ArtificialExtinction(): Remove characters that are absent in a fossil template.WriteTntCharacters(): Write morphological dataset in TNT format.- Improve TNT dataset parsing.
- Documentation improvements.
New functions
RandomTree(): Draw tree from uniform distribution, instead of via ape::rtree().MakeTreeBinary(): Uniform equivalent of ape::multi2di().match.list() method for lists of splits.SplitsInBinaryTree(): How many splits occur in an n-leaf binary tree?vapply64(), sapply64(), replicate64(): helper functions when a function returns a 64-bit integer.
Enhancements
- Use methods for
UnrootTree(), RootTree(), RootOnNode() to support lists of trees.
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.
- Catch hang-inducing bugs in
RootOnNode().
- Update
doubleFactorials cache to fix as.integer() rounding error.
- Support unrooted trees in
AddTipEverywhere().
- Documentation improvements.
RootOnNode(): Quickly root a tree on a specified node.- Improve portability of C++ code.
as.Newick: Fast conversion to Newick format.as.TreeNumber: Tree shape enumeration.
- Add functions to translate trees to mixed base integers.
RenumberTips can extract tip order from phylo and Splits objects.- Documentation changes to attempt to satisfy CRAN submission requirements.
- Pre-release version spun out of ‘TreeSearch’ package. Some functionality is subject to change.