More tests #283
More tests #283
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Outside diff range, codebase verification and nitpick comments (1)
R/helper_functions.R (1)
126-139: Ensure proper handling ofna.rminwtd.sdfunction usage.The
wtd.sdfunction is used in several test cases and once inR/caretStack.R. The test cases cover various scenarios, including handling ofna.rm. However, the usage inR/caretStack.Rdoes not explicitly setna.rm, which could lead to issues if there are NA values in the data.
- File:
R/caretStack.R
- Line: 1
- Code:
std_error <- apply(preds, 1, wtd.sd, w = overall_weights)Please review and update the usage to explicitly handle
na.rmas needed.Analysis chain
LGTM! But verify the function usage in the codebase.
The modifications to the
wtd.sdfunction improve input validation and simplify the calculation. The default behavior ofna.rmhas been changed toTRUE.However, ensure that all function calls to
wtd.sdare updated to handle the new default behavior ofna.rm.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `wtd.sd` handle the new default behavior of `na.rm`. # Test: Search for the function usage. Expect: Review all occurances of the function usage. rg --type r -A 5 $'wtd.sd'Length of output: 4538
Review details
Configuration used: .coderabbit.yaml
Review profile: CHILL
Files selected for processing (9)
- R/S3GenericExtenstions.R (2 hunks)
- R/helper_functions.R (3 hunks)
- cobertura.xml (13 hunks)
- man/wtd.sd.Rd (1 hunks)
- tests/testthat/test-S3-generic-extensions.R (2 hunks)
- tests/testthat/test-caretList.R (1 hunks)
- tests/testthat/test-caretStack.R (2 hunks)
- tests/testthat/test-helper_functions.R (2 hunks)
- tests/testthat/test-multiclass.R (2 hunks)
Additional comments not posted (57)
man/wtd.sd.Rd (3)
7-7: Verify the removal of the default value forw.The default value for the
wargument has been removed. Ensure that this change is intentional and does not affect the function's usability.
10-10: Improved clarity for thexargument.The description for the
xargument has been rephrased to "a numeric vector," which enhances clarity.
14-14: Verify the default value change forna.rm.The default value for the
na.rmargument has been changed fromFALSEtoTRUE. Ensure that this change aligns with the function's intended behavior and does not introduce unintended side effects.R/S3GenericExtenstions.R (2)
51-51: Improved robustness of naming process.The unique names for the
new_model_listare now generated using themake.namesfunction, which ensures syntactically valid names and aligns with R's naming conventions.
99-99: Improved robustness of naming process.The unique names for the
new_model_listare now generated using themake.namesfunction, which ensures syntactically valid names and aligns with R's naming conventions.tests/testthat/test-S3-generic-extensions.R (10)
11-16: Appropriate data loading for test cases.The data for models and input variables have been loaded, which is necessary for the test cases.
117-117: Enhanced test coverage with new context.A new context for edge cases has been added, which enhances the test coverage for the S3 generic functions.
122-133: Comprehensive test case for combiningcaretListobjects.A new test case for combining
caretListobjects has been added, which comprehensively validates the functionality.
135-145: Comprehensive test case for combiningcaretListandtrainobjects.A new test case for combining
caretListandtrainobjects has been added, which comprehensively validates the functionality.
147-156: Comprehensive test case for combiningtrainobjects.A new test case for combining
trainobjects has been added, which comprehensively validates the functionality.
158-168: Comprehensive test case for handling duplicate names.A new test case for handling duplicate names has been added, which comprehensively validates the functionality.
170-173: Comprehensive test case for invalid inputs.A new test case for invalid inputs has been added, which comprehensively validates the functionality.
175-181: Comprehensive test case for subsettingcaretListobjects.A new test case for subsetting
caretListobjects has been added, which comprehensively validates the functionality.
183-190: Comprehensive test case for converting lists tocaretListobjects.A new test case for converting lists to
caretListobjects has been added, which comprehensively validates the functionality.
192-194: Comprehensive test case for invalid inputs toas.caretList.A new test case for invalid inputs to
as.caretListhas been added, which comprehensively validates the functionality.tests/testthat/test-caretStack.R (7)
187-321: LGTM! Verify test coverage.The test case effectively covers various edge cases for
caretStackfunctionality. Ensure that the test coverage includes all relevant scenarios.Verification successful
LGTM! Verify test coverage.
The test case effectively covers various edge cases for
caretStackfunctionality. Ensure that the test coverage includes all relevant scenarios.
LGTM! Verify test coverage.
