Tuesday, January 10, 2012

New version of phytools (v0.1-6)

I just posted a new version of phytools (phytools_0.1-6) to the phytools homepage. I have also submitted this version to CRAN.

Some of the updates in this version:

1) New function sampleFrom which takes a vector of means, a vector of variances, and a vector of sample sizes (or a range on which to pick random sample sizes); and then it generates a vector containing random samples from each population (described here). This is useful for simulating data to be run through the function fitBayes.

2) A new version of the tree plotting function plotTree. This version really just acts as a wrapper for plotSimmap so that it can use the options of plotSimmap, without a mapped trait.

3) A new version of phylosig which also returns the log-likelihood for λ=0.0 if phylosig(...,method="lambda",test=TRUE). This version also has better error checking and new internal functions to match the data (and, optionally, the standard errors) to the tree (described here). These updates were added by user request.

4) A new function for stochastic Yule trees with various options called pbtree (here).

5) A new version of phenogram that can also color the edges by a discrete character mapping on the tree (here).

6) Finally, I new function evolvcv.lite that can be used to fit common correlation models and common rate models for the method of evol.vcv (here).

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