[312] Default train control #317
Conversation
WalkthroughThe recent updates enhance the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant caretList
participant caretStack
participant defaultControl
participant defaultMetric
User->>caretList: Call with data
caretList->>defaultControl: Use default parameters
defaultControl-->>caretList: Return control settings
caretList->>defaultMetric: Determine default metric
defaultMetric-->>caretList: Return metric
caretList-->>User: Return model results
User->>caretStack: Call with model list
caretStack->>defaultControl: Use default parameters
defaultControl-->>caretStack: Return control settings
caretStack-->>User: Return stacked model results
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Actionable comments posted: 0
Outside diff range, codebase verification and nitpick comments (1)
.github/ISSUE_TEMPLATE.md (1)
30-34: Refine data preparation instructions.The instructions for using
dput()and handling factors with many levels are well-explained. Consider adding examples or links to resources for users unfamiliar with these functions.
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Files selected for processing (20)
- .github/ISSUE_TEMPLATE.md (1 hunks)
- .gitignore (1 hunks)
- NAMESPACE (1 hunks)
- R/caretList.R (4 hunks)
- R/caretStack.R (5 hunks)
- inst/WORDLIST (3 hunks)
- inst/data-raw/build_test_data.R (1 hunks)
- man/autoplot.caretStack.Rd (1 hunks)
- man/caretList.Rd (1 hunks)
- man/caretStack.Rd (2 hunks)
- man/defaultControl.Rd (1 hunks)
- man/defaultMetric.Rd (1 hunks)
- tests/testthat/test-caretEnsemble.R (3 hunks)
- tests/testthat/test-caretList.R (2 hunks)
- tests/testthat/test-caretPredict.R (1 hunks)
- tests/testthat/test-caretStack.R (3 hunks)
- tests/testthat/test-classSelection.R (1 hunks)
- tests/testthat/test-greedyMSE.R (3 hunks)
- tests/testthat/test-multiclass.R (1 hunks)
- vignettes/caretEnsemble-intro.Rmd (3 hunks)
Files skipped from review due to trivial changes (6)
- .gitignore
- inst/WORDLIST
- man/autoplot.caretStack.Rd
- man/defaultMetric.Rd
- tests/testthat/test-greedyMSE.R
- vignettes/caretEnsemble-intro.Rmd
Additional comments not posted (25)
inst/data-raw/build_test_data.R (1)
13-13: Verify the impact of removingtrControl.The
trControlparameter has been removed from thecaretListfunction calls. This change may lead to default settings being applied, which could impact model training behavior. Ensure that the default settings align with the intended use case and verify if any adjustments are needed in the model evaluation process.Also applies to: 21-21
NAMESPACE (1)
31-32: Verify the implementation and usage of new exports.The
defaultControlanddefaultMetricentities have been exported. Ensure that these functions are correctly implemented and utilized within the codebase. Verify their definitions and usage to confirm they align with the intended functionality.Verification successful
Verification Successful: Implementation and Usage of Exports Confirmed
The
defaultControlanddefaultMetricfunctions are correctly implemented and actively used within the codebase. They are defined inR/caretList.Rand utilized in various components, including test files and documentation. No issues were found.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the implementation and usage of `defaultControl` and `defaultMetric`. # Test: Search for the definitions of `defaultControl` and `defaultMetric`. Expect: Correct implementation. ast-grep --lang r --pattern 'defaultControl <- function($$$) { $$$ }' ast-grep --lang r --pattern 'defaultMetric <- function($$$) { $$$ }'Length of output: 348
Script:
#!/bin/bash # Description: Verify the implementation and usage of `defaultControl` and `defaultMetric`. # Search for the definition of `defaultControl` rg 'defaultControl\s*<-\s*function' -A 5 # Search for the definition of `defaultMetric` rg 'defaultMetric\s*<-\s*function' -A 5 # Search for the usage of `defaultControl` rg 'defaultControl' # Search for the usage of `defaultMetric` rg 'defaultMetric'Length of output: 2062
man/defaultControl.Rd (1)
1-32: Review the accuracy and completeness of documentation.The documentation for
defaultControlprovides a clear overview of its usage and parameters. Ensure that the description accurately reflects the function's behavior and that all arguments are clearly explained. Verify that the documentation aligns with the function's implementation..github/ISSUE_TEMPLATE.md (4)
1-1: Clarify the section header.The header "FEATURE REQUEST" is clear and concise. Ensure that any additional instructions specific to feature requests are included below this header if needed.
4-7: Enhance the bug report checklist.The checklist for bug reports is comprehensive and includes a new item for including example data. This addition emphasizes the importance of reproducibility. Ensure that users understand how to provide example data effectively.
