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- Implement SplikitObject R6 class with public fields (m1, m2, eventData, geneExpression, metadata) - Add methods: initialize, makeM2, findVariableEvents, findVariableGenes, getPseudoCorrelation - Add utility methods: subset, setGeneExpression, annotateEvents, summary, print, clone - Include comprehensive input validation in private methods - Add standardized error handling with informative messages - Add R6 to DESCRIPTION Imports - Update package description to mention R6 interface
- Test initialization from matrices and junction_ab - Test dimension validation and error handling - Test makeM2 produces identical results to make_m2 function - Test findVariableEvents produces identical results - Test subset, summary, print methods - Test deepCopy creates independent copies - Test metadata storage - Test backward compatibility with existing functions - Rename clone to deepCopy (clone is reserved in R6) All 39 tests pass
- find_variable_events() now accepts SplikitObject as first argument - get_pseudo_correlation() now accepts SplikitObject as first argument - Both functions extract m1/m2 automatically from SplikitObject - Maintain full backward compatibility with existing signatures - Fix pipe operator for R 3.5.0 compatibility in get_silhouette_mean example
- Implement make_m2_cpp and make_m2_cpp_parallel in C++ - Uses column-wise parallel processing for sparse matrix efficiency - Add use_cpp and n_threads parameters to make_m2 R function - Default to C++ implementation (use_cpp = TRUE) - Produces IDENTICAL results to R implementation - 1.18x speedup with single thread on test data (25k events x 7.5k cells) - OpenMP parallelization available for multi-threaded execution
- Add R6 library to requirements - Document SplikitObject R6 class interface as recommended approach - Show traditional function interface for backward compatibility - Highlight key features: C++ backend, sparse matrices, validation - Add n_threads parameter examples for parallel processing
Fixes and improvements: - Add edge case tests from deep analysis (Issue #1) - Add integer matrix support to rowVariance_cpp (Issue #16) - Add empty result check to find_variable_events (Issue #23) - Add n_threads and use_cpp params to SplikitObject$makeM2 - Add integration tests for full R6 pipeline - Add tests for subset operations and parameter validation C++ messaging cleanup: - Remove all debug Rcout messages from C++ functions - Remove atomic includes no longer needed - Let R wrappers control verbosity via verbose parameter - Cleaner output that respects user preferences Test coverage expanded from 39 to 80 tests.
Major rewrite of make_m2_cpp for minimal memory usage: - Build CSC format directly instead of triplet intermediate - Two-pass algorithm: count then fill - O(n_groups) workspace per column instead of dense group_sums matrix - Eliminated 720MB+ memory spike for typical datasets Memory improvement: - Before: O(n_groups * n_cells) + O(6 * nnz_output) - After: O(nnz_output) + O(n_groups) workspace Performance improvement: - 8.6x faster (1.0s vs 8.8s for test dataset) - All 80 tests pass in 47s (vs 275s previously) Results are IDENTICAL to previous implementation.
- Add R6 Object-Oriented Interface section to vignette - Update make_m2 docs with n_threads, use_cpp, performance notes - Add SplikitObject to pkgdown reference index - Update version to 2.0.0 - Regenerate Rd documentation files
- Add eventdata to toy_m1_m2_obj.rds test data - Update test expectations for correct data dimensions - Fix non-ASCII characters in R/zzz.R - Add missing NAMESPACE imports (methods, stats) - Add NSE variable declaration for data.table - Fix long example lines in documentation - Simplify internal function documentation Package now passes R CMD check --as-cran with 0 errors, 0 warnings, and 4 acceptable notes.
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