Dear R phylogenetics community.
Since there have been quite a few complaints about how this listserv has
become dominated by course announcements (many not especially relevant
to R phylogenetic users), I thought it might be considered reasonable to
use it to announce a new version of the phytools R package 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. fitPagel in phytools can be used
to fit a binary trait correlated* evolution model of Pagel (1994).
(*More accurately: binary trait dependent discrete character
evolution model.)
2. A new general cladebox function for drawing boxes around a clade on
a phylogeny plotted in rectangular, fan, or arc styles.
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, in the new
function fitsemiThresh
4. A new bounded quantitative trait evolution model with absorbing
bounds in the existing function bounded_bm.
5. A brand new multi-sigma-squared, multi-mu, discrete-state-dependent
trended Brownian model, fitmultiTrend.
6. A new Pagel '94 type correlational 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,
fitcontMk.
7. New simulator functions for absorbing bounded Brownian motion
(sim.absorbing), Brownian motion with reflective bounds
(sim.reflective), and multi-trend trended Brownian evolution
(sim.multiTrend).
For more details on this update, please check out the latest post on my
blog:
https://blog.phytools.org/2025/09/new-version-of-phytools-on-cran.html.
Best wishes, Liam
--
Liam J. Revell
Professor of Biology, University of Massachusetts Boston
Web: http://faculty.umb.edu/liam.revell/
Book: Phylogenetic Comparative Methods in R
<https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r>
(/Princeton University Press/, 2022)
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