Andrew-Shirk/sGD: Spatially explicit estimation of genetic diversity indices and Wright's neighborhood size (NS)

sGD provides spatially explicit estimates of genetic diversity indices and Wright's neighborhood size in continuous populations isolated by distance or resistance as described in Shirk & Cushman 2014. Inputs include a set of spatially referenced codominant marker genotypes, a matrix of pairwise distances between all sampled individuals (either in Euclidean units or as effective distances quantified by methods such as least-cost-path or circuit theory), and several parameters, including the minimum neighborhood size and the neighborhood radius (specified in Euclidean or effective distances). sGD defines a local neighborhood extent (based on a user-specified radius) around each sample location, and then calculates genetic diversity indices and/or Wright's neighborhood size (a local measure of effective population size that accounts for the continuous structure of populations isolated by distance). Requires the NeEstimator program (version 2.01) available at http://molecularfisherieslaboratory.com.au/neestimator-software.

Getting started

Package details

AuthorAndrew Shirk
MaintainerAndrew Shirk <[email protected]>
LicenseGPL (>= 2)
Version2.11
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("Andrew-Shirk/sGD")
Andrew-Shirk/sGD documentation built on May 26, 2019, 6:38 a.m.