A package for running BayesTraits from R (works on Mac OS only). The functions work by using System to run BayesTraits on your system and delete the output files after importing them into R.
BayesTraits was developed by Mark Pagel and Andrew Meade, and is available from their website as an executable file that can be run from a command line program such as Terminal. Consult the BayesTraits documentation before using btw.
If you have the devtools package installed, you can intall btw from GitHub:
library(devtools)
install_github("rgriff23/btw")
library(btw)
Before using any of the functions that call BayesTraitsV2, you have to download Version 2 of BayesTraits. You then have to tell btw where to find it on your computer by defining the hidden variable .BayesTraitsPath:
.BayesTraitsPath <- "YourPath/BayesTraits"
You will have to define .BayesTraitsPath every time you start a new R session.
The package includes some examples of tree and data files that will work with btw functions. You can load them into your R session after you load btw:
data(primates)
Then you can experiment with the primate data and btw functions. For example, this code fits a Brownian motion model of evolution for a single continuous trait using maximum likelihood, and also finds the maximum likelihood estimate of the phylogenetic signal parameter, lambda:
Continuous(primate.tree1, primate.continuous1, lambda="ML")
Check my website for examples of fitting, comparing, and visualizing BayesTraits output.