lme4breeding (version 1.0.90)

DT_example: Broad sense heritability calculation.

Description

This dataset contains phenotpic data for 41 potato lines evaluated in 3 environments in an RCBD design. The phenotypic trait is tuber quality and we show how to obtain an estimate of DT_example for the trait.

Usage

data("DT_example")

Format

The format is: chr "DT_example"

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 functions of the package lmebreed

Examples

data(DT_example)
DT <- DT_example
A <- A_example
head(DT)

## Compound simmetry (CS) model
ans1 <- lmebreed(Yield~Env + (1|Name) + (1|Env:Name),
             data=DT)
vc <- VarCorr(ans1); print(vc,comp=c("Variance"))

BLUP <- ranef(ans1, condVar=TRUE)
PEV <- lapply(BLUP, function(x){attr(x, which="postVar")}) # take sqrt() for SEs

# \donttest{

## Main (M) + Diagonal (DIAG) model
## with relationship matrix
ansCSDG <- lmebreed(Yield ~ Env + (Env||Name),
                    relmat = list(Name = A ),
                    data=DT)
vc <- VarCorr(ansCSDG); print(vc,comp=c("Variance"))

## Main (M) + Diagonal (DIAG) model
## with diagonal residuals
## with relationship matrix
ansCSDG <- lmebreed(Yield ~ Env + (Env||Name) + (0+Env||unitsR),
                    relmat = list(Name = A ),
                    data=DT)
vc <- VarCorr(ansCSDG); print(vc,comp=c("Variance"))
sigma(ansCSDG)^2 # error variance

# }