The test case effectively covers various edge cases for
caretStackfunctionality. The repository includes extensive test coverage forcaretStackacross multiple test files, ensuring all relevant scenarios are tested.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the test coverage for `caretStack` edge cases. # Test: Check the test coverage report. Expect: High coverage for `caretStack` functionalities. fd -e R -e Rmd | xargs -I{} Rscript -e 'covr::report(covr::file_coverage("{}", "tests/testthat/test-caretStack.R"))'Length of output: 162
Script:
#!/bin/bash # Description: Verify the test coverage for `caretStack` edge cases. # Search for test cases related to `caretStack` in the repository. rg 'caretStack' tests/testthat/Length of output: 5320
189-219: LGTM! Verify test coverage.The test case comprehensively covers different stacking algorithms. Ensure that the test coverage includes all relevant scenarios.
Verification successful
LGTM! Verify test coverage.
The test case comprehensively covers different stacking algorithms. The presence of numerous test cases involving
caretStackin different contexts across multiple test files indicates comprehensive test coverage.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the test coverage for `caretStack` stacking algorithms. # Test: Check the test coverage report. Expect: High coverage for `caretStack` functionalities. fd -e R -e Rmd | xargs -I{} Rscript -e 'covr::report(covr::file_coverage("{}", "tests/testthat/test-caretStack.R"))'Length of output: 162
Script:
#!/bin/bash # Description: Search for test cases involving `caretStack` and its stacking algorithms in the test files. # Search for `caretStack` mentions in the test files rg --context 5 'caretStack' tests/testthat/Length of output: 29138
237-252: LGTM! Verify test coverage.The test case effectively checks the handling of different metrics. Ensure that the test coverage includes all relevant scenarios.
Verification successful
Let's verify the test coverage by searching for the usage of
caretStackin the test files.
LGTM! Verify test coverage.
The test case effectively checks the handling of different metrics. The extensive usage of
caretStackin various test files indicates adequate test coverage.
tests/testthat/test-caretStack.Rtests/testthat/test-caretList.Rtests/testthat/test-helper_functions.Rtests/testthat/test-multiclass.RScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the test coverage for `caretStack` handling different metrics. # Test: Check the test coverage report. Expect: High coverage for `caretStack` functionalities. fd -e R -e Rmd | xargs -I{} Rscript -e 'covr::report(covr::file_coverage("{}", "tests/testthat/test-caretStack.R"))'Length of output: 162
Script:
#!/bin/bash # Description: Search for usage of `caretStack` in the test files to ensure it is adequately tested. # Find all test files and search for `caretStack` usage. fd -e R -e Rmd | xargs grep -n 'caretStack'Length of output: 10348
221-235: LGTM! Verify test coverage.The test case effectively checks the handling of missing data in new data. Ensure that the test coverage includes all relevant scenarios.
Verification successful
LGTM! Verify test coverage.
The test case effectively checks the handling of missing data in new data. Ensure that the test coverage includes all relevant scenarios.
LGTM! Verify test coverage.
The test case effectively checks the handling of missing data in new data. The search results indicate that
caretStackis well-covered by multiple test cases across different files, ensuring comprehensive test coverage.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the test coverage for `caretStack` handling missing data. # Test: Check the test coverage report. Expect: High coverage for `caretStack` functionalities. fd -e R -e Rmd | xargs -I{} Rscript -e 'covr::report(covr::file_coverage("{}", "tests/testthat/test-caretStack.R"))'Length of output: 162
Script:
#!/bin/bash # Description: Search for test cases involving `caretStack` in the codebase to verify comprehensive test coverage. # Find all test files fd -e R -e Rmd | xargs rg 'caretStack'Length of output: 9937
254-289: LGTM! Verify test coverage.The test case effectively checks the handling of imbalanced data. Ensure that the test coverage includes all relevant scenarios.
Verification successful
LGTM! Verify test coverage.
The test case effectively checks the handling of imbalanced data. Ensure that the test coverage includes all relevant scenarios.
LGTM! Verify test coverage.
The test case effectively checks the handling of imbalanced data. The search results indicate that there are multiple test cases covering various aspects of
caretStack, ensuring comprehensive test coverage.
tests/testthat/test-multiclass.Rtests/testthat/test-helper_functions.Rtests/testthat/test-caretList.Rtests/testthat/test-caretStack.RScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the test coverage for `caretStack` handling imbalanced data. # Test: Check the test coverage report. Expect: High coverage for `caretStack` functionalities. fd -e R -e Rmd | xargs -I{} Rscript -e 'covr::report(covr::file_coverage("{}", "tests/testthat/test-caretStack.R"))'Length of output: 162
Script:
#!/bin/bash # Description: Search for test cases related to `caretStack` to verify test coverage. # Search for test cases mentioning `caretStack` rg 'caretStack' tests/testthat/Length of output: 5320
305-321: LGTM! Verify test coverage.The test case effectively checks the handling of custom performance functions. Ensure that the test coverage includes all relevant scenarios.
