v1.12.0

New methods and functions

• TopologyOnly() removes metadata from phylo objects.
• J1Index() computes the robust, universal tree balance measure of
  Lemant et al. 2022 doi:10.1093/sysbio/syac027, incorporating code by Rob Noble.

Enhancements

• Consistent sequence of list entries in phylo objects.
• RandomTree() returns trees for < 3 leaves.
• root_on_node() handles trees with < 2 leaves.
• Support larger trees in TotalCopheneticIndex(), fixing #158.

v1.11.1

• Set random seed and increase tolerance to avoid false negatives on tests.

v1.11.0

New methods and functions

• YuleTree() generates a random tree by the Yule process.
• DescendantTips() complements DescendantEdges(), rewritten in C++, fixing a bug when edges were not in preorder.
• NodeNumbers() returns the indices of nodes within a tree.

Enhancements

• RandomTree(root = TRUE) roots the tree on a random edge.
• RoguePlot()$legendLabels returns suggested labels for legend.
• Support node labels in AddTip(), CollapseNode(), DropTip(), MakeTreeBinary(), Renumber(), Reorder(), SortTree(), Subtree() (#149).
• AddTip(edgeLength = NULL) defaults to lengthBelow. This will become the default in a future release.
• An entry point to the C++ function root_on_node() is now exported (intended for expert use only).
• Fix handling of weighted trees by root_on_node().
• Use KeepTip() internally so SplitFrequency() supports Splits objects as documented.

v1.10.0

New methods and functions

• TipTimedTree() displays trees where leaves are associated with absolute ages.
• ReadMrBayesTrees() samples trees from posterior of MrBayes output.
• is.TreeNumber() method.

Improvements

• Support zero-edge trees in as.Splits() and NSplits().
• Support empty constraints in AddUnconstrained().
• Add space between tokens in WriteTntCharacters() to support continuous characters (#139).

Deprecations and breaking changes

• Change order of parameters in DescendantEdges()
• Deprecate AllDescendantEdges(); use DescendantEdges() instead.
• Deprecate EnforceOutgroup(); use RootTree() instead.
• Remove NonDuplicateRoot() and in.Splits().

v1.9.2

• Improve support for comments in ReadNotes().
• Support Nexus-escaped ''s in ReadCharacters().
• Add legend parameter to RoguePlot().
• RoguePlot() now returns invisibly.
• Deprecate SpectrumLegend() – spun off to separate "PlotTools" package.

v1.9.1

• AddUnconstrained() and ImposeConstraint() handle wider range of inputs.

• PhyDatToMatrix() can (and by default does) override levels to write
  ambiguous tokens in custom formats such as {01}.

• Call C functions using symbols, not strings.

v1.9.0

New methods and functions

• ZeroTaxonTree() creates a phylo object with no leaves.

• DropTip() gains new methods DropTip.list() and DropTip.NULL().

• as.matrix.phylo() converts a tree to a matrix representation, allowing
  a tree to be passed as a constraint to ImposeConstraint().

• as.matrix.Splits() and as.matrix.phyDat() methods added as synonyms to
  as.logical.Splits() and PhyDatToMatrix().

Improvements

• Handle TipLabels(0) and BalancedTree(0).

• Support zero-leaf trees in as.Splits() and duplicated.Splits().

• Support non-identical tip labels in as.Splits().

• Try Latin-1 encoding if ReadCharacters() family fail under UTF-8.

v1.8.0

New methods and functions

• TntOrder() renumbers a tree's nodes to match TNT's convention.

• head() and tail() methods for Splits objects.

• Set names of splits object with names(splits) <- ....

• as.Splits() support character vectors in the form "...***".

Improvements

• ReadTntTree() reads tree tags and follows TNT node numbering conventions.

• SpectrumLegend() gains title parameter and more styling options.

• Support > 32767 trees in Consensus() (#127).

• DropTip() speed improved when branch lengths are present.

v1.7.3

• ReadTntTree() supports multi-line trees.

• as.MixedBase() supports larger trees (44–32767 tips).

• Add deprecation warning to in.Splits().

v1.7.2

• RenumberTips() drops "preorder" attribute, as reordering tip labels may
  break edge ordering guarantee.

• Native implementation of ClusterTable class.

• Replace throw with stop in C++ scripts.