TreeTools 1.3.1

• Improved parsing of TNT files.
• Fix misspecified C++ linkage.

TreeTools 1.3.0

New functions

• SisterSize() and RootNodeDist() measure sister-clade size and root-node distance.
• MSTEdges(): Edges of minimum spanning tree.
• SplitImbalance(): how balanced is each split?
• New C++ functions root_on_node() and root_binary() to root trees quickly and robustly.

Enhancements

• TNTReadTree() handles additional punctuation characters.

• Import RdMacros package ‘Rdpack’.

• C++ implementation of TipsInSplits().

• Export C++ functions preorder_edges_and_nodes() and postorder_edges().

• Remove obsolete copy of C++ code from ‘phangorn’.

TreeTools 1.2.0

• ArtificialExtinction(): Remove characters that are absent in a fossil template.
• WriteTntCharacters(): Write morphological dataset in TNT format.
• Improve TNT dataset parsing.
• Documentation improvements.

TreeTools 1.1.0

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.

TreeTools 1.0.0

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.

TreeTools 0.1.4

• Catch hang-inducing bugs in RootOnNode().
• Update doubleFactorials cache to fix as.integer() rounding error.
• Support unrooted trees in AddTipEverywhere().
• Documentation improvements.

TreeTools 0.1.3

• RootOnNode(): Quickly root a tree on a specified node.
• Improve portability of C++ code.

TreeTools 0.1.2

• as.Newick: Fast conversion to Newick format.
• as.TreeNumber: Tree shape enumeration.

TreeTools 0.1.1

• 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.

TreeTools 0.1.0

• Pre-release version spun out of ‘TreeSearch’ package. Some functionality is subject to change.