meyer {gap.datasets}

A pedigree data on 282 animals deriving from two generations

Description

A data frame attributed to Meyer (1989).

“The pedigrees for each of these 282 animals derive from an additional 24 base population (Generation 0) animals that do not have records of their own but, nevertheless, are of interest with respect to the inference on their own additive genetic values. Furthermore, it is presumed that these original 24 base animals are not related to each other. Therefore, the row dimension of u is 306 (282+24).” (Templeman & Rosa 2004)

Usage

data(meyer)

Format

A data frame containing 306 records

Source

Meyer K (1989). Restricted maximum likelihood to estimate variance components for animal models with several random effects using a derivative-free algorithm. Genetics, Selection, Evolution 21:317-340.

Tempelman RJ, Rosa GJM. Empirical Bayes Approaches to Mixed Model Inference in Quantitative Genetics. in Saxton AM (Ed). Genetic Analysis of Complex Traits Using SAS, chapter 7. SAS Institute Inc., Cary, NC, USA, 2004

Examples

## Not run: 
library(gap)
meyer <- within(meyer,{
   g1 <- ifelse(generation==1,1,0)
   g2 <- ifelse(generation==2,1,0)
})
lm(y~-1+g1+g2,data=meyer)
library(MCMCglmm)
m <-MCMCglmm(y~-1+g1+g2,random=animal~1,pedigree=meyer[,1:3],data=meyer,verbose=FALSE)
summary(m)
plot(m)   

meyer <- within(meyer,{
   id <- animal
   animal <- ifelse(!is.na(animal),animal,0)
   dam <- ifelse(!is.na(dam),dam,0)
   sire <- ifelse(!is.na(sire),sire,0)
})
# library(kinship)
# A <- with(meyer,kinship(animal,sire,dam))*2

A <- kin.morgan(meyer)$kin.matrix*2

library(regress)
regress(y~-1+g1+g2,~A,data=meyer)
prior <- list(R=list(V=1, nu=0.002), G=list(G1=list(V=1, nu=0.002)))
m2 <- MCMCgrm(y~-1+g1+g2,prior,meyer,A,singular.ok=TRUE,verbose=FALSE)
summary(m2)
plot(m2)   

## End(Not run)