post.pairs: Returns pairs of individuals that fall into specific...

In MasterBayes: ML and MCMC Methods for Pedigree Reconstruction and Analysis

Returns pairs of individuals that fall into specific relatedness categories

Description

Computes posterior probabilities of pairs of indiviuals falling into specific relatedness categories (parent-offsping, sibs, full-sibs, half-sibs). Returns those pairs that have a posterior probability greater than some threshold.

Usage

post.pairs(postP, threshold=0, rel="PO")

Arguments

postP	joint posterior distribution of parentage
threshold	threshold probability over which related pairs are returned
rel	relatedness category. Currently "PO" (Parent-Offspring), "S" (Sibs), "FS" (Full-Sibs) and "HS" (Half-Sibs) are supported.

Value

P	pairs of indiviuals that fall into the rel category with posterior probability > threshold
prob	posterior probability

Author(s)

Jarrod Hadfield [e-mail]

See Also

modeP

Examples

## 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, write_postP="JOINT") 

fsib<-post.pairs(model1$P, threshol=0.9, rel="FS")
fsib$P

## End(Not run)

MasterBayes documentation built on June 22, 2022, 5:06 p.m.