gibbs_gl_alt: Gibbs sampler under the alternative of non-random mating...

In hwep: Hardy-Weinberg Equilibrium in Polyploids

Gibbs sampler under the alternative of non-random mating using genotype log-likelihoods.

Description

Gibbs sampler under the alternative of non-random mating using genotype log-likelihoods.

Usage

gibbs_gl_alt(
  gl,
  beta,
  B = 10000L,
  T = 1000L,
  more = FALSE,
  lg = FALSE,
  verbose = TRUE
)

Arguments

gl	The matrix of genotype log-likelihoods. The columns index the dosages and the rows index the individuals. gl[i,j] is the genotype log-likelihood for individual i at dosage j. It is assumed that natural log is used.
beta	The concentration hyperparameter for the genotype frequencies.
B	The number of sampling iterations.
T	The number of burn-in iterations.
more	A logical. Should we also return posterior draws (TRUE) or not (FALSE).
lg	Should we return the log marginal likelihood (true) or not (false).
verbose	A logical. Should we print the progress?

Value

A list with some or all of the following elements

• mx: The estimate of the marginal likelihood

Author(s)

David Gerard

Examples

set.seed(1)
ploidy <- 8

## Simulate under the alternative
q <- stats::runif(ploidy + 1)
q <- q / sum(q)
nvec <- c(stats::rmultinom(n = 1, size = 100, prob = q))
gl <- simgl(nvec)

gibbs_gl_alt(gl = gl, beta = rep(1, ploidy + 1), lg = TRUE)

hwep documentation built on May 31, 2023, 9:06 p.m.