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v2.4.0

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@ms609 ms609 released this 02 Jun 18:54
· 7 commits to main since this release

New features

  • RandomTree(), YuleTree(), PectinateTree(), BalancedTree(), StarTree(), and SingleTaxonTree() allow lengths to accept a function that generates edge lengths (e.g. RandomTree(8, lengths = runif)).
  • PaintTree() assigns colours to every edge, leaf, and internal node such that sister clades occupy adjacent hue bands proportional to their tip counts, with saturation growing from zero at the root to one at every tip.
  • NexusTokensToInteger() converts character data to integers, mapping uncertain tokens to NA.
  • ReadTntCharacters() attaches an xgroup attribute (factor) when a TNT xgroup partition block is present.

Performance

  • Consensus() computes majority-rule and threshold consensus trees in time linear in the number of trees (previously quadratic), after Jansson, Shen & Sung (2016); implementation informed by their FACT package.
    SplitFrequency() inherits the same single-pass speed-up.

Fixes

  • NexusTokens() once again handles polymorphism tokens with internal whitespace (e.g. (1 2), {0 1}).