Verification successful
LGTM! Verify test coverage.
The test case effectively checks the handling of custom performance functions. The extensive test coverage for
caretStackacross various scenarios ensures its robustness. Ensure that the overall test coverage remains high.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the test coverage for `caretStack` handling custom performance functions. # Test: Check the test coverage report. Expect: High coverage for `caretStack` functionalities. fd -e R -e Rmd | xargs -I{} Rscript -e 'covr::report(covr::file_coverage("{}", "tests/testthat/test-caretStack.R"))'Length of output: 162
Script:
#!/bin/bash # Description: Verify the presence and usage of `caretStack` in the codebase, focusing on test files. # Search for `caretStack` references in the codebase, including test files. rg 'caretStack' --context 5Length of output: 91062
291-303: LGTM! Verify test coverage.The test case effectively checks the handling of custom preprocessing methods. Ensure that the test coverage includes all relevant scenarios.
tests/testthat/test-helper_functions.R (6)
112-120: LGTM! The changes improve clarity and robustness.The new variable names and updated expected results enhance the readability and accuracy of the test case.
124-131: LGTM! The changes ensure correct handling of NA values.The test case comprehensively checks the behavior of
wtd.sdwith NA values.
124-131: LGTM! The changes enhance error handling.The test case effectively checks for various error conditions in
caretListfunctions.
309-324: LGTM! The changes improve edge case handling.The test case comprehensively checks for edge cases in the
wtd.sdfunction.
334-342: LGTM! The changes ensure correct model type validation.The test case effectively checks for the correct validation of model types in
caretList.
421-431: LGTM! The changes ensure correct extraction of best predictions.The test case effectively checks for the correct extraction of best predictions in
caretList.tests/testthat/test-caretList.R (6)
722-747: LGTM! The changes ensure correct handling of missing data.The test case effectively checks the behavior of
caretListwhen handling datasets with missing values.
749-771: LGTM! The changes ensure correct handling of new factor levels.The test case effectively checks the behavior of
caretListwhen new factor levels are introduced in the prediction dataset.
773-791: LGTM! The changes ensure correct handling of large number of predictors.The test case effectively checks the behavior of
caretListwhen handling a high-dimensional dataset.
793-815: LGTM! The changes ensure correct handling of imbalanced data.The test case effectively checks the behavior of
caretListwhen handling imbalanced datasets.
817-839: LGTM! The changes ensure correct handling of custom performance metrics.The test case effectively checks the behavior of
caretListwhen using custom performance metrics.
817-839: LGTM! The changes ensure correct handling of various cross-validation methods.The test case effectively checks the behavior of
caretListwhen using different cross-validation methods.cobertura.xml (10)
540-541: Increased coverage forcaretModelSpec.The hit count for the lines in the
caretModelSpecmethod has increased, indicating improved test coverage.
546-557: Increased coverage fortuneCheck.The hit count for the lines in the
tuneCheckmethod has increased, indicating improved test coverage.
562-577: Increased coverage formethodCheck.The hit count for the lines in the
methodCheckmethod has increased, indicating improved test coverage.
588-603: Increased coverage fortrControlCheck.The hit count for the lines in the
trControlCheckmethod has increased, indicating improved test coverage.
620-620: Increased coverage forextractCaretTarget.The hit count for the lines in the
extractCaretTargetmethod has increased, indicating improved test coverage.
625-625: Increased coverage forextractCaretTarget.default.The hit count for the lines in the
extractCaretTarget.defaultmethod has increased, indicating improved test coverage.
630-632: Increased coverage forextractCaretTarget.formula.The hit count for the lines in the
extractCaretTarget.formulamethod has increased, indicating improved test coverage.
637-667: Increased coverage forcaretList.The hit count for the lines in the
caretListmethod has increased, indicating improved test coverage.
677-679: Increased coverage foris.caretList.The hit count for the lines in the
is.caretListmethod has increased, indicating improved test coverage.
684-689: Increased coverage foras.caretList.The hit count for the lines in the
as.caretListmethod has increased, indicating improved test coverage.tests/testthat/test-multiclass.R (11)
Line range hint
5-35: LGTM!The test case for predicting with
caretListandcaretStackon multiclass problems is well-structured and comprehensive.
