#Modern Measures of Differentiation

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

##Quickstart

###Install

mmod isn't 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 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 (2008) G'st and Jost's (2008) D to R, along with an implementation of Nei's Gst that uses nearly unbiased estimators for Hs and Ht, the two key parameters from which all these stats are calculated. All these functions work on genind objects from the library adegenet so data can be read in from standard genepopfiles. An overview of a typical usage is provided in a vignette called "demo", acessable from vignette("demo", package="mmod")

Briefly yhere are functions for each of these measures which give values for each locus in a genind object and a global estimate:D_Jost(), Gst_Hedrick(), Gst_Nei(). Because most of the heavy-lifting in calculating all these stats is finding Hs and Ht, a function, diff_stats() is provided to calculate each at once.

Each of the stats can be calculated for each pairwise comparison of populations in a dataset: pairwise_D(), pairwise_Gst_Hedrick(), pairswise_Gst_Nei().

Finally, the function jacknife_population() can, as the name suggests, calculate these statistics in a sample jacknifed across populations

mmod is still very much in development, so I'm happy to receive and suggestions contributions or bugs you might find