Standardized reproducibility seeds across examples, demos, tests,
and archived simulation scripts to 12345.
Consolidated the former standalone examples into three
non-redundant, reproducible visual demos. They cover one-dimensional
Bayesian FDR, observed-versus-shuffled two-dimensional scans, pooled
versus replicate-aware fitting across small, medium, and large replicate
counts, both ANDOVA integration methods, baseline effects, and
representative multiresolution trees.
Restored current CRAN metadata and registered all native
routines.
Replaced deprecated Armadillo index-returning max()
calls and fixed an uninitialized-variable path in the C++ tree
traversal.
Added input validation that prevents invalid dimensions, labels,
bounds, and tuning parameters from reaching the C++ core.
Restored the version 1.2.6 ANDOVA midpoint-quadrature default;
deterministic and randomized compatibility suites now reproduce legacy
numerical and tree results.
Preserved the legacy default sample-space bounds for ordinary data
while safely supporting constant and non-positive dimensions.
Documented posterior sampling, effect-size baselines, numerical
integration, and Bayesian-FDR plotting introduced on the development
branch.
Fixed posterior sample matrix shaping and direction probabilities,
multidimensional sampling, sampling without a representative tree,
Bayesian-FDR matrix indexing, and a Riemann-quadrature second-moment
error.
Kept sampled ANDOVA probabilities inside their valid domain and
removed undefined behavior in dyadic bin conversion and region
reconstruction.
Removed the unused optimx dependency and replaced the
igraph-backed representative-tree renderer with a deterministic
base-graphics renderer.
Added explicit return-value documentation for all exported plotting
and print methods, including the meaning of their graphical or printed
side effects.