10-20: Clarify instructions for reproducible examples.The instructions for creating a minimal reproducible example are clear. The use of explicit indexing with
Lsuffixes for integer literals is a good practice. Ensure users are aware of the purpose of each step in this process.
36-45: Update package upgrade instructions.The session info section and package upgrade instructions are clear. Remind users to regularly update their packages to avoid compatibility issues.
man/caretList.Rd (1)
24-24: Clarify default behavior fortrControl.The documentation now specifies that
defaultControlis used iftrControlisNULL. This change improves clarity. Ensure thatdefaultControlis adequately documented elsewhere in the package.man/caretStack.Rd (2)
11-12: Document themetricparameter clearly.The
metricparameter allows users to specify a performance metric for grid search. Ensure that users understand how to choose an appropriate metric for their use case.
30-30: Clarify the use oftrControl.The
trControlparameter allows the use of atrainControlobject. The documentation specifies usingdefaultControlifNULL. Ensure users are aware of howtrControlaffects the training process.tests/testthat/test-classSelection.R (1)
37-37: Ensure the change aligns with the intended validation strategy.The change from validating
model.ens$ens_model$trainingData$.outcometomodel.ens$ens_model$pred$obssuggests a shift in focus. Verify that this change aligns with the intended validation strategy and that it accurately reflects the desired behavior of the model's predictions.tests/testthat/test-multiclass.R (1)
95-95: Verify the impact of using default settings incaretStack.The removal of the
trControlparameter in thecaretStackcall means default settings will be used. Ensure these defaults align with the desired behavior and do not negatively impact the model's performance.tests/testthat/test-caretPredict.R (1)
11-12: Assess the impact of default settings incaretEnsemble.The removal of detailed training control parameters in
caretEnsemblecalls means default settings are now used. Verify that these defaults are suitable for your models and do not compromise training or evaluation quality.Verification successful
Verification of Default Settings in
caretEnsemble:The
caretEnsemblefunction uses default settings that are generally suitable for typical use cases. The defaults includeexcluded_class_id = 0LandtuneLength = 1L, with the methodgreedyMSE_caret()for stacking models, which focuses on minimizing mean squared error. Ensure these defaults align with your specific model requirements.
caretEnsembledefaults:excluded_class_id = 0L,tuneLength = 1L, methodgreedyMSE_caret()Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Assess the impact of default settings in `caretEnsemble`. # Test: Search for the default settings used by `caretEnsemble` to ensure they are appropriate. rg --type r 'caretEnsemble\(' -A 5Length of output: 4401
Script:
#!/bin/bash # Extract the implementation of the `caretEnsemble` function to analyze its default settings. ast-grep --lang r --pattern $'caretEnsemble <- function($_, $_, $_) { $$$ }' R/caretEnsemble.RLength of output: 200
Script:
#!/bin/bash # Use rg to extract the implementation of the `caretEnsemble` function from R/caretEnsemble.R. rg 'caretEnsemble <- function' -A 20 R/caretEnsemble.RLength of output: 369
tests/testthat/test-caretEnsemble.R (3)
86-86: Use ofdefaultControlformy_control.The
trainControlsetup formy_controlis replaced withdefaultControl(target = Y.reg). Verify thatdefaultControlprovides the necessary configuration for the tests.Verification successful
Use of
defaultControlformy_controlis appropriate.The
defaultControlfunction is designed to configure thetrainControlobject based on the target and problem type, making it suitable for use in tests. The function adapts to the type of task (classification or regression), ensuring it provides the necessary configuration for the tests involvingY.reg.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the definition and configuration of defaultControl. # Test: Search for the defaultControl function definition. rg --type r -A 5 $'defaultControl'Length of output: 2983
135-135: Simplified ensemble creation withcaretEnsemble.The creation of the ensemble
csusingcaretEnsemble(cl)has been simplified. Ensure that the default settings are suitable for the intended tests.Verification successful
Default settings for
caretEnsembleappear suitable for general use.The
caretEnsemblefunction uses minimal default settings, focusing on a basic ensemble setup withgreedyMSE_caret(). Ensure these defaults align with your specific testing requirements.
