#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.
mmod is still very much in development, so I'm happy to receive any suggestions contributions or bugs you might find
chao_bootstrap
diff_stats
diff_test
dist.codom
D_Jost
Gst_Hedrick
Gst_Nei
harmonic_mean
jacknife_populations
mmod
(mmod-package)pairwise_D
pairwise_Gst_Hedrick
pairwise_Gst_Nei
Phi_st_Meirmans
rgenotypes
summarise_bootstrap