README.md

In radamsRHA/GppFst: Posterior Predictive Simulations for generating theoretical distributions of Fst and Dxy under the neutral coalescent model for two species

GppFst: Genomic Posterior Predictive Fst simulations

NOTE See the file https://github.com/radamsRHA/GppFst/blob/master/vignettes/GppFst_Tutorial.pdf for detailed instructions

Steps for conducting posterior predictive simulations for Fst and Dxy.

1. Estimate joint posterior distributions for coalescent parameters of a two population coalescent model (population size parameters 4Neu, divergence times). This can be accomplished using a number of programs that estimate mutispecies coalescent model parameters.
2. Input a sample of this posterior distribution using the function read.posterior.
3. Input the empirical locus coverage (for both populations) and locus length for all loci
4. Conduct Fst and Dxy PPS using the input MCMC and empirical pararmeters

Installing R package GppFst from github

The R package GppFst is freely available to download and distribute from github https://github.com/radamsRHA/GppFst/. To install and load GppFst, you must first install the R packages devtools, phybase, and Geneland.

install.packages("devtools")
install.packages("Geneland")

The packages, phybase should be downloaded http://faculty.franklin.uga.edu/lliu/content/phybase. Save it to your desktop and then use this code to install it from source:

install.packages("~/Desktop/phybase", repos = NULL, type = "source")

Now using devtools we can install GppFst from github:

library(devtools)
install_github("radamsRHA/GppFst")
library(GppFst) # Load package GppFst
library(phybase) # Load dependancy phybase
library(Geneland) # Load dependancy Geneland

UPDATE: it seems that Geneland has been removed from Cran. As a potential work around, you can install gfortran for mac, for example (https://github.com/fxcoudert/gfortran-for-macOS/releases), and then use the command:

install_github("https://github.com/cran/Geneland")

To begin using GppFst try using our vignette with example files provided with this package. See the directory ./GppFst_Tutorial/ for example files and tutorial.

radamsRHA/GppFst documentation built on Nov. 9, 2019, 7:08 p.m.