sommer (version 3.6)

gryphondata: 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("gryphondata")

Format

The format is: chr "gryphondata"

References

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

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 and mmer2

Examples

# NOT RUN {
####=========================================####
#### For CRAN time limitations most lines in the 
#### examples are silenced with one '#' mark, 
#### remove them and run the examples using
#### command + shift + C |OR| control + shift + C
####=========================================####
data(gryphondata)

gryphon <- gryphondata$gryphon
ppedig <- gryphondata$pedi
## obtained using the 'getA()' function from the pedigreemm package
A <- gryphondata$A 

#### look at the data
head(gryphon)

#### fit the model with no fixed effects (intercept only)
#mix1 <- mmer2(BWT~1,random=~g(ANIMAL), G=list(ANIMAL=A), data=gryphon)
#summary(mix1)

#### fit the model with SEX as fixed effects 
#mix2 <- mmer2(BWT~1+SEX,random=~g(ANIMAL), G=list(ANIMAL=A), data=gryphon)
#summary(mix2)

# }