Imports #296
Imports #296
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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 primarily focus on refactoring the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant CaretEnsemble
participant DataTable
participant Stats
User->>CaretEnsemble: Call method
CaretEnsemble->>DataTable: Use data.table::function()
CaretEnsemble->>Stats: Use stats::function()
CaretEnsemble-->>User: Return result
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Actionable comments posted: 0
Outside diff range, codebase verification and nitpick comments (1)
NAMESPACE (1)
Reinstate the removed import statements.
The removed import statements from
caret,data.table,ggplot2, and other packages are still required as their functions are used in the codebase. Removing these imports will cause errors.
caret: Functions liketrain,trainControl,modelLookup, etc., are used.data.table: Functions likeas.data.table,data.table,dcast.data.table, etc., are used.ggplot2: Functions likeaes,geom_bar,geom_hline,geom_linerange,geom_point,ggplot, etc., are used.Please verify and reinstate the necessary import statements to ensure the code functions correctly.
Analysis chain
Line range hint
1-31:
Verify the removal of import statements.The removal of imports from
caret,data.table,ggplot2,gridExtra,lattice,methods,pbapply, andstatssuggests that these functions are no longer needed. Verify that these functions are not used elsewhere in the codebase.Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that removed import functions are not used elsewhere in the codebase. # Test: Search for the usage of removed functions. Expect: No occurrences of these functions. rg --type r -e 'modelLookup|resamples|train|trainControl|as.data.table|data.table|dcast.data.table|merge.data.table|rbindlist|set|setcolorder|setkeyv|setnames|setorderv|aes|geom_bar|geom_hline|geom_linerange|geom_point|geom_pointrange|geom_smooth|ggplot|labs|scale_x_continuous|scale_y_continuous|theme_bw|grid.arrange|dotplot|is|pblapply|coef|median|model.frame|model.response|na.omit|qnorm|reshape|resid|residuals|weighted.mean|weights'Length of output: 116888
Review details
Configuration used: .coderabbit.yaml
Review profile: CHILL
Files selected for processing (16)
- NAMESPACE (1 hunks)
- R/caretEnsemble-package.R (1 hunks)
- R/caretEnsemble.R (12 hunks)
- R/caretList.R (8 hunks)
- R/caretPredict.R (3 hunks)
- R/caretStack.R (11 hunks)
- R/caretTrain.R (1 hunks)
- cobertura.xml (18 hunks)
- man/dotplot.caretStack.Rd (1 hunks)
- man/extractPredObsResid.Rd (1 hunks)
- tests/testthat/test-caretEnsemble.R (1 hunks)
- tests/testthat/test-caretStack.R (1 hunks)
- tests/testthat/test-ensembleMethods.R (3 hunks)
- tests/testthat/test-helper_functions.R (1 hunks)
- tests/testthat/test-parallel.R (1 hunks)
- vignettes/caretEnsemble-intro.Rmd (2 hunks)
Files skipped from review due to trivial changes (9)
- R/caretEnsemble-package.R
- man/dotplot.caretStack.Rd
- man/extractPredObsResid.Rd
- tests/testthat/test-caretEnsemble.R
- tests/testthat/test-caretStack.R
- tests/testthat/test-ensembleMethods.R
- tests/testthat/test-helper_functions.R
- tests/testthat/test-parallel.R
- vignettes/caretEnsemble-intro.Rmd
Additional comments not posted (34)
R/caretTrain.R (2)
24-24: LGTM! Explicit namespace usage enhances clarity.The explicit use of
caret::trainensures that the correct function is called, reducing potential errors related to function name conflicts.
29-29: LGTM! Explicit namespace usage enhances clarity.The explicit use of
caret::trainensures that the correct function is called, reducing potential errors related to function name conflicts.R/caretPredict.R (3)
58-58: LGTM! Explicit use ofmethods::isenhances robustness.The explicit use of
methods::isensures that the type-checking is performed using the S4 class system, which is more robust for certain object types in R.
77-77: LGTM! Explicit use ofmethods::isenhances robustness.The explicit use of
methods::isensures that the type-checking is performed using the S4 class system, which is more robust for certain object types in R.
