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…ions() with get_grouping_levels(), add missing value checks for grouping variables, update tests and documentation accordingly
…ocumentation and unit tests for resolve_family_obj
…e, and add tests to assure the ordering
…) that converts outcome columns to continuous (integer) type columns
…iables are extracted
…te_analysis_type helpers, improved handling of survival and factor variables, and introduced varname_to_modelframe utility function.
… non-survival models now result in an error
…d to get the correct term name for event indicator colums such as status != "censored" (was removed in commit cb787a6)
… column names for event indicators
…else regarding grouping levels
…resolve_family_obj, and merge_call_args
…dn't work for tibble)
… on unnamed lists; update NEWS and docs
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Pull request overview
This pull request focuses on code cleanup and refactoring across the test suite and documentation. The changes primarily improve code formatting consistency, add new test coverage for helper functions, and update documentation files. The PR includes reformatting of existing test files to follow consistent style guidelines (improved indentation and line breaks), addition of new test files for previously untested helper functions, updates to snapshot tests reflecting minor numerical changes, and generation of new documentation files for internal helper functions.
Key Changes
- Reformatted multiple test files with consistent indentation and line breaks for better readability
- Added comprehensive test coverage for
factor_to_integer(), grouping-related functions, and validation functions - Updated snapshot test files with minor numerical precision changes
- Added documentation for internal helper functions and a
.lintrconfiguration file
Reviewed changes
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Show a summary per file
| File | Description |
|---|---|
| tests/testthat/test-survival.R | Reformatted with improved indentation and line breaks |
| tests/testthat/test-helpfunctions_survival.R | New test file for factor_to_integer() function |
| tests/testthat/test-helpfunctions_formulas_general.R | Reformatted with consistent spacing; added test for single formula case |
| tests/testthat/test-helpfunctions_formulas.R | Reformatted and reorganized; removed multi-column outcome test, added I() transformation test |
| tests/testthat/test-helpfunctions_checks.R | Added extensive test coverage for validation and helper functions |
| tests/testthat/test-helpfunctions2.R | New test file for grouping level checking functions |
| tests/testthat/test-groupings.R | Renamed function references and reformatted |
| tests/testthat/_snaps/glmm.md | Updated with minor numerical precision changes |
| tests/testthat/_snaps/clmm.md | Updated with minor numerical precision changes |
| man/varname_to_modelframe.Rd | New documentation file for internal helper function |
| man/resolve_family_obj.Rd | New documentation file for internal helper function |
| man/rd_vcov.Rd | Fixed duplicate description text in documentation |
| man/paste_analysis_type.Rd | New documentation file for internal helper function |
| .lintr | Added linter configuration file |
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… cause of failure of R CMD ubuntu-latest run.
…erences on different platforms and to avoid warnings bein printed in testthat output,
…4.5.0 and should never happen anyway
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This pull request contains several improvements and refactorings to the data handling and model setup logic. Key changes include allowing tibbles as input data, enabling overwriting elements in the data list, refactoring of matrix division and model type functions for clarity.