Data files, code and analyses involving summer flounder larvae from 1989-2012.
- 15outlier_PCA.R script examines 15 spatial outliers in adult PADE w/ PCA, calculates regional allele frequencies, identifies these SNPs in larvae, and calculates genotype likelihoods
- fallvswinter.R exploratory code examining allele frequency differences between larvae ingressing in the fall and the winter
- keepfirstsnponly.R script reads in a vcf, removes SNPs existing on the same contig & writes a new file
- larvaevadults.R exploratory code examining allele frequency differences between adult and larval PADE
- larvaevadults_fst.R calculates FST between adult and larval populations caught over time
- larval_sampling_simulations.R creates and plots a null model that examines allele frequency change over time that depends on sampling size
- larval_tempovertime.R preliminary analysis of temperature change over time using RUMFS bridgenetting & NOAA Beaufort datasets
- larvalstructure.R PCA broken down by region
- structurethrutime.R exploratory code for larval PADE, including PCA broken down by time period, summary statistics, DAPC, AMOVA and allele frequency change over time