Lint #297
Lint #297
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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 changes reflect significant updates across the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant CaretPackage
participant ErrorHandler
participant Linter
User->>CaretPackage: Execute code with linter checks
CaretPackage->>Linter: Run linters
Linter-->>CaretPackage: Return results
CaretPackage->>ErrorHandler: Handle any errors
ErrorHandler-->>CaretPackage: Return refined error message
CaretPackage-->>User: Display results
sequenceDiagram
participant User
participant CaretPackage
participant TestSuite
User->>TestSuite: Run tests on CaretPackage
TestSuite->>CaretPackage: Execute functions
CaretPackage-->>TestSuite: Return outputs
TestSuite->>TestSuite: Validate outputs with expect_identical
TestSuite-->>User: Report test results
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Actionable comments posted: 1
Review details
Configuration used: .coderabbit.yaml
Review profile: CHILL
Files selected for processing (18)
- .lintr (1 hunks)
- R/S3GenericExtenstions.R (2 hunks)
- R/caretEnsemble.R (4 hunks)
- R/caretList.R (11 hunks)
- R/caretPredict.R (2 hunks)
- R/caretStack.R (5 hunks)
- R/caretTrain.R (1 hunks)
- cobertura.xml (1 hunks)
- man/check_caretStack.Rd (1 hunks)
- man/set_excluded_class_id.Rd (1 hunks)
- tests/testthat/test-S3-generic-extensions.R (2 hunks)
- tests/testthat/test-caretEnsemble.R (6 hunks)
- tests/testthat/test-caretList.R (19 hunks)
- tests/testthat/test-caretStack.R (8 hunks)
- tests/testthat/test-classSelection.R (1 hunks)
- tests/testthat/test-ensembleMethods.R (4 hunks)
- tests/testthat/test-helper_functions.R (13 hunks)
- tests/testthat/test-multiclass.R (9 hunks)
Files skipped from review due to trivial changes (5)
- R/S3GenericExtenstions.R
- R/caretTrain.R
- cobertura.xml
- man/check_caretStack.Rd
- man/set_excluded_class_id.Rd
Additional comments not posted (110)
.lintr (3)
2-2: LGTM!Setting
tagstoNULLremoves all categorization tags for linters, which might be intentional to simplify the configuration.
3-3: LGTM!Setting
todo_comment_lintertoNULLdisables the linter for TODO comments, which might be intentional to allow TODO comments in the code.
4-4: LGTM!Setting
object_name_lintertoNULLdisables the linter for object names, which might be intentional to allow flexibility in naming objects.tests/testthat/test-classSelection.R (1)
39-39: LGTM!Replacing
sapplywithvapplyenhances type safety and performance by ensuring that the output is consistently of typecharacter(1L).R/caretPredict.R (7)
11-11: LGTM!Adding
call. = FALSEto the warning suppresses the call stack, making the warning message cleaner.
15-15: LGTM!Adding
call. = FALSEto the error suppresses the call stack, making the error message cleaner.
18-18: LGTM!Adding
call. = FALSEto the error suppresses the call stack, making the error message cleaner.
25-25: LGTM!Adding
call. = FALSEto the warning suppresses the call stack, making the warning message cleaner.
29-29: LGTM!Using
suppressWarningsensures that any warnings during the conversion are suppressed, making the code cleaner.
34-34: LGTM!Adding
call. = FALSEto the error suppresses the call stack, making the error message cleaner.
37-37: LGTM!Adding
call. = FALSEto the error suppresses the call stack, making the error message cleaner.tests/testthat/test-S3-generic-extensions.R (2)
180-180: Good use ofvapplyfor type safety.Replacing
sapplywithvapplyensures that the result is explicitly a character vector, improving type safety and clarity.
192-202: Stricter validation withexpect_identical.Replacing
expect_equalwithexpect_identicalensures that the structure and type of the data tables returned by the predictions match the expected dimensions precisely.tests/testthat/test-ensembleMethods.R (3)
42-42: Stricter validation withexpect_identical.Replacing
expect_equalwithexpect_identicalensures that the variable names are not only equal in value but also of the same type and structure.
51-54: Stricter validation withexpect_identical.Replacing
expect_equalwithexpect_identicalensures that the structure and type of the data tables returned by the predictions match the expected dimensions precisely.
129-133: Stricter validation withexpect_identicalandexpect_named.Replacing
expect_equalwithexpect_identicalandexpect_namedensures that the structure and type of the data tables and the names of the columns match the expected values precisely.tests/testthat/test-multiclass.R (6)
14-14: Stricter validation withexpect_identical.Replacing
expect_equalwithexpect_identicalensures that the number of rows in the predictions matches the expected value precisely.
24-24: Stricter validation withexpect_identical.Replacing
expect_equalwithexpect_identicalensures that the number of rows in the predictions matches the expected value precisely.
43-43: Stricter validation withexpect_identical.Replacing
expect_equalwithexpect_identicalensures that the dimensions of the predictions match the expected values precisely.
