New version of phytools on CRAN

This past weekend I was able to get a new version of phytools on CRAN (phytools 2.5-2).

This new phytools version includes various new models & updates previously documented on this blog. Among these (in mostly chronological order, not in order of importance):

1. Minor improvements in the model objects and optimization diagnostics returned to the user by fitPagel (here). fitPagel in phytools can be used to fit a binary trait correlated evolution model of Pagel (1994).

2. A new general cladebox function for drawing boxes around a clade on a phylogeny plotted in rectangular, fan, or arc styles (1, 2).

3. A totally new ‘semi-threshold’ trait evolution model where evolution of the liability behaves as a quantitative trait on some interval, but as a discrete threshold character outside of it (1, 2), fitsemiThresh

4. A new bounded quantitative trait evolution model with absorbing bounds (1, 2) in bounded_bm.

5. A brand new multi-σ², multi-μ, discrete-state-dependent trended Brownian model (1, 2, 3), fitmultiTrend.

6. A new Pagel ’94 type correlation model with one binary trait and one continuous character, in which the state of the continuous trait is allowed to affect the transition rate of the discrete character (1, 2), fitcontMk.

7. New simulator functions for absorbing bounded Brownian motion (sim.absorbing: 1, 2), Brownian motion with reflective bounds (sim.reflective), and multi-trend trended Brownian evolution (sim.multiTrend: here).

Getting the new version of phytools is easy, just update from CRAN! To get the most recent development phytools version, I recommend first installing the remotes CRAN package and then running:

remotes::install_github("liamrevell/phytools")

Thanks for reading!