We use R for a variety of tasks, and 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.2.4). You can also download the bleeding edge version directly from GitHub: https://github.com/thej022214/OUwie
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 (v.2.3). You can also download the bleeding edge version directly 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. It is currently available on CRAN (v.1.9.8). You can also download the bleeding edge version directly from GitHub: https://github.com/thej022214/hisse
selac – (pronounced "sel-ac") – Sets up and executes a SelAC model (Selection on Amino acids and codons) for testing the presence of selection in amino acid or codon among a set of genes on a fixed phylogeny. It is currently available on CRAN (v.1.7.5). You can also download the bleeding edge directly from GitHub: https://github.com/bomeara/selac
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")
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.2.4). You can also download the bleeding edge version directly from GitHub: https://github.com/thej022214/OUwie
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 (v.2.3). You can also download the bleeding edge version directly 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. It is currently available on CRAN (v.1.9.8). You can also download the bleeding edge version directly from GitHub: https://github.com/thej022214/hisse
selac – (pronounced "sel-ac") – Sets up and executes a SelAC model (Selection on Amino acids and codons) for testing the presence of selection in amino acid or codon among a set of genes on a fixed phylogeny. It is currently available on CRAN (v.1.7.5). You can also download the bleeding edge directly from GitHub: https://github.com/bomeara/selac
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")