119-119: LGTM! Explicit use ofmethods::isenhances robustness.The explicit use of
methods::isensures that the type-checking is performed using the S4 class system, which is more robust for certain object types in R.R/caretStack.R (7)
57-57: LGTM!Explicitly using
data.table::as.data.tableimproves code clarity and prevents potential conflicts.
78-78: LGTM!Explicitly using
caret::trainimproves code clarity and prevents potential conflicts.
97-97: LGTM!Explicitly using
stats::weighted.meanimproves code clarity and prevents potential conflicts.
133-133: LGTM!Explicitly using
stats::predictimproves code clarity and prevents potential conflicts.
159-160: LGTM!Explicitly using
methods::isimproves code clarity and ensures proper type checking for S4 objects.
218-218: LGTM!Explicitly using
caret::varImpimproves code clarity and prevents potential conflicts.
259-259: LGTM!Explicitly using
methods::isimproves code clarity and ensures proper type checking for S4 objects.R/caretList.R (6)
67-67: LGTM!Explicitly using
caret::modelLookupimproves code clarity and prevents potential conflicts.
123-123: LGTM!Explicitly using
stats::model.responseandstats::model.frameimproves code clarity and prevents potential conflicts.
249-249: LGTM!Explicitly using
methods::isimproves code clarity and ensures proper type checking for S4 objects.
285-285: LGTM!Explicitly using
methods::isimproves code clarity and ensures proper type checking for S4 objects.
325-325: LGTM!Explicitly using
stats::predictimproves code clarity and prevents potential conflicts.
366-368: LGTM!Explicitly using
data.table::setnamesimproves code clarity and prevents potential conflicts.R/caretEnsemble.R (8)
10-10: LGTM!Explicitly using
methods::isimproves code clarity and ensures proper type checking for S4 objects.
61-61: LGTM!Explicitly using
methods::isimproves code clarity and ensures proper type checking for S4 objects.
99-99: LGTM!Explicitly using
data.table::data.tableimproves code clarity and prevents potential conflicts.
123-123: LGTM!Explicitly using
stats::coefimproves code clarity and prevents potential conflicts.
167-168: LGTM!Explicitly using
caret::varImpimproves code clarity and prevents potential conflicts.
Line range hint
206-238:
LGTM!Explicitly using
ggplot2functions improves code clarity and prevents potential conflicts.
248-260: LGTM!Explicitly using
methods::is,data.table::data.table, anddata.table::setimproves code clarity and ensures proper type checking for S4 objects.
Line range hint
285-335:
LGTM!Explicitly using
methods::is,ggplot2, anddata.tablefunctions improves code clarity and prevents potential conflicts.cobertura.xml (8)
52-52: Improved Test Coverage forextractModelMetrics.The addition of line 98 with 12 hits indicates better test coverage for the
extractModelMetricsmethod.
Line range hint
64-73:
Enhanced Test Coverage forsummary.caretEnsemble.The addition of multiple new lines with 2 hits each indicates improved test coverage for the
summary.caretEnsemblemethod.
79-83: Enhanced Test Coverage forvarImpDataTable.The addition of multiple new lines with 60 hits each indicates improved test coverage for the
varImpDataTablemethod.
92-97: Improved Test Coverage forvarImp.caretEnsemble.The modification of line numbers and additional hits for specific lines indicate better test coverage for the
varImp.caretEnsemblemethod.
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112-131:
Enhanced Test Coverage forplot.caretEnsemble.The addition of multiple new lines with 8 hits each indicates improved test coverage for the
plot.caretEnsemblemethod.
145-145: Increased Test Hits forextractPredObsResid.The increase in hits for line 257 from 10 to 20 indicates better test coverage for the
extractPredObsResidmethod.
160-177: Improved Test Coverage forautoplot.caretEnsemble.The modification of line numbers and additional hits for specific lines indicate better test coverage for the
autoplot.caretEnsemblemethod.
563-583: Enhanced Test Coverage forpredict.caretList.The modification of line numbers and additional hits for specific lines indicate improved test coverage for the
predict.caretListmethod.
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