Releases: ms609/TreeTools
Releases · ms609/TreeTools
v1.3.0
New functions
SisterSize()
andRootNodeDist()
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()
androot_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()
andpostorder_edges()
. -
Remove obsolete copy of C++ code from 'phangorn'.
v1.2.0
v1.1.0
New functions
RandomTree()
: Draw tree from uniform distribution, instead of via
ape::rtree()
.MakeTreeBinary()
: Uniform equivalent ofape::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.
v0.1.4
- Catch hang-inducing bugs in
RootOnNode()
. - Update
doubleFactorials
cache to fixas.integer()
rounding error. - Support unrooted trees in
AddTipEverywhere()
. - Documentation improvements.
v1.0.0
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()
: usePostorder()
instead.NonDuplicateRoot()
: unused internal function.match.Splits()
: usematch()
instead.in.Splits()
: use%in%.Splits()
instead.
Enhancements
- Improve support for unrooted trees in
as.Splits()
. - Use methods so
Reorder
functions can handlemultiPhylo
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.
0.1.3
0.1.2
as.Newick
: fast conversion to Newick format.as.TreeNumber
: Tree shape enumeration.- Add functions to translate trees to mixed base integers.
RenumberTips
can extract tip order fromphylo
andSplits
objects.- Documentation changes to satisfy CRAN submission requirements.
Development release
- New package spun out of TreeSearch
- Splits handled using new class, and represented as bitwise integers rather than logicals