MLE.beta {MasterBayes}R Documentation

Maximum Likelihood Estimation of Beta

Description

Finds MLE for beta given a pedigree, via a call to optim. Beta is the paramater vector of a multinomial log-linear model.

Usage

MLE.beta(X.list, ped, beta=NULL, nUSdam=NULL, nUSsire=NULL,...)

Arguments

X.list list of design matrices for each offspring derived using getXlist
ped pedigree with id, dam and sire in ech column
beta optional starting vector for beta
nUSdam optional number of unsampled females. Only required if unsampled females have known phenotype.
nUSsire optional number of unsampled males. Only required if unsampled males have known phenotype.
... Further arguments to be passed

Value

beta vector of MLE's for beta
C large sample variance-covariance matrix of beta MLE's

Author(s)

Jarrod Hadfield j.hadfield@ed.ac.uk

References

Hadfield J.D. et al (2006) Molecular Ecology 15 3715-31 Smouse P.E. et al (1999) Journal of Evolutionary Biology 12 1069-1077

See Also

MCMCped, beta.loglik

Examples

data(WarblerP)
data(WarblerG)

GdP<-GdataPed(WarblerG)

res1<-expression(varPed("offspring", restrict=0))
var1<-expression(varPed(c("lat", "long"), gender="Male", 
  relational="OFFSPRING"))
res2<-expression(varPed("terr", gender="Female", relational="OFFSPRING",
  restrict="=="))

PdP<-PdataPed(formula=list(var1,res1,res2), data=WarblerP, USsire=FALSE)

X.list<-getXlist(PdP=PdP, GdP=GdP, E2=0.005)

ped<-MLE.ped(X.list)
beta<-MLE.beta(X.list, ped) 
beta

[Package MasterBayes version 2.42 Index]