DT_example: Broad sense heritability calculation.

In covaruber/sommer: Solving Mixed Model Equations in R

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"

Source

This data was generated by a potato study.

References

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

See Also

The core functions of the package mmes

Examples

####=========================================####
#### For CRAN time limitations most lines in the 
#### examples are silenced with one '#' mark, 
#### remove them and run the examples
####=========================================####
####=========================================####
#### EXAMPLES
#### Different models with sommer
####=========================================####

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

####=========================================####
#### Univariate homogeneous variance models  ####
####=========================================####

## Compound simmetry (CS) model
ans1 <- mmes(Yield~Env,
             random= ~ Name + Env:Name,
             rcov= ~ units,
             data=DT)
summary(ans1)$varcomp

# ####===========================================####
# #### Univariate heterogeneous variance models  ####
# ####===========================================####
# 
# ## Compound simmetry (CS) + Diagonal (DIAG) model
# DT=DT[with(DT, order(Env)), ]
# ans2 <- mmes(Yield~Env,
#              random= ~Name + vsm(dsm(Env),ism(Name)),
#              rcov= ~ vsm(dsm(Env),ism(units)),
#              data=DT)
# summary(ans2)

# ####===========================================####
# #### Multi-trait variance models               ####
# ####===========================================####
# 
# # stack traits
# DT2 <- stackTrait(DT, traits = c("Yield","Weight") )
# DTx <- DT2$long
# head(DTx)
# 
# DTx=DTx[with(DTx, order(trait, Env)), ]
# 
# ## model
# ans1 <- mmes(valueS~ trait + trait:Env,
#              random= ~ vsm(dsm(trait), dsm(Env), ism(Name)), 
#              rcov= ~ vsm(dsm(trait), dsm(Env), ism(units)), 
#              data=DTx)
# summary(ans1)$varcomp

covaruber/sommer documentation built on June 14, 2025, 11 p.m.