Sunday, November 12, 2017

New phytools version on CRAN

A new version of phytools (0.6-44) was just posted to CRAN. Binary versions have yet to be built, but since phytools does not require compilation, it can be easily installed by any user from source. Normally it takes a few days for new package binaries to be built and to percolate through all the CRAN mirrors.

I submitted the last CRAN phytools update on July 28, 2017, consequently there have been many updates since that time. All changes to phytools can easily be tracked on its GitHub page, but the following are some of the highlights:

  1. An update to anc.ML for ML ancestral state reconstruction to add the EB or 'early-burst' model of trait evolution. (Also see 1.)

  2. A bug fix in the popular phytools co-phylogenetic plotting method.

  3. An update to the function ratebytree to permit comparison between trees under different trait evolution models.

  4. An extension of ratebytree to compare the rate or process of evolution for discrete characters between trees. (Also see 1.)

  5. A new posthoc S3 method for the object class produced by ratebytree. (Also see 1.)

  6. New custom tip label spacing in the phytools plotting method phenogram.

  7. A further update to ratebytree to permit flexible user control of the regimes hypothesized for different trees. (For instance, that trees 1 & 3 are evolving by one rate, and trees 2 & 4 by another.)

  8. A new AIC method for ratebytree objects to facilitate comparison of alternative models.

  9. A bug fix for directional, ordered character evolution models in fitMk.

  10. An update to plotTree.barplot to permit trees & barplots to be plotted in an array. (Also see 1.)

  11. A new function,, to fit a birth-death diversification model with incomplete sampling in phytools. (Also see 1, 2, 3.)

  12. Another extension of ratebytree to allow comparison of the rates of diversification among trees. (Also see 1, 2, 3, 4, 5.)

  13. Clean print & plot methods for the old phytools function ancThresh for Bayesian ancestral character estimation under the threshold model, plus a significant speed-up by calling a pre-compiled version of the internal function threshState in phangorn.

  14. New print method for an old phytools function evol.rate.mcmc for identifying the phylogenetic position of a rate shift in the pace of continuous character evolution on the tree.

  15. An update & some new S3 methods for the old phytools function threshBayes for modeling correlated trait evolution under the threshold model.

  16. New print and plot methods for the ancestral state reconstruction function, rerootingMethod.

  17. New methods for the Bayesian MCMC function fitBayes for fitting continuous trait evolution models with intraspecific variation.

  18. A clean print method for the always popular simulation-based phylogenetic ANOVA function phylANOVA.

  19. A new print method, and object class, for the function pgls.Ives for bivariate phylogenetic regression with (correlated) sampling error in x and y.

  20. Some new methods & functionality in the phytools function anc.Bayes for Bayesian ancestral state reconstruction of continuous characters.

Along with some other stuff, of course.

Feedback & bug reports are always welcome - and the latest (non-CRAN) phytools version can always be installed directly from GitHub using devtools as follows:


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