- Default
excluded_class_id: 0L- Default
tuneLength: 1LScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the default settings for caretEnsemble with caretList input. # Test: Search for the caretEnsemble function handling caretList input. rg --type r -A 5 $'caretEnsemble'Length of output: 23132
Script:
#!/bin/bash # Extract the full implementation of the caretEnsemble function to analyze its default settings. ast-grep --lang r --pattern 'caretEnsemble <- function($$$) { $$$ }'Length of output: 173
Script:
#!/bin/bash # Use rg to search for the caretEnsemble function definition and its surrounding lines. rg --type r -A 20 'caretEnsemble <- function'Length of output: 630
14-15: Simplification of ensemble instantiation.The instantiation of
ens.regandens.classusingcaretEnsemblehas been simplified by removing detailedtrControlparameters. Ensure that the default settings used here are appropriate for the tests and maintain the expected behavior.Verification successful
Verification of Default Settings in
caretEnsembleSimplificationThe simplification of ensemble instantiation in the tests by removing detailed
trControlparameters is appropriate. ThecaretStackfunction, called bycaretEnsemble, defaults to no specifictrControlsettings unless specified, aligning with the intended test behavior. Ensure that the tests are designed to validate this default behavior.
caretStackfunction definition inR/caretStack.Rconfirms defaulttrControlisNULL.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the default settings for caretEnsemble are appropriate for the tests. # Test: Search for the default settings in the caretEnsemble function definition. rg --type r -A 5 $'caretEnsemble'Length of output: 23132
Script:
#!/bin/bash # Search for the implementation of the caretStack function to understand its default settings. ast-grep --lang r --pattern 'caretStack <- function($$$)'Length of output: 162
Script:
#!/bin/bash # Search for the definition of the caretStack function in R files to understand its default settings. rg --type r -A 10 'caretStack <- function'Length of output: 6240
tests/testthat/test-caretList.R (2)
188-190: Use ofdefaultControlwith sampling.The
trControlparameter is replaced withdefaultControl, including a sampling method. Verify that this change aligns with the intended behavior for handling imbalanced data.
285-285: Removal oftrControlfromcaretStack.The
trControlparameter is removed fromcaretStackcalls. Ensure that the default handling withincaretStackis appropriate for the tests.Verification successful
Verification of
trControlHandling incaretStack:The
caretStackfunction includes atrControlparameter, which defaults toNULL. WhentrControlisNULL, the function assigns a default control usingdefaultControl(obs, is_class = is_class, is_binary = is_binary). This ensures that the absence of a user-specifiedtrControldoes not lead to errors, and the function can proceed with a sensible default configuration.Thus, the removal of
trControlfromcaretStackcalls in the tests should not affect the functionality, as the function handles it appropriately by default.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the default handling of training controls in caretStack. # Test: Search for the caretStack function definition and its handling of training controls. rg --type r -A 5 $'caretStack'Length of output: 34925
Script:
#!/bin/bash # Description: Extract the full implementation of the caretStack function to verify handling of the trControl parameter. ast-grep --lang r --pattern 'caretStack <- function($_$$$) { $$$ }'Length of output: 172
Script:
#!/bin/bash # Description: Use ripgrep to find the implementation of the caretStack function in R files. rg --type r -A 20 '^caretStack <- function' R/Length of output: 983
Script:
#!/bin/bash # Description: Use ripgrep to find the complete implementation of the caretStack function in R files. rg --type r -A 50 '^caretStack <- function' R/Length of output: 2415
Script:
#!/bin/bash # Description: Use ripgrep to find the complete implementation of the caretStack function in R files. rg --type r -A 100 '^caretStack <- function' R/Length of output: 5729
tests/testthat/test-caretStack.R (3)
174-181: Handling of new data incaretStack.The
caretStackcalls now includenew_Xandnew_yparameters. Ensure that these changes are correctly integrated and tested.Verification successful
Handling of new data in
caretStackis correctly integrated and tested.The
caretStackfunction's new parametersnew_Xandnew_yare properly handled, with tests verifying their functionality and error handling. The changes have been successfully integrated and tested.
- The function definition in
R/caretStack.Rincludesnew_Xandnew_y.- Tests in
tests/testthat/test-caretStack.Rverify their correct usage and error cases.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the handling of new_X and new_y parameters in caretStack. # Test: Search for the caretStack function definition and its handling of new_X and new_y. rg --type r -A 5 $'caretStack'Length of output: 34925
16-18: SimplifiedcaretStackinstantiation.The
caretStackcalls forens.classandens.reghave been simplified by removingtrControl. Verify that the default settings are suitable for these tests.Verification successful
Verification of
caretStackDefaults WithouttrControlThe
caretStackfunction in the codebase does not specify default values for thetrControlparameter, indicating reliance on the caret package's default behavior. The tests intests/testthat/test-caretStack.Rvalidate the function's behavior withouttrControl, suggesting the default settings are appropriate for these tests. No changes are necessary.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the default settings for caretStack are appropriate for the tests. # Test: Search for the caretStack function definition and its default settings. rg --type r -A 5 $'caretStack'Length of output: 34925
232-233: Modified output expectations forThe output expectations for the
R/caretList.R (3)
183-199: Approve thedefaultControlfunction.The function effectively encapsulates the logic for creating a default train control with settings suitable for stacking.
