Changelog

Source: NEWS.md

TreeTools 1.12.0 (2024-07-25)

CRAN release: 2024-07-25

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.

TreeTools 1.11.1 (2024-06-06)

CRAN release: 2024-06-07

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

TreeTools 1.11.0 (2024-05-23)

CRAN release: 2024-06-05

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.

TreeTools 1.10.0 (2023-08-18)

CRAN release: 2023-08-18

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().

TreeTools 1.9.2 (2023-04-25)

CRAN release: 2023-04-27

• 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.

TreeTools 1.9.1 (2023-03-21)

CRAN release: 2023-03-20

• 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.

TreeTools 1.9.0 (2022-11-29)

CRAN release: 2022-11-28

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.

TreeTools 1.8.0 (2022-09-15)

CRAN release: 2022-09-15

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.

TreeTools 1.7.3 (2022-07-20)

CRAN release: 2022-07-20

• ReadTntTree() supports multi-line trees.

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

• Add deprecation warning to in.Splits().

TreeTools 1.7.2 (2022-05-24)

CRAN release: 2022-05-24

• 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.

TreeTools 1.7.1 (2022-03-25)

CRAN release: 2022-03-25

• AddTip(): Fix bug when adding tip to root of weighted tree.

TreeTools 1.7.0 (2022-03-21)

CRAN release: 2022-03-21

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).

TreeTools 1.6.0 (2022-01-12)

CRAN release: 2022-01-12

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().

TreeTools 1.5.1 (2021-10-06)

CRAN release: 2021-10-06

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

• Implement sort.multiPhylo().

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

TreeTools 1.5.0 (2021-09-13)

CRAN release: 2021-09-08

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.

• 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.

TreeTools 1.4.5 (2021-06-23)

CRAN release: 2021-06-23

• 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.

TreeTools 1.4.4 (2021-04-23)

CRAN release: 2021-04-20

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

TreeTools 1.4.3 (2021-04-12)

CRAN release: 2021-04-12

• 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).

TreeTools 1.4.2 (2021-01-26)

CRAN release: 2021-01-26

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

TreeTools 1.4.1 (2020-12-09)

CRAN release: 2020-12-09

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

TreeTools 1.4.0 (2020-10-20)

CRAN release: 2020-10-19

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.

TreeTools 1.3.1

CRAN release: 2020-10-03

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

TreeTools 1.3.0 (2020-09-22)

CRAN release: 2020-09-22

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 (2020-08-30)

CRAN release: 2020-08-03

• 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 (2020-07-07)

CRAN release: 2020-07-07

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 (2020-06-08)

CRAN release: 2020-06-08

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 (2020-03-04)

CRAN release: 2020-03-04

• 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 (2020-01-07)

CRAN release: 2019-12-19

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

TreeTools 0.1.2 (2020-12-18)

CRAN release: 2019-12-18

• 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 satisfy CRAN submission requirements.

TreeTools 0.1.0 (2019-10-30)

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