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.
Package details |
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Author | Andrew Shirk |
Maintainer | Andrew Shirk <ashirk@uw.edu> |
License | GPL (>= 2) |
Version | 2.11 |
Package repository | View on GitHub |
Installation |
Install the latest version of this package by entering the following in R:
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