hdm: Half Diallel Matrix

Description

THIS FUNCTION HAS BEEN OVERPASSED BY THE 'overlay' FUNCTION WHICH IS MORE FLEXIBLE AND FASTER.

This function uses a dataframe with 2 columns named "female" and "male" in numeric format and creates an incidence matrix for a single explanatory variable corresponding to the GCA effect. The resulting incidence matrix can be used in the mmer function as a 'Z' argument in the 2-level list argument for random effects.

Usage

hdm(dat)

Arguments

dat

a dataframe with 2 columns named 'female' and 'male' with numeric or factor values indicating the male or female used to produce such hybrid.

Value

$Z: an incidence matrix with as many columns as parents in the dataframe indicating with ones the parents used for a particular hybrid (in rows).

References

Fikret Isik. 2009. Analysis of Diallel Mating Designs. North Carolina State University, Raleigh, USA.

Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744

Examples

Run this code

# 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)
####=========================================####
#### GCA matrix for half diallel using male and female columns
#### use the 'hdm' function to create the half diallel matrix
####=========================================####
Z1 <- hdm(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)
# }