Description Usage Arguments Details Value Author(s) See Also Examples

Finds the mode of the posterior marginal distribution of parents

1 |

`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 [email protected]

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ```
## 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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