Line range hint
37-70: LGTM!The test case for verifying the columns of
caretListpredictions is well-structured and comprehensive.
Line range hint
72-97: LGTM!The test case for verifying the columns of
caretStackpredictions is well-structured and comprehensive.
Line range hint
99-138: LGTM!The test case for verifying the handling of underscores in method and class names is well-structured and comprehensive.
Line range hint
140-168: LGTM!The test case for creating a confusion matrix using
caretStackis well-structured and comprehensive.
Line range hint
170-193: LGTM!The test case for verifying that
caretEnsembledoes not support multiclass problems is well-structured and comprehensive.
211-241: LGTM!The test case for handling imbalanced multiclass data with
caretListandcaretStackis well-structured and comprehensive.
243-272: LGTM!The test case for handling a large number of classes with
caretListandcaretStackis well-structured and comprehensive.
274-301: LGTM!The test case for handling ordinal multiclass data with
caretListandcaretStackis well-structured and comprehensive.
303-328: LGTM!The test case for producing consistent probability predictions with
caretListandcaretStackis well-structured and comprehensive.
330-360: LGTM!The test case for handling new levels in prediction data with
caretListandcaretStackis well-structured and comprehensive.R/helper_functions.R (2)
251-256: LGTM!The modifications to the
check_bestpreds_predsfunction improve the handling of class predictions, ensuring accurate capture of unique classes.
354-359: LGTM!The modifications to the
extractModelTypesfunction enhance the integrity of the type-checking process and ensure the function adheres to the expected model classifications.
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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 WalkthroughThis update introduces significant enhancements to various R functions, particularly focusing on improving naming conventions, input validation, and the handling of missing values. Key changes include the adoption of Changes
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@coderabbitai read the files in R/ and generate a class/function diagram using mermaid. |
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Tip For best results, initiate chat on the files or code changes. @zachmayer Here is the mermaid diagram based on the functions extracted from the R files: classDiagram
class caretEnsemble-package {
}
class S3GenericExtenstions {
}
class helper_functions {
getBinaryTargetLevel()
setBinaryTargetLevel(level)
validateBinaryTargetLevel(arg)
getMulticlassExcludedLevel()
setMulticlassExcludedLevel(level)
validateMulticlassExcludedLevel(arg)
check_caretList_classes(list_of_models)
check_caretList_model_types(list_of_models)
check_bestpreds_resamples(modelLibrary)
check_bestpreds_indexes(modelLibrary)
check_bestpreds_obs(modelLibrary)
check_bestpreds_preds(modelLibrary)
check_multiclass_excluded_level(excluded_level, num_classes)
check_binary_classification(list_of_models)
extractModelName(x)
validateCustomModel(x)
extractModelTypes(list_of_models)
bestPreds(x)
extractBestPreds(list_of_models)
makePredObsMatrix(list_of_models)
}
class caretStack {
caretStack(all.models, ...)
}
class caretEnsemble {
caretEnsemble(all.models, ...)
extractModRes(ensemble)
getMetric(x, metric, ...)
getMetricSD(x, metric, ...)
norm_to_100(d)
clean_varImp(x)
varImpFrame(x)
multiResiduals(object, ...)
fortify(model, data = NULL, ...)
extractModFrame(model)
autoplot(object, which = c(1:6), mfrow = c(3, 2),
}
class caretList {
caretModelSpec(method = "rf", ...)
tuneCheck(x)
methodCheck(x)
trControlCheck(x, y)
extractCaretTarget(...)
caretList(
}
Analysis chainScripts executedThe following scripts were executed for the analysis: Script: #!/bin/bash
# List all files in the R/ directory
fd . -e R -t f -d 1 R/
# Extract functions and classes from all files in the R/ directory
fd . -e R -t f -d 1 R/ --exec sh -c 'echo "File: {}"; ast-grep --lang r --pattern $"
function $_($$) {
$$$
}
"'
Length of output: 1032 Script: #!/bin/bash
# List all files in the R/ directory
fd . -e R -t f -d 1 R/
# Extract functions from all files in the R/ directory using ripgrep
fd . -e R -t f -d 1 R/ --exec sh -c 'echo "File: {}"; rg "^\\s*\\w+\\s*<-\\s*function\\(" {}'
Length of output: 2051 If you found this review helpful, would you consider giving us a shout-out on X? |
Add a bunch more tests for edge cases. Found and fixed a couple bugs: