DT_gryphon {lme4breeding}

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"

Source

This data comes from the Journal of Animal Ecology. Please, if using this data cite Wilson et al. publication. If using our mixed model solver please cite Covarrubias' publication.

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)



## 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"))