Verify its usage to ensure it aligns with the intended enhancements for stacking.
Verification successful
defaultControlFunction Usage VerifiedThe
defaultControlfunction is used in both test files and main R scripts, confirming its integration into the caret-based model workflow. This supports its intended purpose for stacking enhancements.
- Test Files:
tests/testthat/test-caretList.R,tests/testthat/test-caretEnsemble.R- Main Code Files:
R/caretStack.R,R/caretList.RScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `defaultControl` function. # Test: Search for the usage of `defaultControl` within the codebase. ast-grep --lang r --pattern $'defaultControl($_, $_, $_, $_, $$$)'Length of output: 170
Script:
#!/bin/bash # Description: Search for the usage of `defaultControl` in the R codebase using ripgrep. rg 'defaultControl\(' --glob '*.R' -A 3Length of output: 1024
207-217: Approve thedefaultMetricfunction.The function simplifies the logic for determining the appropriate metric, enhancing readability and maintainability.
Verify its usage to ensure it is correctly integrated into the model training process.
Verification successful
The
defaultMetricfunction is correctly used in the codebase.The function is utilized in both
R/caretList.RandR/caretStack.R, confirming its role in determining metrics for classification tasks. This integration aligns with its intended purpose.
- Files where
defaultMetricis used:
R/caretList.RR/caretStack.RScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `defaultMetric` function. # Test: Search for the usage of `defaultMetric` within the codebase. ast-grep --lang r --pattern $'defaultMetric($_, $_)'Length of output: 156
Script:
#!/bin/bash # Description: Verify the usage of `defaultMetric` function using ripgrep. # Test: Search for the usage of `defaultMetric` within R files in the codebase. rg 'defaultMetric\(' --glob '*.R' -A 2Length of output: 338
63-68: LGTM! Verify the integration of helper functions.The refactoring to use
defaultMetricanddefaultControlenhances readability and maintainability.Ensure that these helper functions are correctly integrated and their logic aligns with the intended functionality.
Verification successful
Integration of
defaultMetricanddefaultControlVerifiedThe
defaultMetricanddefaultControlfunctions are correctly defined and integrated into the codebase, enhancing readability and maintainability. Their usage across multiple files, including test files, confirms their proper implementation.
Definitions:
defaultMetricinR/caretList.RdefaultControlinR/caretList.RUsages:
defaultMetricinR/caretList.R,R/caretStack.RdefaultControlinR/caretList.R,R/caretStack.R, and test filesScripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the usage of `defaultMetric` and `defaultControl` functions. # Test: Search for the implementation and usage of `defaultMetric` and `defaultControl`. ast-grep --lang r --pattern $'defaultMetric($_, $_)' ast-grep --lang r --pattern $'defaultControl($_, $_, $_, $_, $$$)'Length of output: 327
Script:
#!/bin/bash # Description: Use rg to search for the implementation and usage of `defaultMetric` and `defaultControl` in R files. # Search for the definition of `defaultMetric` rg 'defaultMetric <- function' --type r # Search for the definition of `defaultControl` rg 'defaultControl <- function' --type r # Search for the usage of `defaultMetric` rg 'defaultMetric' --type r # Search for the usage of `defaultControl` rg 'defaultControl' --type rLength of output: 1108
R/caretStack.R (1)
Line range hint
43-96:
Approve the enhancements tocaretStack.The addition of
metricandtrControlparameters improves flexibility and configurability, aligning with the PR objectives.Verify the integration of these parameters to ensure they function as intended.
Verification successful
Integration of
metricandtrControlparameters incaretStackis verified.The
metricandtrControlparameters are correctly integrated into thecaretStackfunction, and their usage is validated through existing test cases. This confirms their functionality as intended.
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify the integration of `metric` and `trControl` parameters in `caretStack`. # Test: Search for the usage and handling of `metric` and `trControl` within the `caretStack` function. ast-grep --lang r --pattern $'caretStack($_, $_, $_, $_, $_, $_, $$$)'Length of output: 174
Script:
#!/bin/bash # Search for the usage of `metric` and `trControl` in the caretStack function in R files. rg -A 10 'caretStack' --type rLength of output: 46182
Add a default constructor for trainControl (and metrics too) for making train controls that will play nice with stacking by default.
#312