Dev feat: Merge dev into main - #23
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- Introduced a comprehensive guide for the Statistical Test Validation Framework in `Statistical_Test_Framework_Guide.Rmd`. - Created configuration file `test_framework_config.R` to define available statistical tests, their properties, and tolerance settings. - Implemented report generation script `generate_test_reports.R` for creating validation reports for statistical tests. - Developed a master template `statistical_test_template.Rmd` for generating detailed validation reports with dynamic content. - Established a modular design for easy extension and integration of new statistical tests within the framework.
- Implemented a comprehensive test script (test_comprehensive.R) to verify the correct matching logic for data, focusing on the Myriophyllum study (MOCK0065) and other studies. - Created a focused test script (test_matching_issue.R) to demonstrate specific matching problems and the correct logic for handling measurement variables. - Developed a test script (test_matching_logic.R) to verify the structure of test data and results, ensuring the matching logic is correctly applied. - Added a validation test script (test_validation.R) to simulate actual testing functions and confirm the matching logic works as intended. - Enhanced documentation and comments throughout the scripts to clarify the matching rules and logic applied.
…t tests - Implemented a new script to analyze which endpoints have count vs continuous data. - Added detailed output for each endpoint, including data presence checks for Total, Alive, and Dead columns. - Developed a corrected validation function that checks count data per endpoint instead of per study. - Enhanced the function to handle both count and continuous data appropriately, including control level determination. - Tested the fixed validation logic across multiple function groups with comprehensive output.
…nnett Test - Created a comprehensive validation summary for the Dunnett Test, detailing data quality issues and actions taken. - Implemented a test script (`test_dunnett_call.R`) to evaluate the functionality of the `dunnett_test` function with specific study data. - Developed a validation script (`test_fixed_patterns.R`) to compare actual results against expected values using corrected patterns. - Added a script (`test_updated_tolerances.R`) to test the Dunnett Test with updated tolerances for t-values and p-values. - Included data cleaning steps to handle invalid placeholders and ensure proper statistical comparisons. - Enhanced error handling in test scripts to capture and report issues during validation.
- Implemented `run_dunnett_validation` function to support multi-endpoint validation. - Created scripts to check study IDs, data columns, and expected results for function groups. - Added debugging scripts to investigate issues with expected results and data linking for FG00225. - Developed tests for individual function groups and multi-endpoint validation. - Enhanced error handling and output reporting in validation functions. - Included checks for European decimal notation in dose conversion. - Established a framework for validating T-statistics, P-values, and means against expected results.
…d validate results
…t tests - Introduced USER_QUESTIONS_ANSWERED.md for detailed answers to user queries regarding validation results and data quality issues. - Implemented comprehensive_multi_study_analysis.R to analyze multiple studies with Dunnett tests, summarizing results and endpoints. - Created detailed_individual_analysis.R for in-depth validation of individual function groups, including actual vs expected comparisons. - Developed detailed_validation_functions.R with enhanced validation functions providing detailed row-by-row results for Dunnett tests. - Generated final_validation_summary.R to summarize the overall validation results, including success rates and study breakdowns. - Added working_detailed_analysis.R for a practical demonstration of validation processes and handling of data quality issues. - Created definitive_multi_study_multi_endpoint_demo.R to showcase the package's capability to handle multiple studies and endpoints effectively.
Updated devcontainer configuration to include R features and customizations.
…r structure improvements
…r improved navigation and clarity
…lper.Rmd for clarity
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This pull request merges the extensive updates from the dev branch into main. Changes include:
R/,dev/debug_and_test/, andinst/SystemTesting/. Includes new statistical tests, debugging scripts, and a comprehensive testing framework.pkgdownsite configuration (_pkgdown.yml) and updated numerous vignettes invignettes/articles/to fix broken links and missing figures. Added new system testing reports and guides.This PR represents a significant step forward in the package's development, bringing in a large volume of work on testing, validation, and documentation.