Friday, September 28, 2018

New phytools version (0.6-60) on CRAN

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:

  1. A small but important fix to fitMk and make.simmap that affects some internals running matrix exponentiation which is otherwise sometimes very slow.

  2. A significant update to the function phyl.pairedttest for a phylogenetic paired t-test.

  3. Significant increases in user control of the S3 plotting method for "cophylo" objects (1, 2).

  4. A new object class and S3 methods for the multiple (partial) Mantel test function, multi.mantel.

  5. A new function, ctt, for visualizing the number of reconstructed changes on stochastic map trees through time (1, 2).

  6. 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).

  7. A function gtt, along with print and plot methods, 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:::gtt or by updating with the fix I just pushed to GitHub.)

  8. A totally new function, sim.multiMk, to simulate evolution by a variable-rate Mk process on the tree (1, 2).

  9. A small fix to the "static" method of phylomorphospace3d.

  10. A totally new plotting method (plotTree.datamatrix) to visualize a discrete character data matrix next to a tree (1, 2, 3, 4).

  11. Another new plotting function, but to animate the projection of a tree into morphospace called project.phylomorphospace (1, 2).

  12. Several different updates to the phytools function plotTree.wBars (1, 2).

  13. Some small updates to plotTree.barplot.

  14. 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!


  1. I was happy with myself after a couple of hours playing with the options of plot.phylo and the package phytools. Feeling like an R-badass again muahahaha!

    And now after wandering through the blog I must admit that I feel floored like a sloth XDDDD. Fantastic plots and code. Thanks and keep up the good work :-)

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