sommer (version 4.4.1)

DT_ige: Data to fit indirect genetic effects.

Description

This dataset contains phenotpic data for 98 individuals where they are measured with the purpose of identifying the effect of the neighbour in a focal individual.

Usage

data("DT_ige")

Format

The format is: chr "DT_ige"

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_ige)
DT <- DT_ige
# # Indirect genetic effects model without covariance between DGE and IGE
# modIGE <- mmes(trait ~ block, dateWarning = FALSE,
#                random = ~ focal + neighbour,
#                rcov = ~ units, nIters=100,
#               data = DT)
# summary(modIGE)$varcomp
# pmonitor(modIGE)
# 
# # Indirect genetic effects model with covariance between DGE and IGE using relationship matrices
# modIGE <- mmes(trait ~ block, dateWarning = FALSE,
#                random = ~ covm( vsm(ism(focal)), vsm(ism(neighbour)) ),
#                rcov = ~ units, nIters=100,
#               data = DT)
# summary(modIGE)$varcomp
# pmonitor(modIGE)
# 
# # form relationship matrix
# Ai <- solve(A_ige + diag(1e-5, nrow(A_ige),nrow(A_ige) ))
# Ai <- as(as(as( Ai,  "dMatrix"), "generalMatrix"), "CsparseMatrix")
# # Indirect genetic effects model with covariance between DGE and IGE using relationship matrices
# modIGE <- mmes(trait ~ block, dateWarning = FALSE,
#                random = ~ covm( vsm(ism(focal), Gu=Ai), vsm(ism(neighbour), Gu=Ai) ),
#                rcov = ~ units, nIters=100,
#               data = DT)
# summary(modIGE)$varcomp
# pmonitor(modIGE)