v1.7.0

TreeTools 1.7.0

New methods and functions

• rev.Splits() reverses order in which splits are listed.

• KeepTip.Splits() is a faster alternative to SubSplit().

• %in%.Splits() retains names when comparing small splits
  (#40).

• sort.multiPhylo() sorts lists of trees according to their mixed base
  representation (#84).

• Bitwise manipulation of splits with |, &, xor.

• as.MixedBase() uniquely represents binary trees as a mixed-base vector.

• PathLengths() describes all paths within a tree.

• KeptVerts() and KeptPaths() identify elements in reduced trees.

• PostorderOrder() describes a sequence of edges corresponding to a
  postorder traversal of a tree.

• SpectrumLegend() adds gradients to plot legends.

Improvements

• Improve handling of zero-split trees.

• DropTip() no longer adds a root to unrooted trees, and retains edge lengths.

• Improve speed of DropTip(), by an order of magnitude in some cases.

• Support edge lengths in Preorder(), RootTree(), UnrootTree() and
  Postorder() (#49,
  #89).

• Fix bug when tree is rooted on a discontinuous outgroup.

• SortTree() handles weighted and non-binary trees
  (#25,
  #25),
  and gains option to sort by tip labels.

• TipsInSplits(smallest = TRUE) counts tips in smaller bipartition.

• Fix a bug with phyDat objects in ArtificialExtinction().

• RenumberTips() allows tipOrder to contain elements not present in tree.

• Use lighter Rcpp headers.

• Small improvements to computational efficiency.

Deprecations

• Remove deprecated function PostorderEdges()
  (#35).

v1.6.0

New functions

• RoguePlot() plots the positions of rogue taxa.

Improvements

• DropTip() gains check parameter to allow slightly faster operation where
  input is guaranteed to be valid.

• RandomTree() gains nodes parameter allow the inclusion of polytomies.

• Infer tips parameter if missing in StringToPhyDat().

• Remove dependency on "phangorn" (allowing use on R < 4.1)

• Improve parsing of information from nexus files.

• Export DropTipPhylo() as wrapper to DropTip.phylo().

v1.5.1

• PhyDatToMatrix() optionally encodes ambiguous / inapplicable tokens as NA.

• Update test suite for compatibility with "testthat" > 3.0.4 (@hadley, #83).

v1.5.0

New functions

• ConstrainedNJ() returns an approximation to a neighbour-joining tree that respects constraints.
• PolarizeSplits() marks a specified taxon as representing the ingroup of all splits.
• Add KeepTip() and improve performance of DropTip().
• ImposeConstraint() makes a tree consistent with topological constraints.
• as.phylo.Splits() represents a Splits object as a tree.
• Consensus() is a faster C++ implementation of ape::consensus().
• ClusterTable() C++ functionality imported from "TreeDist".

Improved functions

• Warn when empty cells passed to MatrixToPhyDat().
• Warn when LabelSplits(labels) lack names.
• SplitFrequency() drops tips from forest that aren't in reference.
• AddTipEverywhere() supports trees with < 3 leaves.
• Make RootTree() and PhyDatToMatrix() more robust.
• Read[Tnt]AsPhyDat() passes additional parameters to Read[Tnt]Characters().
• Support encoding option in ReadCharacters() function family.
• Support CHARSTATELABELS in ReadCharacters().
• Support for more formatting quirks in ReadNotes().
• Better support ambiguous tokens in WriteTntCharacters().

Optimization

• Fast matching functions from "fastmatch".
• Improve efficiency of Preorder() and Postorder(), and lift limit on tree size.

v1.4.5

• Correct calculation of minimum value in TCIContext().
• Extract tip labels from objects in StringToPhyDat().
• Support AddTip(tree, where = "tip name").
• SplitFrequency() supports four-leaf trees.
• Add RootTree.matrix() method for edge matrices.
• Add TipLabels.phyDat() method.
• Add NULL methods for tree reordering functions.
• Additions and improvements to text parsing functions.

v1.4.4

• Add NTip.phyDat() method.
• Update MakeTreeBinary() docs and tests to reflect updated behaviour of
  ape::multi2di() in 'ape' v5.5.

v1.4.3

• AddTip() supports edge lengths.
• CladisticInfo() supports Splits objects.
• as.multiPhylo() converts trees, datasets and Splits objects into
  multiPhylo objects.
• LabelSplits(labels = NULL) labels each split with its associated node.
• PhyDatToMatrix() supports integer-only levels.
• SortTree() supports lists of trees.
• Improvements to ReadTntCharacters() character block extraction
  (#50).

v1.4.2

• Support star trees in RootTree().
• Improve memory handling in root_on_node().
• Documentation linkage.

v1.4.1

• MSTEdges() supports distance matrices with > 256 entries.
• Package 'vdiffr' used conditionally.

v1.4.0

New functions

• MSTLength() reports length of minimum spanning tree.
• AllTipLabels() returns all labels from all trees in a list.
• PairwiseDistances() (from 'TreeDistData') computes distances between all
  pairs of trees in a list.
• ArtificialExtinction() gains replaceAll option.
• WriteTntCharacters(types = ...) writes different character types to TNT
  file.
• Tree characterization S3 methods: add .default and .NULL.

Enhancements

• MSTEdges() implemented in C++, improving runtime by orders of magnitude.
• Improved parsing of TNT character files.