modeP: Posterior Mode of Parents

Description

Finds the mode of the posterior marginal distribution of parents

Usage

modeP(postP, threshold=0, marginal=FALSE, USasNA=TRUE)

Arguments

postP

posterior distribution of parentage

threshold

threshold probability under which ML parents are replaced by NA

marginal

logical; should the marginal mode be calculated from the joint distribution?

USasNA

logical; should usampled parents be replaced by NA?

Value

pedigree with id in the first column, and dam and sire in the second and third columns

prob

marginal posterior probability of the most likely parental combination (joint) or the most likely mother (marginal)

prob.male

marginal posterior probability of the most likely father (marginal)

Details

Individuals that do not have a parent assignment with a posterior probability exceeding the threshold, or whose parents belong to the base or unsampled population (if USasNA=TRUE), have NA as their parents. Please bear in mind that the mode of the marginal distribution (returned by MCMCped if write_postP="MARGINAL") may be different from the mode of the joint distribution (write_postP="JOINT"). For example the male that has the highest marginal probability (marginal with respect to potential mothers) may not be the male that is in the parental category (i.e. dam/sire combination) with the highest probability. If write_postP="JOINT" was sepcified, then the mode of the marginal distribution can be obtained by specifying marginal=TRUE. The modes are marginal with respect to other offspring and with multigenerational pedigrees may not coincide with the mode of the distribution of pedigrees.

Examples

Run this code

# NOT RUN {
data(WarblerP)
data(WarblerG)
GdP<-GdataPed(WarblerG)

var1<-expression(varPed(c("lat", "long"), gender="Male", 
  relational="OFFSPRING"))

# paternity is to be modelled as a function of distance 
# between offspring and male territories

res1<-expression(varPed("offspring", restrict=0))

# indivdiuals from the offspring generation are excluded as parents

res2<-expression(varPed("terr", gender="Female", relational="OFFSPRING", 
  restrict="=="))

# mothers not from the offspring territory are excluded
 
PdP<-PdataPed(formula=list(var1,res1,res2), data=WarblerP, USsire=FALSE)
tP<-tunePed(beta=30)

model1<-MCMCped(PdP=PdP, GdP=GdP, tP=tP, nitt=3000, thin=2, burnin=1000) 

ped<-modeP(model1$P, threshol=0.9)
ped
# }