NEWS.md

In Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees

Rogue v2.2.1 (2026-06-24)

• Improve performance of TipInstability() (and thence ColByStability(), QuickRogue()) through full C++ processing, removing Rfast dependency.

Rogue v2.2.0 (2026-03-20)

Performance

• 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.

Rogue v2.1.7 (2025-07-01)

• Improve tip instability calculation in identical tree sets (#29).

• Improve variable protection.

Rogue v2.1.6 (2023-11-29)

• Legend annotations in documentation.
• Disable parallel evaluation by default in TipInstability(), adding parallel parameter to allow user to override.
• Use format string in REprintf().

Rogue v2.1.5 (2023-03-20)

• Call C functions using symbols, not strings.

Rogue v2.1.4 (2023-01-16)

• C2X compliant function prototypes.

• Remove unused sprintf() calls.

Rogue v2.1.3 (2022-09-26)

• ColByStability() gains pal argument to allow specification of custom palettes.

Rogue v2.1.2 (2022-08-16)

• Faster rogue detection when edge lengths provided, per report by Joe Keating.

• Don't list neverDrop in QuickRogue(fullSeq = TRUE).

Rogue v2.1.1 (2022-07-20)

• Handle ColByStability(trees = NULL).

Rogue v2.1.0 (2022-01-13)

• 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.

Rogue v2.0.0 (2021-09-13)

• Information theoretic rogue detection (per Smith, 2022).

Rogue v1.0.0 (2021-06-28)

• R interface to RogueNaRok.

Rogue documentation built on June 24, 2026, 5:08 p.m.