R
- Line:
class_preds <- predict(models.class, newdata = X.class, excluded_class_id = 0L)- Line:
reg_preds <- predict(models.reg, newdata = X.reg)- Line:
class_probs <- predict(models.class, newdata = X.class, excluded_class_id = 0L)Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `predict.caretList` match the updated functionality. # Test: Search for the function usage. Expect: Only occurrences of the updated functionality. rg --type r -A 5 $'predict.caretList'Length of output: 2939
136-139: LGTM! But verify the function usage in the codebase.The new parameter
trimis correctly implemented and the documentation is accurate.However, ensure that all function calls to
caretListmatch the updated functionality.Also applies to: 148-150, 180-181
75-77: LGTM! But verify the function usage in the codebase.The conversion to
data.tableand usage ofrbindlistare correctly implemented.However, ensure that all function calls to
methodCheckmatch the updated functionality.Also applies to: 86-86
Verification successful
LGTM! But verify the function usage in the codebase.
The conversion to
data.tableand usage ofrbindlistare correctly implemented.The function
methodCheckis used and tested adequately in the codebase:
R/caretList.Rtests/testthat/test-caretList.RScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `methodCheck` match the updated functionality. # Test: Search for the function usage. Expect: Only occurrences of the updated functionality. rg --type r -A 5 $'methodCheck'Length of output: 1972
R/caretEnsemble.R (1)
320-321: LGTM! But verify the function usage in the codebase.The conversion to
data.tableand usage ofsetare correctly implemented.However, ensure that all function calls to
autoplot.caretEnsemblematch the updated functionality.Verification successful
To confirm that the
autoplot.caretEnsemblefunction is not used elsewhere in the codebase, we need to perform a broader search.
The function
autoplot.caretEnsembleis defined and documented but not called elsewhere in the codebase. This suggests that it is either not used internally or is intended for external use.
- No internal calls to
autoplot.caretEnsemblewere found.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `autoplot.caretEnsemble` match the updated functionality. # Test: Search for the function usage. Expect: Only occurrences of the updated functionality. rg --type r -A 5 $'autoplot.caretEnsemble'Length of output: 470
Script:
#!/bin/bash # Description: Verify all function calls to `autoplot.caretEnsemble` in the codebase. # Test: Search for any occurrences of `autoplot.caretEnsemble` in the codebase. rg 'autoplot.caretEnsemble'Length of output: 576
tests/testthat/test-caretList.R (9)
85-85: LGTM!The changes ensure compatibility with
data.tableand maintain the original functionality.
97-97: LGTM!The changes ensure compatibility with
data.tableand maintain the original functionality.
111-111: LGTM!The changes ensure compatibility with
data.tableand maintain the original functionality.
264-264: LGTM!The changes ensure compatibility with
data.tableand improve performance and memory efficiency.
549-549: LGTM!The changes ensure compatibility with
data.tableand improve performance and memory efficiency.
631-631: LGTM!The changes ensure compatibility with
data.tableand improve performance and memory efficiency.
733-733: LGTM!The changes ensure compatibility with
data.tableand improve performance and memory efficiency.
805-805: LGTM!The changes ensure compatibility with
data.tableand improve performance and memory efficiency.
829-829: LGTM!The changes ensure compatibility with
data.tableand improve performance and memory efficiency.cobertura.xml (10)
3-3: Updated coverage metrics.The coverage metrics have been updated to reflect the latest changes, with an increase in the number of lines covered.
475-475: Updated hit count forcaretListmethod.The hit count for this line has been updated, indicating changes in how many times this line was executed during testing.
476-476: Updated hit count forcaretListmethod.The hit count for this line has been updated, indicating changes in how many times this line was executed during testing.
477-477: Updated hit count forcaretListmethod.The hit count for this line has been updated, indicating changes in how many times this line was executed during testing.
481-481: Updated hit count forcaretListmethod.The hit count for this line has been updated, indicating changes in how many times this line was executed during testing.
482-482: Updated hit count forcaretListmethod.The hit count for this line has been updated, indicating changes in how many times this line was executed during testing.
485-485: Updated hit count forcaretListmethod.The hit count for this line has been updated, indicating changes in how many times this line was executed during testing.
486-486: Updated hit count forcaretListmethod.The hit count for this line has been updated, indicating changes in how many times this line was executed during testing.
487-487: Updated hit count forcaretListmethod.The hit count for this line has been updated, indicating changes in how many times this line was executed during testing.
488-488: Updated hit count forcaretListmethod.The hit count for this line has been updated, indicating changes in how many times this line was executed during testing.
