mmod is an R package for calculating modern population divergence statistics.
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")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)
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.
All functions are documented and there is Vignette describing a basic usage of the pacakge.