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# NOT RUN {
####=========================================####
#### For CRAN time limitations most lines in the
#### examples are silenced with one '#' mark,
#### remove them and run the examples
####=========================================####
data(HDdata)
head(HDdata)
####=========================================####
#### Example 1 (formula-based)
#### using overlay with mmer2 function
####=========================================####
data(HDdata)
head(HDdata)
HDdata$female <- as.factor(HDdata$female)
HDdata$male <- as.factor(HDdata$male)
HDdata$geno <- as.factor(HDdata$geno)
#### model using overlay
modh <- mmer2(sugar~1, random=~female + and(male) + geno,
data=HDdata)
summary(modh)
#### model using overlay [and(.)] and covariance structures [g(.)]
# A <- diag(7); A[1,2] <- 0.5; A[2,1] <- 0.5 # fake covariance structure
# colnames(A) <- as.character(1:7); rownames(A) <- colnames(A);A
#
# modh2 <- mmer2(sugar~1, random=~g(female) + and(g(male)) + geno,
# G=list(female=A, male=A),data=HDdata)
# summary(modh2)
#
# ####=========================================####
# #### Example 2 (matrix-based)
# #### using overlay with mmer function
# ####=========================================####
#
# #### GCA matrix for half diallel using male and female columns
# #### use the 'overlay' function to create the half diallel matrix
# Z1 <- overlay(HDdata[,c(3:4)])
#
# #### Obtain the SCA matrix
# Z2 <- model.matrix(~as.factor(geno)-1, data=HDdata)
#
# #### Define the response variable and run
# y <- HDdata$sugar
# ETA <- list(list(Z=Z1), list(Z=Z2)) # Zu component
# modHD <- mmer(Y=y, Z=ETA, draw=FALSE, silent=TRUE)
# summary(modHD)
# }
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