Improvements#1
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- Fix documentation bugs: correct max_control_af default (0.25) and data_source parameter name in examples - Add comprehensive input validation with informative error messages - Improve error handling for Canopy clustering with tryCatch - Enhance TiNDA object with classification_summary and parameters - Add S3 methods: print.TiNDA, summary.TiNDA - Add get_tinda_params() to retrieve default parameters - Add run_pipeline() convenience function for file-based workflow - Add test infrastructure with testthat - Add CITATION file for publication credit Bug fixes: - Fix parameter mismatch in documentation (max_control_af: 0.45 -> 0.25) - Fix parameter mismatch in documentation (max_control_af_chip: 0.35 -> 0.40) - Fix example code using wrong parameter name (data_type -> data_source)
- Add testthat package installation - Add explicit test execution step - Keep testthat output display for debugging
Canopy was removed from CRAN (archived 2026-01-22), so install from the archive before running checks.
Add ape, fields, pheatmap, scatterplot3d as prerequisities for Canopy.
Skip setup-r-dependencies which uses lockfile that can't find Canopy. Instead install all dependencies directly with install.packages().
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