FDK_BLUEs

#Use lme4 to develop BLUEs

library(data.table)
library(lme4)
library(emmeans)
library(dplyr)

#upload pheno data
DT <- read.csv("/Users/ackerman/FDK/FDK_Data/FDK_Pheno/FDK_BLUEs", header = TRUE)

#Adjusted for FDK dataset
mixed.mod <- lmer(DON_ppm ~ taxa + (1|Env) + (1|Trial:Env) + (1|taxa:Env), data = DT)

#calcuate with emmeans

emmeans.out1 <- emmeans(mixed.mod, "taxa", lmer.df = "asymptotic")
emmeans.out2 <- summary(emmeans.out1)
emmeans.out3 <- emmeans.out2[,1:2] #save columns

summary(mixed.mod)

#Alternative extraction - calculate with lme4(fixef)

blues <- as.data.frame(fixef(mixed.mod))

#Push to excel and finish there

write.csv(blues, "/Users/ackerman/FDK/FDK_Data/FDK_Pheno/FDK_BLUEs/FDK_BLUEs_DON.csv")