DT_h2 {lme4breeding}

Broad sense heritability calculation.

Description

This dataset contains phenotpic data for 41 potato lines evaluated in 5 locations across 3 years in an RCBD design. The phenotypic trait is tuber quality and we show how to obtain an estimate of DT_h2 for the trait.

Usage

data("DT_h2")

Format

The format is: chr "DT_h2"

Source

This data was generated by a potato 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_h2)
DT <- DT_h2
head(DT)



DT=DT[with(DT, order(Env)), ]

Z <- with(DT, smm(Env))
for(i in 1:ncol(Z)){DT[,colnames(Z)[i]] <- Z[,i]}
csdiagFormula <- paste0( "y ~ Env + (", paste(colnames(Z), collapse = "+"), "|| Name)")
blockFormula <- paste0( "(0+", paste(colnames(Z), collapse = "+"), "|| Block)")
form <- paste(csdiagFormula , blockFormula, sep="+")

ans1b <- lmebreed(as.formula(form),
                  data=DT)
vc <- VarCorr(ans1b); print(vc,comp=c("Variance"))