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Differentiation statistics in R
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README.md

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 download mmod_*.tar.gz and install via the command line (or with the GUI if you'd prefer):

    $R CMD INSTALL mmod_*.tar.gz 

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

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 library 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, there are pretty versions of the help pages here.

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