There is a new version of phytools on CRAN.
Here are some of the updates since the previous version:
A bug fix in
A new function
fastDistto compute the patristic distance between two species.
A minor bug fix in
plotSimmapwhen the edge order of the input tree is
The addition of a scale bar for the
A total re-write of the internally used function
phyloDesign. (It's also now in the name space.)
A small update to the phytools function to fix malconformed trees (
cophylofor trees without edge lengths (here).
Functionality to add node, edge, and tip labels to a plotted object of class
New functionality in
plotTree.wBarsfor user control of the bar colors (here).
New interactive modes for the phytools functions
phylo.to.mapto permit right- facing trees.
phylo.to.mapto permit use with
edgelabelsfrom ape (here).
An important update for
describe.simmap(and thus the S3
summarymethod for objects of class
"multiSimmap") when trees have potentially incongruent topologies.
A new function to simulate a stochastic species-level tree from a genus backbone tree.
An update to
contMapto permit user-supplied node states.
A new feature in
fastAncto permit some node states to be fixed.
A new function for computing the relative frequency of different types of state changes along edges in a set of stochastic-mapped trees.
A function to comute the matrix-representation of a tree for
mrp.supertree- although it can also be used on it's own (here).
A variety of bug fixes in
rerootingMethod, detailed here.
And, finally, separate user control of edge & legend line widths in
Along with some other changes & bug fixes. Check it out!