TipInstability() operates on the lower triangle of distance matrices only,
halving the work for row statistics (rowMads, rowVars, rowMedians).
New batch C function LOG_GRAPH_GEODESIC_MULTI computes log-geodesic
distances for all trees in a single .Call(), reusing one interim buffer
and returning lower-triangle entries directly.
Cache-friendly extraction loop in graph_geodesic.c (stride-1 access
instead of stride-all_nodes).
Auto-enable OpenMP parallelism in Rfast operations (rowMads, rowVars)
when the distance matrix exceeds 1 000 rows.
Use Rfast::rowMedians() in place of matrixStats::rowMedians().
RogueTaxa() now calls .PrepareTrees() once and passes .prepared = TRUE
to QuickRogue() / Roguehalla(), avoiding redundant tree preparation.
QuickRogue() precomputes information upper bounds for all iterations rather
than recomputing each step.
Improve tip instability calculation in identical tree sets (#29).
Improve variable protection.
TipInstability(),
adding parallel parameter to allow user to override.C2X compliant function prototypes.
Remove unused sprintf() calls.
ColByStability() gains pal argument to allow specification of custom
palettes.Faster rogue detection when edge lengths provided, per report by Joe Keating.
Don't list neverDrop in QuickRogue(fullSeq = TRUE).
ColByStability(trees = NULL).Early termination of QuickRogue() when no further improvement possible.
Cophenetic() renamed to the more accurate GraphGeodesic().
Calculate information content of consensus trees with p > 0.5 (#15).
Improve support for multiPhylo objects.
New vignette detailing rogue detection with Bayesian tree samples.