In advance of a workshop that I will be teaching next week in Spain with Luke Harmon, I just submitted a new phytools version (0.6-60) to CRAN and overnight it was posted. (As of this morning, binaries have yet to be built but it can already be installed from source.)
It's been a while since my last CRAN update of phytools, so there is are a number of new features & functions in this version. As usual, all changes to phytools can be tracked via its GitHub page, but the following are nonetheless some highlights:
A small but important fix to
make.simmapthat affects some internals running matrix exponentiation which is otherwise sometimes very slow.
A significant update to the function
phyl.pairedttestfor a phylogenetic paired t-test.
Significant increases in user control of the S3 plotting method for
"cophylo"objects (1, 2).
A new object class and S3 methods for the multiple (partial) Mantel test function,
A new function,
ctt, for visualizing the number of reconstructed changes on stochastic map trees through time (1, 2).
A totally new method, implemented in
fitmultiMk, for fitting a multi-rate Mk model in which the rate (or process) of character transition between states changes between different edges or clades in the tree (1, 2).
gtt, along with
plotmethods, for plotting Pybus & Harvey's γ-statistic through time. (I actually forgot to put this in the namespace, but it can still be called using
phytools:::gttor by updating with the fix I just pushed to GitHub.)
A totally new function,
sim.multiMk, to simulate evolution by a variable-rate Mk process on the tree (1, 2).
A small fix to the
A totally new plotting method (
plotTree.datamatrix) to visualize a discrete character data matrix next to a tree (1, 2, 3, 4).
Another new plotting function, but to animate the projection of a tree into morphospace called
Several different updates to the phytools function
Some small updates to
And numerous other smaller things that are all catalogued on my GitHub.
Please check out the new version by updating from CRAN or GitHub & let me know if you run into any problems!