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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
…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)
- Fix warning_once to use environment pattern instead of <<- - Split extractor_functions.Rd into individual documentation pages for each S3 method (extract_rhat.bgms, extract_rhat.bgmCompare, etc.) - Each extractor method now has its own title and description - Generic functions use plain comments, methods use @exportS3Method - Deprecated functions (extract_edge_indicators, extract_pairwise_thresholds) marked with @Keywords internal
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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.