Cleanup todos and spacing #307
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zachmayer
commented
Aug 8, 2024
zachmayer
commented
- add todo linter
- cleanup some double spaces after a period
- refactor the Makefile
- Reorg some exports vs keywords internal objects (everything that is not exported should now be keyword internal)
- remove is methods to just use the builtin methods::is
- remove dontrun from most examples (except autoplot which is slow)
WalkthroughThe recent changes focus on enhancing the structure, documentation, and usability of an R package. Key updates include the introduction of a Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Makefile
participant R_Functions
participant Documentation
User->>Makefile: Request help
Makefile->>User: List available targets
User->>R_Functions: Request documentation
R_Functions->>Documentation: Fetch detailed usage
Documentation->>User: Provide updated examples
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Files selected for processing (31)
- Makefile (4 hunks)
- NAMESPACE (1 hunks)
- R/caretEnsemble.R (1 hunks)
- R/caretList.R (11 hunks)
- R/caretPredict.R (2 hunks)
- R/caretStack.R (9 hunks)
- R/package.R (1 hunks)
- man/X.class.Rd (1 hunks)
- man/X.reg.Rd (1 hunks)
- man/Y.class.Rd (1 hunks)
- man/Y.reg.Rd (1 hunks)
- man/aggregate_mean_or_first.Rd (1 hunks)
- man/autoplot.caretStack.Rd (2 hunks)
- man/c.caretList.Rd (1 hunks)
- man/c.train.Rd (1 hunks)
- man/caretEnsemble.Rd (1 hunks)
- man/caretList.Rd (2 hunks)
- man/caretStack.Rd (1 hunks)
- man/dotplot.caretStack.Rd (1 hunks)
- man/extractCaretTarget.Rd (1 hunks)
- man/extractCaretTarget.default.Rd (1 hunks)
- man/extractCaretTarget.formula.Rd (1 hunks)
- man/models.class.Rd (2 hunks)
- man/models.reg.Rd (1 hunks)
- man/plot.caretStack.Rd (1 hunks)
- man/predict.caretStack.Rd (1 hunks)
- man/print.caretStack.Rd (1 hunks)
- man/summary.caretList.Rd (1 hunks)
- man/summary.caretStack.Rd (1 hunks)
- tests/testthat/test-caretList.R (2 hunks)
- tests/testthat/test-caretStack.R (1 hunks)
Files skipped from review due to trivial changes (22)
- R/caretPredict.R
- R/package.R
- man/X.class.Rd
- man/X.reg.Rd
- man/Y.class.Rd
- man/Y.reg.Rd
- man/aggregate_mean_or_first.Rd
- man/caretList.Rd
- man/caretStack.Rd
- man/dotplot.caretStack.Rd
- man/extractCaretTarget.Rd
- man/extractCaretTarget.default.Rd
- man/extractCaretTarget.formula.Rd
- man/models.class.Rd
- man/models.reg.Rd
- man/plot.caretStack.Rd
- man/predict.caretStack.Rd
- man/print.caretStack.Rd
- man/summary.caretList.Rd
- man/summary.caretStack.Rd
- tests/testthat/test-caretList.R
- tests/testthat/test-caretStack.R
Additional comments not posted (30)
man/c.train.Rd (1)
19-31: Improved Example Clarity with Common Dataset.The examples now use the
irisdataset, which is widely recognized and simplifies understanding. The addition oftuneLength = 1Lin the random forest model provides a clearer demonstration of model tuning. The renaming ofbigListtomodel_listenhances readability and follows best practices for variable naming.man/c.caretList.Rd (1)
20-31: Enhanced Example Accessibility with Standard Dataset.Switching to the
irisdataset makes the examples easier to understand for users familiar with R. The updated model specifications and tuning parameters offer a more practical illustration of thecaretListfunctionality. These changes improve the educational value of the examples.NAMESPACE (1)
Line range hint
4-4:
Confirm Removal of Exports.The exports for
is.caretListandis.caretStackhave been removed. Ensure that this change aligns with the intended simplification of the public API and verify that no external dependencies rely on these functions.man/autoplot.caretStack.Rd (1)
25-27: Documentation improvement approved.The added note clarifies the requirement for using
savePredictions = "final", enhancing user understanding of the function's prerequisites.R/caretEnsemble.R (1)
32-34: Example update approved.The change to use "rpart" and "rf" in the example provides a diverse illustration of model usage. The removal of the
\dontrun{}directive allows the example to be executed directly.man/caretEnsemble.Rd (1)
52-54: Documentation example update approved.The update to use "rpart" and "rf" in the example aligns with the source code changes, providing a consistent and relevant example for users.
Makefile (16)
3-20: LGTM: Well-structured help target.The
helptarget clearly lists available make targets and their descriptions, enhancing usability.
22-22: LGTM: Comprehensivealltarget.The
alltarget effectively combines multiple tasks, ensuring a complete build process.
25-32: LGTM: Correct dependency installation.The
install-depstarget installs all necessary dependencies, ensuring a smooth setup process.
33-35: LGTM: Proper installation sequence.The
installtarget correctly depends oninstall-deps, ensuring a proper installation flow.
37-39: LGTM: Documentation generation.The
documenttarget correctly generates documentation, maintaining up-to-date package information.
41-43: LGTM: Test fixtures update.The
update-test-fixturestarget correctly updates test data, ensuring tests are current.
45-47: LGTM: Test execution and cleanup.The
testtarget correctly runs unit tests and cleans up test artifacts, ensuring a clean environment.
70-78: LGTM: Consolidated coverage tasks.The
coveragetarget effectively consolidates related tasks, improving organization and clarity.
81-84: LGTM: Comprehensive check process.The
checktarget ensures documentation is up-to-date before running checks, maintaining package integrity.
86-88: LGTM: Code style enforcement.The
fix-styletarget correctly applies code style standards, ensuring consistent formatting.
91-93: LGTM: Linting process.The
linttarget effectively identifies code issues, supporting code quality maintenance.
Line range hint
95-104:
LGTM: Spelling check.The
spelltarget correctly identifies potential spelling errors, aiding in documentation quality.
106-108: LGTM: Package build process.The
buildtarget correctly builds the package, ensuring the package is ready for distribution.
110-112: LGTM: Vignettes build process.The
build-vignettestarget correctly builds vignettes, ensuring comprehensive package documentation.
114-116: LGTM: Package release process.The
releasetarget correctly facilitates package release, streamlining the deployment process.
Line range hint
118-131:
LGTM: Cleanup process.The
cleantarget effectively removes generated files, maintaining a clean development environment.R/caretList.R (4)
6-7: LGTM: Improved documentation clarity.The documentation improvements provide clearer guidance on using
caretList, especially regardingdata.table.
120-120: LGTM: Robust type checking.The use of
methods::isfor type checking improves robustness and aligns with S3 method conventions.
436-436: LGTM: Function export.Exporting
extractMetric.caretListaligns with the package's API design, increasing accessibility for users.
401-401: LGTM: Internal function designation.Marking
extractCaretTargetas internal clarifies its usage scope, aligning with best practices.R/caretStack.R (4)
43-43: LGTM: Improved type checking.The use of
methods::isfor type checking reduces redundancy and aligns with best practices.
367-367: LGTM: Enhanced documentation clarity.The improved documentation for
predict.caretStackenhances clarity and usability for users.
431-433: LGTM: Clearer function documentation.The documentation updates for
autoplot.caretStackimprove user understanding and clarity.
337-338: LGTM: Improved example clarity.The updated examples for
dotplot.caretStackenhance readability and focus on essential usage.