54-54: Stricter validation withexpect_named.Replacing
expect_equalwithexpect_namedensures that the names of the columns in the predictions match the expected values precisely.
76-76: Stricter validation withexpect_identical.Replacing
expect_equalwithexpect_identicalensures that the dimensions of the predictions match the expected values precisely.
Line range hint
213-251:
Stricter validation withexpect_identicalandexpect_named.Replacing
expect_equalwithexpect_identicalandexpect_namedensures that the structure and type of the data tables and the names of the columns match the expected values precisely.tests/testthat/test-caretEnsemble.R (10)
25-25: Approved: Stricter equality checks for metrics extraction.The use of
expect_identicalensures that the metrics are not only equal in value but also identical in type and attributes.
29-29: Approved: Stricter equality checks for metrics extraction with standard deviation.The use of
expect_identicalensures that the metrics with standard deviation are not only equal in value but also identical in type and attributes.
73-73: Approved: Stricter equality checks for ensemble predictions.The use of
expect_identicalensures that the number of columns in the predictions is identical.
114-115: Approved: Stricter equality checks for predictions with different predictors.The use of
expect_identicalensures that the number of rows and columns in the predictions is identical.
183-185: Approved: Stricter equality checks for classification model predictions.The use of
expect_identicalensures that the number of rows in the stacked, in-sample, and one-row predictions is identical.
188-190: Approved: Stricter equality checks for classification model predictions.The use of
expect_identicalensures that the number of columns in the stacked, in-sample, and one-row predictions is identical.
236-236: Approved: Stricter equality checks for custom model names.The use of
expect_namedensures that the names of the ensembled models are as expected.
249-251: Approved: Stricter equality checks for custom model predictions.The use of
expect_identicalensures that the number of rows in the stacked, in-sample, and one-row predictions is identical.
254-256: Approved: Stricter equality checks for custom model predictions.The use of
expect_identicalensures that the number of columns in the stacked, in-sample, and one-row predictions is identical.
Line range hint
157-160: Approved: Stricter equality checks for predictions with high excluded class level.The use of
expect_identicalensures that the number of rows and columns in the predictions is identical. The helper functionall_finiteimproves readability and maintainability.tests/testthat/test-caretStack.R (12)
35-35: Approved: Stricter equality checks for classification model predictions.The use of
expect_identicalensures that the number of rows in the predictions is identical.
134-137: Approved: Stricter equality checks for caretStack object identification.The use of
expect_identicalensures that the identification of caretStack objects is accurate.
157-160: Approved: Stricter equality checks for predictions with high excluded class level.The use of
expect_identicalensures that the number of rows and columns in the predictions is identical. The helper functionall_finiteimproves readability and maintainability.
187-187: Approved: Stricter equality checks for stacking algorithm predictions.The use of
expect_identicalensures that the method of the ensemble model is as expected.
356-357: Approved: Stricter equality checks for predictions with new data.The use of
expect_identicalensures that the number of rows in the predictions is identical.
359-360: Approved: Stricter equality checks for predictions with new data.The use of
expect_identicalensures that the number of columns in the predictions is identical.
368-369: Approved: Stricter equality checks for predictions with new data.The use of
expect_identicalensures that the number of rows in the predictions is identical.
371-372: Approved: Stricter equality checks for predictions with new data.The use of
expect_identicalensures that the number of columns in the predictions is identical.
296-301: Approved: Stricter equality checks for predictions without excluded_class_id.The use of
expect_identicalensures that the number of rows and columns in the predictions is identical and that the predictions are named correctly.
311-312: Approved: Stricter equality checks for caretStack object coercion.The use of
expect_warningensures that the coercion warning is captured, and the use ofexpect_identicalensures that the models are correctly coerced to a caretList.
314-315: Approved: Stricter equality checks for caretStack failure conditions.The use of
expect_errorensures that the correct error message is produced whennew_Xandnew_yare not both NULL or both non-NULL.
356-372: Approved: Stricter equality checks for predictions with new data.The use of
expect_identicalensures that the number of rows and columns in the predictions is identical.R/caretStack.R (8)
42-42: Approved: Improved handling of warnings.The warning message now suppresses the call stack, improving the user experience.
48-48: Approved: Improved validation of inputs.The validation ensures that both
new_Xandnew_yare either NULL or non-NULL, improving the robustness of the function.
85-96: Approved: Added caretStack object validation.The
check_caretStackfunction ensures that the object has the expected structure, improving robustness.
98-110: Approved: Added function to set excluded class ID.The
set_excluded_class_idfunction centralizes the logic for managing the excluded class ID, improving modularity and readability.
183-183: Approved: Improved caretStack object validation.The use of
check_caretStackensures that the object is validated early in the execution, improving robustness.
189-189: Approved: Improved handling of excluded class ID.The use of
set_excluded_class_idcentralizes the logic for managing the excluded class ID, improving readability and modularity.
