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.