Code to correct phenotypes and genotypes for confounding factors

This is the R script that was used to correct the phenotypes and imputed genotypes for possible confounding factors prior to conducting Random Forest analyse

Phenotype comparisons for 2010

R code to quantify phenotypic differences between fish from the integrated and segregated hatchery lines in 201

Input files for Random Forest analyses

This file contains the original phenotypes and imputed genotypes for individuals prior to Random Forest analyses, along with the corrected phenotypes and genotypes that were analyzed by Random Forest for each of the six fitness traits

PacSNP chum data for MER

The file is formatted for GenAlEx software, but can easily be converted to Genepop or similar formats. Genotypes are in two-column format with missing data designated with a “0”. Population code and locus code worksheets follow the rawdata. The population order differs between the rawdata which is in numeric order and Table 1 of the manuscript which is ordered geographically. This is particularly noticeable in the order of the Western Alaska populations including the Yukon River. The rawdata includes laboratory names for the SNPs; a key to published names is in the locus code worksheet. The mtDNA SNPs are listed independently and have not been combined into composite haplotypes