Data and analysis scripts for "Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow"

Phenotypic, genotype, and analysis scripts for "Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow" Main growth analysis of the 5,051 seedlings can be reproduced by running the "04a-fit-full-model.R" script and loading the "full growth analysis.Rdata" dataset in R Data for GEBV estimation with cross-validation not across families is contained within the directories in: run_642454_tmax_sum_dif_rgr_10fold_notacross_seed300.zip Data for GEBV estimation with cross-validation across families is in: run_648224_tmax_sum_dif_rgr_10fold_acrossfams_seed300.zip To reproduce the GEBV estimation and analysis, download the corresponding zip files that contains the R environment and datasets and use the "04d-analyze-models-cluster.R" script "valley oak growth data - all seedlings.csv" contains the relative growth rates and relevant covariates for the 5,051 seedlings in an easy to read format "gbs451_FIL-4_noLD.recode.vcf" contains the genotypes of each maternal tree in the study in VCF format All data preparation and analysis scripts are available on Github: https://github.com/lukembrowne/Valley-oak-common-garden-growth-analysis