SinglefReject: Samples from the posterior for the single f model

In HWEBayes: Bayesian investigation of Hardy-Weinberg Equilibrium via estimation and testing.

Description

Function to generate samples from the posterior for allele frequencies and f, under the single f model. Samples are generated using a rejection algorithm that simulates from the prior.

Usage

SinglefReject(nsim, bvec, lambdamu, lambdasd, nvec)

Arguments

nsim	number of samples to generate from the prior.
bvec	vector of size k that is the specification for the Dirichlet prior on the allele frequencies.
lambdamu	prior mean for λ.
lambdasd	prior standard deviation for λ.
nvec	vector of genotype frequencies in the order n_{11}, n_{21}, n_{22}, ..., n_{k1}, n_{k2}, ..., n_{kk}.

Value

psamp	samples for k allele frequencies.
fsamp	samples for inbreeding coefficient f.
accrate	acceptance rate of the rejection algorithm.
PrnH1	estimate of normalizing constant (which may be used in Bayes factor calculations). Calculated by averaging the likelihood over the sampled points.
varest	estimated variance of the estimate of the normalizing constant.

Author(s)

Jon Wakefield ([e-mail])

References

Wakefield, J. (2010). Bayesian methods for examining Hardy-Weinberg equilibrium. Biometrics; Vol 66:257-65

Examples

data(DiabRecess)
postsampf1 <- SinglefReject(nsim=100,bvec=rep(1,4),lambdamu=-2.95,
   lambdasd=1.07,nvec=DiabRecess)

HWEBayes documentation built on May 2, 2019, 11:07 a.m.