priorPed {MasterBayes}R Documentation

priorPed Object

Description

An object containing the prior specifiactions for a model fitted using MCMCped. If prior distributions are not specified then improper priors are used, and a proper posterior distribution cannot be gauranteed.

Usage

priorPed(E1=999, E2=999, beta=list(mu=999, sigma=999),
         USdam=list(mu=999, sigma=999),  
         USsire=list(mu=999, sigma=999), ...)

Arguments

E1 matrix of parameters for the beta distribution specifying the prior distribution of allelic dropout for codominat markers or the probability of mis-scoring a dominant allele as recessive for dominant markers. Rows correspond to error rate categories, columns to the beta shape parameters. The order of rows in E1 are the order in which the error rate categories appear in the categories argument of GdataPed (see dbeta). If perlocus=TRUE was passed to GdataPed, then the error rate categories are replicated across loci
E2 matrix of parameters for the beta distribution specifying the prior distribution of stochastic genotyping error rates for codominat markers or the probability of mis-scoring a recessive allele as dominant for dominant markers. Rows correspond to error rate categories, columns to the beta shape parameters. The order of rows in E2 are the order in which the error rate categories appear in the categories argument of GdataPed (see dbeta). If perlocus=TRUE was passed to GdataPed, then the error rate categories are replicated across loci
beta list containing a vector for the mean, and a matrix for the variance-covariances of a multivariate normal distribution, that specifies the prior distribution for the population level parameters. The order of beta is the order in which the parameters appear in the MCMC ouput.
USdam list containing vectors of means and standard deviations for log normal distributions that specify the prior distribution for the number of unsampled females. The order of USdam is the order in which the unsampled dam populations appear in the USdam argument of PdataPed (see dlnorm)
USsire list containing vectors of means and standard deviations for log normal distributions that specify the prior distribution for the number of unsampled males. The order of USsire is the order in which the unsampled sire populations appear in the USsire argument of PdataPed (see dlnorm)
... further arguments to be passed

Value

list containing the arguments passed

Author(s)

Jarrod Hadfield j.hadfield@ed.ac.uk

See Also

MCMCped

Examples

# When each individual has only been genotyped once, and no pedigree 
# information exists, there is virtually no information available
# to estimate error rates.  The tiny amount of information comes 
# (dangerously) from the assumption of Hardy-Weinburg equilibrium.  
# The posterior distribution is similar to the prior:

data(WarblerG)
A<-extractA(WarblerG)

ped<-matrix(NA, 100,3)
ped[,1]<-1:100

G<-simgenotypes(A, E1=0.01, E2=0.01, ped=ped, no_dup=1)
GdP<-GdataPed(G=G$Gobs, id=G$id)
pP<-priorPed(E1=matrix(c(40,1600), nrow=1), E2=matrix(c(40,1600), nrow=1))

model1<-MCMCped(GdP=GdP, pP=pP)

#The posterior distribution recovers the prior distribution 

summary(model1$E1)
quantile(rbeta(1000, 40, 1600), prob=c(0.025, 0.25, 0.5, 0.75, 0.975))


[Package MasterBayes version 2.42 Index]