moc.gapbk 0.2.1

Performance

This release rewrites the hot inner loops of the algorithm using vectorised R primitives. Numerical results are bit-identical to 0.2.0 under the same random seed; only the runtime changes.

generate.groups(): the original nested for-loop is replaced by a single max.col(-dmatrix[, medoids]) call, which runs in C.
calculate.objective.functions(): the original triple for-loop over individuals, clusters and objects is replaced by a single matrix slice plus sum(). The minimum medoid-to-medoid squared distance is now obtained from a (k x k) submatrix with diag(sub) <- Inf and min(sub), also vectorised.
singletons.delete() and singletons.repair() use tabulate() to count cluster sizes in C instead of which() + length() in R.
singletons.repair() no longer resets the column index to 1 on every replacement; it now retries on the same column up to num_objects attempts, eliminating an O(n^2) worst case.
moc.gapbk() precomputes the element-wise squared distance matrix for each input matrix once and caches it via an attribute, instead of squaring entries inside the inner loop on every call.
Path-Relinking caches the symmetric difference between the initial and guide solutions across each while iteration (it was recomputed three times per cycle in 0.2.x).
Path-Relinking builds the batch of intermediate solutions in a single replicate-and-overwrite step rather than chained rbind() calls on a growing data frame.
Pareto Local Search replaces apply(A, 1, function(x) all(x == B)) with vectorised rowSums(A != B) == 0L.

Observed speedups on the internal benchmark (synthetic data, seed=42):

Scenario	0.2.2	0.3.0	Speedup
NSGA-II, n=200, G=3	0.049 s	0.003 s	17.8x
NSGA-II, n=300, G=3	0.070 s	0.003 s	22.3x
NSGA-II, n=500, G=3	0.124 s	0.006 s	22.3x
Full algo, n=50	0.011 s	0.002 s	4.3x
Full algo, n=60	0.009 s	0.002 s	5.3x
Full algo, n=70	0.009 s	0.003 s	3.6x

The asymptotic complexity of the algorithm itself is unchanged (Pareto Local Search is still O(m^2 * n^2 * k) per generation, where m is the size of the Pareto front). What changes is the constant factor: the inner operations now execute in compiled C through R primitives rather than at the interpreter level. For very large instances with local_search = TRUE a future Rcpp-backed release will be needed.

moc.gapbk 0.2.0

GitHub infrastructure and developer experience

New README.Rmd (dynamic, generates README.md via devtools::build_readme()) with CRAN, R-CMD-check, pkgdown, Codecov, lifecycle and license badges.
Added GitHub Actions workflows under .github/workflows/:
- R-CMD-check.yaml on Ubuntu (devel, release, oldrel-1), macOS and Windows.
- pkgdown.yaml that deploys the documentation site to gh-pages.
- test-coverage.yaml that pushes coverage to Codecov.
Added _pkgdown.yml (Bootstrap 5, cosmo theme, navbar, structured reference index, OpenGraph metadata, ORCID link).
Added codecov.yml with informational thresholds.
Added CODE_OF_CONDUCT.md (Contributor Covenant 2.1) and .github/CONTRIBUTING.md, .github/pull_request_template.md, .github/ISSUE_TEMPLATE/{bug_report,feature_request}.md.
Added a hex-style package logo at man/figures/logo.png (and logo.svg source).
Added the Language: en-US field to DESCRIPTION.
Updated .Rbuildignore and .gitignore to keep all of the above out of the CRAN bundle while preserving them on GitHub.
Moved amap from Imports to Suggests. The package code itself does not use amap; it only appeared in the example and in the vignette. The example was rewritten to use stats::dist() from base R, and the vignette wraps the amap::Dist() call with requireNamespace() so it knits in either configuration. This removes the R CMD check NOTE “Namespace in Imports field not imported from: ‘amap’”.

Breaking changes

The main function has been renamed from moc.gabk() to moc.gapbk() to match the package name. The previous name is preserved as a deprecated alias that emits a warning and forwards its arguments to moc.gapbk(). The alias will be removed in a future release.

CRAN compliance

Removed doMPI from the dependency list. The MPI backend was never actually used by the package code and doMPI currently fails CRAN checks on macOS because it requires Rmpi, which depends on a system-level MPI installation.
nsga2R, foreach, doParallel, parallel, utils, stats and amap are now declared with explicit importFrom directives.
registerDoParallel() is now called with its namespace prefix.
The Author: field has been removed from DESCRIPTION in favor of a single Authors@R: declaration. The Date: field has been removed.
A copyright-holder role (cph) has been added for the maintainer.
Examples no longer call library() on the package itself or on imported packages.

Code quality

The single 1100-line R/main.R has been split into thematic files: population.R, groups.R, genetic-ops.R, objectives.R, pareto-local-search.R, path-relinking.R, results.R and moc-gapbk.R.
Fixed a latent bug in singletons.repair() which returned a list with duplicated element names. The list now uses distinct, meaningful names; callers were updated accordingly.
Added input validation with informative error messages at the beginning of moc.gapbk().
parallel::makeCluster() now uses on.exit(parallel::stopCluster()) to guarantee cluster shutdown even if the parallel section fails.

Documentation and tests

Added tests/testthat/ with smoke tests for moc.gapbk() and the deprecated alias.
Added a vignettes/moc-gapbk-intro.Rmd introductory vignette.
Added README.md, NEWS.md and cran-comments.md.
Minimum R version raised from 3.2.5 to 3.5.0.