hdm: Half Diallel Matrix

Description

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(data)

Arguments

data

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

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


####=========================================####
#### 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)