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Changelog

Source: NEWS.md

treestructure 1.0.1

  • The default target false discovery rate is now fdr = 0.2 (was 0.1). The stricter 0.1 default was conservative on real trees and interacted awkwardly with minCladeSize; at 0.2 the number of designated clusters decreases monotonically as minCladeSize grows, and more genuine structure is recovered while the whole-tree error rate remains controlled.
  • The node-support vignette was revised to the new default (fdr = 0.2).

treestructure 1.0.0

Calibrating to a false discovery rate

  • trestruct() now calibrates the split threshold to a target false discovery rate by default (fdr = 0.1). At each scan the algorithm splits at the most extreme eligible candidate clade only if it clears a multiple-testing correction over the eligible candidates in that scan. The fdr is a property of the whole tree: under the global null of a single unstructured coalescent, the probability of designating any structure equals fdr; when real structure is present, fdr bounds the expected fraction of spurious splits among all splits. The analytic calibration requires no simulation and is deterministic. Supplying an explicit level (without fdr) selects the previous subjective-threshold behaviour, and level = NULL selects the CH index. Arguments were reordered (fdr, level, minCladeSize, ...) and minCladeSize now defaults to 10.

  • The multiple-testing correction is selectable with split: 'bonferroni' (the default) or 'bh', a Benjamini-Hochberg step-up that is less conservative and retains more power on large trees with abundant moderate structure, while still controlling the false discovery rate.

  • The returned TreeStructure object now carries a global-null test in $global.test (the root-scan max|z|, the number of candidates, and a Bonferroni p-value for the presence of any structure at all), reported by print().

  • In fdr mode a heterochronous-sampling diagnostic is computed ($hetero) and printed. On serially sampled trees the coalescent statistic carries a small positive bias that can modestly inflate the realized FDR; this is reported as a caveat and discussed in the vignette. fdr composes with the existing nodeSupportValues/nodeSupportThreshold node-support filtering.

Fast, simulation-free statistic

  • The coalescent rank-sum null is characterized by exact analytic moments by default (method = 'analytic') — a fast, deterministic alternative to Monte-Carlo simulation (method = 'sim', the previous behaviour). trestruct() and treestructure.test() both gain the method argument.

  • Fixed an error in the exact (Ei = 3) rank-sum transition used for monophyletic/monophyletic contrasts.

Documentation and tests

  • Added a testthat test suite covering the FDR calibration, the global-null test, the heterochronous diagnostic, and composition with node support.

  • Vignettes updated to lead with the FDR calibration and document the precise meaning of the FDR, to show the isochronous FWER validation, and to present node support and the CH index as complementary ways of refining clusters.