DT_halfdiallel {lme4breeding}

half diallel data for corn hybrids

Description

This dataset contains phenotpic data for 21 corn hybrids, with 2 technical repetitions, coming from a half diallel design and evaluated for sugar content. The column geno indicates the hybrid and male and female origin columns are included as well.

Usage

data("DT_halfdiallel")

Format

The format is: chr "DT_halfdiallel"

Source

This data was generated by a corn study.

References

Giovanny Covarrubias-Pazaran (2024). lme4breeding: enabling genetic evaluation in the age of genomic data. To be submitted to Bioinformatics.

Douglas Bates, Martin Maechler, Ben Bolker, Steve Walker (2015). Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67(1), 1-48.

See Also

The core function of the package lmebreed

Examples

data("DT_halfdiallel")
DT <- DT_halfdiallel
head(DT)
DT$femalef <- as.factor(DT$female)
DT$malef <- as.factor(DT$male)
DT$genof <- as.factor(DT$geno)
# overlay matrix to be added to the addmat argument
Z <- with(DT, overlay(femalef,malef) )
## inital values for incidence matrix but irrelevant
## since these will be replaced by admat argument
fema <- (rep(colnames(Z), nrow(DT)))[1:nrow(DT)]
## model using overlay without relationship matrix
modh <- lmebreed(sugar ~ (1|genof) + (1|fema),
                 addmat = list(fema=Z),
             data=DT)
vc <- VarCorr(modh); print(vc,comp=c("Variance"))



## model using overlay with relationship matrix
## relationship matrix to be added to the relmat argument
A <- diag(7); colnames(A) <- rownames(A) <- 1:7;A
modh <- lmebreed(sugar ~ (1|genof) + (1|fema),
                 addmat = list(fema=Z),
                 relmat = list(fema=A),
                 data=DT)
vc <- VarCorr(modh); print(vc,comp=c("Variance"))