grmunjal / mmod

Differentiation statistics in R

#Modern Measures of Differentiation

mmod is an R package for calculating modern population divergence statistics.

##Quickstart

###Install

mmod is on CRAN, so you can install the latest stable version using install.packages("mmod"). This github repository may be running ahead of the version on CRAN, if you really want the latest version you can use devtools to install the code in thes repo:

library(devtools)
install_github("dwinter/mmod")

###Usage Once it's up an running all you need is genepop (or fstat) file with your data

    >library(mmod)
    >my_data <- read.genepop("my_file.gen")
    >diff_stats(my_data)

##Overview

Population geneticists have traditionally used Nei's Gst (often confusingly called Fst...) to measure divergence between populations. It turns out, Gst doesn't really measure divergence so, [a set of new measures have been developed] (http://www.molecularecologist.com/2011/03/should-i-use-fst-gst-or-d-2/)

mmod is a package that brings two of these measures; Hedricks (2005, 2011) G''st Jost's (2008) D and Meirman's (2005) φ'st to R, along with a function that calculates Nei's Gst using nearly unbiased estimators for Hs and Ht (the two key parameters from which most of these stats are calculated). All these functions work on genind objects from the package adegenet so data can be read in from standard genepop for fstat files. An overview of a typical usage is provided in a vignette called "demo", acessable from vignette("demo", package="mmod"), I suggest new users read this before that start.

##Help All functions are documented and there is Vignette describing a basic usage of the pacakge.