lme4breeding (version 1.0.50)

DT_gryphon: Gryphon data from the Journal of Animal Ecology

Description

This is a dataset that was included in the Journal of animal ecology by Wilson et al. (2010; see references) to help users understand how to use mixed models with animal datasets with pedigree data.

The dataset contains 3 elements:

gryphon; variables indicating the animal, the mother of the animal, sex of the animal, and two quantitative traits named 'BWT' and 'TARSUS'.

pedi; dataset with 2 columns indicating the sire and the dam of the animals contained in the gryphon dataset.

A; additive relationship matrix formed using the 'getA()' function used over the pedi dataframe.

Usage

data("DT_gryphon")

Format

The format is: chr "DT_gryphon"

References

Wilson AJ, et al. (2010) An ecologist's guide to the animal model. Journal of Animal Ecology 79(1): 13-26.

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_gryphon)
DT <- DT_gryphon
A <- A_gryphon
P <- P_gryphon
#### look at the data
head(DT)

# \donttest{

## fit the model with no fixed effects (intercept only)
mix1 <- lmebreed(BWT~ (1|ANIMAL),
                 relmat = list(ANIMAL=A),
                 control = lmerControl(
                   check.nobs.vs.nlev = "ignore",
                   check.nobs.vs.rankZ = "ignore",
                   check.nobs.vs.nRE="ignore"
                 ),
                 data=DT)
vc <- VarCorr(mix1); print(vc,comp=c("Variance"))

# }