KMA-Sockeye-Mixtures

This repository holds all scripts associated with analyzing sockeye salmon mixtures from Kodiak Management Area commercial fisheries sampled over three seasons, 2014--2016.

KMASockeyeMixtures.R

Purpose

The goal of this script is to analyze sockeye salmon mixtures from the KMA commercial harvest from 2014-2016 using a coastwide sockeye baseline containing 473 populations in 15 reporting groups characterized by 48 SNPs grouped into 46 loci (2 sets of linked SNPs are combined as haplotypes). All mixtures are to be analyzed with the program BAYES.

Specific Objectives

This script will:

1. Import mixture data

2. Define spatio-temporal strata

3. Perform a data QC on mixtures

4. Prepare BAYES input files

5. Summarize BAYES results

6. Generate plots and tables of results