uploaded

code/BLUES.R

+
+###B6 Script Specialized for MPI experiment August-September 2018 by Tom Theeuwen###################################
+
+library(lme4); library(lmerTest); library(pbkrtest)
+setwd('../data/')
+data <- na.omit(as.data.frame(read.table("s8.csv", sep = ",", header = TRUE)))
+data$Basin <- factor(data$Basin)
+data$Replicate <- factor(data$Replicate)
+data$Table_pos <- factor(data$Table_pos)
+data$Image_pos <- factor(data$Image_pos)
+data$x <- factor(data$x)
+data$y <- factor(data$y)
+data$Sowing_X <- factor(data$Sowing_X)
+data$Sowing_Y <- factor(data$Sowing_Y)
+data$Sowing_Block <- factor(data$Sowing_Block)
+
+BLUES_overview <- NULL
+extract_names <- sapply(data$Genotype,levels)[,1]
+BLUES_overview<-rbind(BLUES_overview,extract_names)
+BLUE_new <- NULL
+start_point = 13 # enter column where you want to start
+
+for(x in start_point:ncol(data)){
+  name <- colnames(data)[x]
+  variable <- data[,x]
+  mm1 <- lmer(variable ~ Genotype + (1|Image_pos) + (1|x) + (1|y) + (1|Sowing_Block), data=data,REML=TRUE)
+  BLUE <- fixef(mm1)
+  MN1 <- BLUE[1]
+  BLUE_new[1] <- MN1
+  for(i in 2:length(BLUE)){
+    BLUE_new[i] <- MN1 + BLUE[i]
+  }
+  BLUES_overview <- rbind(BLUES_overview, BLUE_new)
+  print(name)
+}
+rownames(BLUES_overview)=c()
+mat=t(BLUES_overview)
+colnames(mat)=c("Genotype","T13_1","T13_2","T13_3","T13_4","T14_1","T14_2","T14_3","T14_4","T14_5","T14_6","T14_7","T14_8","T15_1","T15_2","T15_3","T15_4","T15_5","T15_6","T15_7","T15_8","T16_1","T16_2","T16_3","T16_4","T16_5","T16_6","T16_7","T16_8","T17_1","T17_2","T17_3","T17_4","T17_5","T17_6","T17_7","T17_8","T18_1","T18_2","T18_3","T18_4","T18_5","T18_6","T18_7","T18_8","T19_1","T19_2","T19_3","T19_4","T19_5","T19_6","T19_7","T19_8","T20_1","T20_2")
+write.csv(mat, "s9.csv",quote=F,row.names=F)
+