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There appears to be a mismatch between function documentation and signatures. |
Conflicts resolved: - mcmc_memoization.h: Keep single-entry cache (benchmarked equivalent to hash-map) - mcmc_nuts.h: Use main's joint-only API - mcmc_utils.cpp: Use main's refactored step-size heuristic - RcppExports.R: Regenerated via rebuild Updated ggm_mixed files to use main's API: - adaptive_gradient_sampler.h: Pass (grad, joint) instead of (log_post, grad) - hmc_sampler.h: Same API update
C++ (GGMModel): - Store observations matrix and missing-data index when na_impute=true - impute_missing(): Gibbs sweep from conditional Gaussian - update_suf_stat_for_imputation(): incremental O(p) rank-1 update Interface (sample_ggm.cpp / RcppExports): - Add na_impute and missing_index_nullable parameters R side: - Remove GGM+impute guard in validate_data.R; add entire-column guard - Wire na_impute/missing_index through run_sampler.R - Remove column_means from spec, build_arguments, predict, simulate - predict now self-centers newdata; simulate uses zero mean vector - center_continuous_data() returns centered matrix only - Add Missing Data section to bgm() roxygen docs Tests: - 7 GGM imputation integration tests (test-bgm.R) - 3 GGM impute validation tests (test-validate-missing-data.R) - Remove obsolete impute-not-supported-for-GGM spec test - Update build-arguments and predict tests for column_means removal
…rder Fixes -Wreorder warnings on windows-latest GHA builds. The initializer lists in both the raw-observations constructor and the copy constructor had precision_proposal_ before observations_, but the class declares observations_ first.
…dit #1) - Remove @Keywords internal from exported extractor functions - Fix ##' to #' roxygen comment marker - Add @return with per-function descriptions - Add @examples block with runnable examples - Add @Seealso and @family extractors - Move %||% polyfill from extractor_functions.R to zzz.R - Add dev/documentation/ (strategy, audit, reviews)
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- Add .github/workflows/lint.yaml (runs lintr on PRs) - Remove line_length_linter from .lintr (cosmetic, would block CI) - Fix T/F symbol lints: rename T -> n_total in mcmc_summary.R - Fix seq lints: 1:length() -> seq_along(), 1:nrow() -> seq_len(nrow()) - Fix vector logic lints: | -> || and & -> && in scalar if() conditions - Fix styler-broken tests: result = -> result <- inside expect_*() calls - Fix scaffolding fixtures: use test_path() for relative path resolution - Improve styler to preserve <- inside function-call arguments - Update copilot-instructions.md with <- exception rule
…plog_macros.h (phase 4.6, 4.7)
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https://github.com/Bayesian-Graphical-Modelling-Lab/issues/issues/19
Does not add classes for priors.
Needs a thorough review and validation of the functionality and computational speed.