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).