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Published June 8, 2020 | Version 1.0.0
Software Open

ms609/TreeTools: v1.0.0

Authors/Creators

  • 1. Department of Earth Sciences, Durham University

Description

New functions
  • CladisticInfo(): Calculate the information content of a tree.
  • RootNode(): Which node is a tree's root?
  • UnrootTree(): Safely remove a root node.
  • NodeDepth(): Discriminate shallow from deep nodes.
  • NodeOrder(), NDescendants(): Count edges incident to each node.
  • CladeSizes(): Count leaves / nodes descended from each node.
  • ListAncestors(): List ancestors of a node.
  • LabelSplits(): Label splits on plotted tree.
  • DropTip(): Remove tip, handling weird node orders.
  • LeafLabelInterchange(): Exchange position of n tips.
  • StarTree(): Generate unresolved tree.
  • TotalCopheneticIndex() integrated from 'tci' package.
Deprecations
  • PostorderEdges(): use Postorder() instead.
  • NonDuplicateRoot(): unused internal function.
  • match.Splits(): use match() instead.
  • in.Splits(): use %in%.Splits() instead.
Enhancements
  • Improve support for unrooted trees in as.Splits().
  • Use methods so Reorder functions can handle multiPhylo objects and edges.
  • Handle funny node orders.
  • Support continuous characters in ReadCharacters().
  • Improve performance of as.logical.Splits() and related functions.
  • Fail nicely when trees are too large for memory.
  • Fix memory leak in as.Splits().
  • Various under-the-hood improvements to functions.
  • Documentation improvements.

Files

ms609/TreeTools-1.0.0.zip

Files (818.2 kB)

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md5:697a6fffad7480ccf10a6e6f026901b8
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Additional details

Related works

Is supplement to
https://github.com/ms609/TreeTools/tree/1.0.0 (URL)