MLE.beta | R Documentation |
Finds MLE for beta given a pedigree, via a call to optim. Beta is the paramater vector of a multinomial log-linear model.
MLE.beta(X.list, ped, beta=NULL, nUSdam=NULL, nUSsire=NULL, shrink=NULL)
X.list |
list of design matrices for each offspring derived using |
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. |
shrink |
optional scalar for the variance defining the ridge-regression likelihood penalisation. |
beta |
vector of MLE's for beta |
C |
large sample variance-covariance matrix of beta MLE's |
Jarrod Hadfield j.hadfield@ed.ac.uk
Hadfield J.D. et al (2006) Molecular Ecology 15 3715-31 Smouse P.E. et al (1999) Journal of Evolutionary Biology 12 1069-1077
MCMCped
, beta.loglik
## Not run: 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)$P beta<-MLE.beta(X.list, ped) beta ## End(Not run)
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