247-247: Approved: Improved handling of warnings for standard errors.The warning message now suppresses the call stack, improving the user experience.
318-318: Approved: Improved output formatting.The use of
toStringfor formatting the base model names enhances the readability of the printed output.R/caretList.R (14)
27-27: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.
40-40: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.
52-56: Improvement: Cleaner error messages.Including
call. = FALSEin thestopfunction suppresses the function call in the error message, resulting in cleaner output.
79-79: Improvement: Cleaner error messages.Including
call. = FALSEin thestopfunction suppresses the function call in the error message, resulting in cleaner output.
82-84: Improvement: Cleaner error messages.Including
call. = FALSEin thestopfunction suppresses the function call in the error message, resulting in cleaner output.
94-95: Improvement: Cleaner error messages.Including
call. = FALSEin thestopfunction suppresses the function call in the error message, resulting in cleaner output.
182-182: Improvement: Cleaner error messages.Including
call. = FALSEin thestopfunction suppresses the function call in the error message, resulting in cleaner output.
235-235: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.
239-239: Improvement: Cleaner error messages.Including
call. = FALSEin thestopfunction suppresses the function call in the error message, resulting in cleaner output.
261-261: Improvement: Cleaner error messages.Including
call. = FALSEin thestopfunction suppresses the function call in the error message, resulting in cleaner output.
272-272: Improvement: Cleaner error messages.Including
call. = FALSEin thestopfunction suppresses the function call in the error message, resulting in cleaner output.
283-283: Improvement: Cleaner error messages.Including
call. = FALSEin thestopfunction suppresses the function call in the error message, resulting in cleaner output.
287-288: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.
295-295: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.R/caretEnsemble.R (10)
11-11: Improvement: Cleaner error messages.Including
call. = FALSEin thestopfunction suppresses the function call in the error message, resulting in cleaner output.
101-103: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.
122-122: Enhancement: Use oftoStringfor better readability.Replacing
pastewithtoStringsimplifies the code and ensures a more readable output format.
126-126: Enhancement: Use oftoStringfor better readability.Replacing
pastewithtoStringsimplifies the code and ensures a more readable output format.
128-129: Enhancement: Use oftoStringfor better readability.Replacing
pastewithtoStringsimplifies the code and ensures a more readable output format.
132-132: Enhancement: Use oftoStringfor better readability.Replacing
pastewithtoStringsimplifies the code and ensures a more readable output format.
175-175: Enhancement: Use ofMapfor better readability.Replacing
mapplywithMapimproves readability and aligns better with the intended use of the functions involved.
Line range hint
213-215:
Enhancement: Stricter assertions withexpect_identical.Using
expect_identicalensures both value and type equality, tightening validation criteria.
Line range hint
219-221:
Enhancement: Stricter assertions withexpect_identical.Using
expect_identicalensures both value and type equality, tightening validation criteria.
Line range hint
276-279:
Enhancement: Stricter assertions withexpect_identical.Using
expect_identicalensures both value and type equality, tightening validation criteria.tests/testthat/test-helper_functions.R (11)
26-26: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.
48-50: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.
159-159: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.
166-167: Enhancement: Stricter assertions withexpect_identical.Using
expect_identicalensures both value and type equality, tightening validation criteria.
173-174: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.
213-215: Enhancement: Stricter assertions withexpect_identical.Using
expect_identicalensures both value and type equality, tightening validation criteria.
219-221: Enhancement: Stricter assertions withexpect_identical.Using
expect_identicalensures both value and type equality, tightening validation criteria.
276-279: Enhancement: Stricter assertions withexpect_identical.Using
expect_identicalensures both value and type equality, tightening validation criteria.
358-359: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.
364-364: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.
368-369: Enhancement: Use ofvapplyfor type safety.The replacement of
sapplywithvapplyensures that the output type is consistent, enhancing type safety and reliability.tests/testthat/test-caretList.R (23)
26-26: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
32-32: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
55-58: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
114-115: Approved: Improved readability and stricter comparison in test case.Assigning
expect_warningto a variable improves readability. Replacingexpect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
157-157: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
168-170: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
239-240: Approved: Improved readability and stricter comparison in test case.Assigning
expect_warningto a variable improves readability. Replacingexpect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
252-252: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
289-290: Approved: Improved readability and stricter comparison in test case.Assigning
expect_warningto a variable improves readability. Replacingexpect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
299-301: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
409-411: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
435-437: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
472-474: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
495-495: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
509-510: Approved: Improved readability and stricter comparison in test case.Assigning
expect_warningto a variable improves readability. Replacingexpect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
517-518: Approved: Improved readability and stricter comparison in test case.Assigning
expect_warningto a variable improves readability. Replacingexpect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
529-530: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
568-571: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
590-590: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
595-597: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
601-603: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
665-665: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
718-718: Approved: Stricter comparison in test case.Replacing
expect_equalwithexpect_identicalensures both value and type equality, improving test robustness.
Fully delint, only todo linter and object linter left