startmrca

This package implements a hidden Markov model to estimate the time at which a beneficial allele begins increasing in frequency. More specifically, we assume a "star" genealogy among carriers of the benefical allele to estimate time to the most recent common ancestor (TMRCA). See Smith et al. (2018) for details of the model.

Setup

In R, install the latest version of the package using these commands:

library(devtools)
install_github("jhavsmith/startmrca")
library(startmrca)

Usage

After installing the package, usage options and an example are available by typing:

help(run.startmrca)