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Refactor Varimp #289
Refactor Varimp #289
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WalkthroughThe recent updates streamline functionality related to variable importance calculations by refactoring existing functions and enhancing documentation. Key changes include the removal of the Changes
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Actionable comments posted: 0
Review details
Configuration used: .coderabbit.yaml
Review profile: CHILL
Files selected for processing (7)
- DESCRIPTION (1 hunks)
- NAMESPACE (1 hunks)
- R/caretEnsemble.R (3 hunks)
- cobertura.xml (9 hunks)
- man/varImp.caretEnsemble.Rd (1 hunks)
- man/varImpDataTable.Rd (1 hunks)
- tests/testthat/test-ensembleMethods.R (2 hunks)
Files skipped from review due to trivial changes (2)
- man/varImp.caretEnsemble.Rd
- man/varImpDataTable.Rd
Additional comments not posted (10)
DESCRIPTION (1)
Line range hint
1-38
:
Verify the impact of removing thedigest
package.The
digest
package is commonly used for hashing and generating checksums. Ensure that its removal does not affect any critical functionality.Verification successful
The removal of the
digest
package does not impact any critical functionality.The search results indicate that the
digest
package is not used in the codebase, documentation, or configuration files.
- No references to
digest
were found in the R scripts.- No references to
digest
were found in the documentation files (e.g., README, DESCRIPTION).- No references to
digest
were found in the configuration files (e.g., .Rbuildignore, .Rprofile).Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify that the `digest` package removal does not affect any critical functionality. # Test: Search for any usage of the `digest` package in the codebase. Expect: No usage found. rg --type r 'digest'Length of output: 20
Script:
#!/bin/bash # Re-run the search for any usage of the `digest` package in the codebase, including documentation and configuration files. # Search for `digest` in R scripts rg --type r 'digest' # Search for `digest` in documentation files (e.g., README, DESCRIPTION) rg 'digest' --glob '*.md' --glob 'DESCRIPTION' # Search for `digest` in configuration files (e.g., .Rbuildignore, .Rprofile) rg 'digest' --glob '.*'Length of output: 89
NAMESPACE (2)
41-45
: LGTM! The addition ofdata.table
import statements enhances data handling capabilities.The functions
dcast.data.table
,merge.data.table
, andsetcolorder
are essential for reshaping, merging, and rearranging columns in data tables.
Line range hint
1-38
:
Verify the impact of removing thedigest
package.The
digest
package is commonly used for hashing and generating checksums. Ensure that its removal does not affect any critical functionality.tests/testthat/test-ensembleMethods.R (3)
19-23
: LGTM! The test case for variable importance in ensembles is clear and efficient.The test case checks variable importance in ensemble models using the
varImp
function.
Line range hint
30-43
:
LGTM! The test case forvarImp
function incaretEnsembles
is clear and efficient.The test case checks the output structure of the
varImp
function forcaretEnsembles
.
51-55
: LGTM! The test case for dimensions of variable importance output is clear and efficient.The test case checks the dimensions of the variable importance output.
R/caretEnsemble.R (2)
120-138
: LGTM! But verify the function usage in the codebase.The code changes are approved.
However, ensure that all function calls to
varImpDataTable
match the new signature.Verification successful
All function calls to
varImpDataTable
match the new signature.The function
varImpDataTable
is correctly used with the new signature in the following instances:
- Line 145:
mapply(varImpDataTable, object$models, model_names, MoreArgs = list(...), SIMPLIFY = FALSE)
- Line 151:
varImpDataTable(object$ens_model, "ensemble")
Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Description: Verify all function calls to `varImpDataTable` match the new signature. # Test: Search for the function usage. Expect: Only occurrences of the new signature. rg --type r -A 5 $'varImpDataTable'Length of output: 1258
148-180
: LGTM! But verify the function usage in the codebase.The code changes are approved.
However, ensure that all function calls to
varImp.caretEnsemble
match the new logic.cobertura.xml (2)
3-3
: Coverage metrics updated.The overall line coverage has been updated to reflect the current state of the codebase.
66-75
: Method name updated.The method name has been updated from
varImpFrame
tovarImpDataTable
to reflect the new function name.
No description provided.