This repository contains data and scripts for the manuscript "Genetic variation reveals Individual-level climate tracking across the full annual cycle of a migratory bird"
Breeding_96snps(.loc,.ped,.map) - PED formated genotypes from 96 assayed SNPs for all breeding individuals (including RAD sequenced
Unknowns_96snps(.loc,.ped,.map) - PED formated genotypes from 96 assayed SNPs for wintering and migrating birds
Breeding_157snps.str - STRUCTURE input with all breeding individuals assayed at 157 snps
Morphology.csv - Subset of morphological data from Wiedenfeld 1991 (The Auk)
Format.R - filters and formats genotypes from Fluidigm assays for downstream analysis
MakeMapStacks.R - takes Q-matrix from STRUCTURE and creates spatial layers
NewMap.R - Plots layers from MakeMapStacks.R
SNPrelate.R - performs PCA
Rubias.R - performs population assignments in rubias
OriGen.R - creates probability surfaces for wintering individuals
Morphology.R - test for morphological correlates of precipitation with the Wiedenfeld 1991 data
ClimateMatchingAnalysis.R - test for correlation between breeding and wintering climate
FormatBBSdata.R - extract yellow warbler counts from BBS data and format for JAGS input
make.jags.data.R - adding cliamte to BBS data for JAGS input
run_jags_final.R - run JAGS model for abundance/climate associations
bbs_model_final.txt - JAGS model