modeP | R Documentation |
Finds the mode of the posterior marginal distribution of parents
modeP(postP, threshold=0, marginal=FALSE, USasNA=TRUE)
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? |
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.
P |
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) |
Jarrod Hadfield j.hadfield@ed.ac.uk
MCMCped
## 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 ## End(Not run)
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