sommer (version 4.3.5)

DT_btdata: Blue Tit Data for a Quantitative Genetic Experiment

Description

a data frame with 828 rows and 7 columns, with variables tarsus length (tarsus) and colour (back) measured on 828 individuals (animal). The mother of each is also recorded (dam) together with the foster nest (fosternest) in which the chicks were reared. The date on which the first egg in each nest hatched (hatchdate) is recorded together with the sex (sex) of the individuals.

Usage

data("DT_btdata")

Format

The format is: chr "DT_btdata"

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 mmer, mmec

Examples

# ####=========================================####
# #### For CRAN time limitations most lines in the 
# #### examples are silenced with one '#' mark, 
# #### remove them and run the examples
# ####=========================================####
# ####=========================================####
# ####=========================================####
# #### EXAMPLE 1
# #### simple example
# ####=========================================####
# ####=========================================####
# data(DT_btdata)
# DT <- DT_btdata
# head(DT)
# mix4 <- mmer(tarsus ~ sex,
#              random = ~ dam + fosternest,
#              rcov=~units,
#              data = DT)
# summary(mix4)$varcomp
# 
# mix5 <- mmec(tarsus ~ sex,
#              random = ~ dam + fosternest,
#              rcov=~units,
#              data = DT)
# summary(mix5)$varcomp
# 
# ####=========================================####
# ####=========================================####
# ####=========================================####
# #### EXAMPLE 2
# #### more complex multivariate model
# ####=========================================####
# ####=========================================####
# data(DT_btdata)
# DT <- DT_btdata
# mix3 <- mmer(cbind(tarsus, back) ~ sex,
#                 random = ~ vsr(dam) + vsr(fosternest),
#                 rcov= ~ vsr(units, Gtc=diag(2)),
#                 data = DT)
# summary(mix3)
# #### calculate the genetic correlation
# cov2cor(mix3$sigma$`u:dam`)
# cov2cor(mix3$sigma$`u:fosternest`)