I use R for a variety of tasks, and I have contributed several R packages that are freely available on CRAN and GitHub:
OUwie– (pronounced “au-wi”) – Calculates and compares rate differences of continuous character evolution under a new set of Ornstein-Uhlenbeck-based models that allow the strength of selection and the rate of stochastic motion to vary across selective regimes. It is currently available on CRAN (v.1.45), but is now continuously developed and maintained on github: https://github.com/thej022214/OUwie
NOTE: As of version 1.33, OUwie no longer supports the OUwie.contour function. This is due to with licensing issues with a particular dependency (akima), which required that we remove it from OUwie completely. I have plans to restore this functionality at some point. In the meantime, the code can be downloaded here and the manual here.
corHMM -- (pronounced "kor-um") – Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution. It is currently available on CRAN. You can also download from source from github: https://github.com/thej022214/corHMM
hisse -- (pronounced "hissy") – Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and a binary character set to test for hidden shifts in trait-dependent rates of diversification. You can also download from source from github: https://github.com/thej022214/hisse
How do you install any of these packages from GitHub instead of CRAN?
First, you need to install the devtools package. Start R and type: install.packages("devtools") Now, load the devtools package: library(devtools) To download, say, OUwie: install_github("thej022214/OUwie")
Archived folder containing R scripts used to conduct analyses inBeaulieu, J.M., and B.C. O'Meara (2015). Extinction can be estimated from moderately sized molecular phylogenies.Evolution.They are found here
Archived folder containing scripts written in Ruby and R for calculating a composite AIC weights as described in Beaulieu et al (2013). They are found h