Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Differentiation statistics in R
R
Branch: master

Fetching latest commit…

Cannot retrieve the latest commit at this time

Failed to load latest commit information.
R
inst
man
tests
vignettes
.Rbuildignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
README.md

README.md

Travis-CI Build
Status Current CRAN release

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

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.

Something went wrong with that request. Please try again.