The procedure used for the prediction of trait stability in coffee was described here. Phenotypic file contains yield data for two populations: Premature (Prec) and Intermediate (Inter). Both populations differ by coffee bean maturity date, Prec matures earlier than Inter population. Genotypic file contains imputed ~56k snps for both populations. The codes implemented can be found in "R code for trait stability prediction.Rmd".
Before running the code, install bglr, FW, metan and dplyr R packages.