hpySampler: Hierarchical Pitman-Yor Gibbs sampler

In kevinmcgregor/hpy: Hierarchical Pitman Yor Model for Microbial Abundance Data

Description

Hierarchical Pitman-Yor Gibbs sampler

Usage

hpySampler(
  Y,
  n.iter,
  n.burn,
  p.shape,
  p.scale,
  p.shape.pop = NULL,
  p.scale.pop = NULL,
  type = c("py", "dp"),
  quiet = FALSE
)

Arguments

Y	Matrix of taxon counts (rows are populations, columns are species)
n.iter	Number of MCMC iterations (after burn-in)
n.burn	Number of burn-in iterations
p.shape	Shape parameter for gamma prior on top-level concentration parameter
p.scale	Scale parameter for gamma prior on top-level concentration parameter
p.shape.pop	Vector with length equal to number of populations containing shape parameters for gamma priors on population-level concentration parameter
p.scale.pop	Vector with length equal to number of populations containing scale parameters for gamma priors on population-level concentration parameter
type	Type of hierarchical process: "py" for Pitman-Yor process, "dp" for Dirichlet process
quiet	Set to TRUE to suppress console output

Value

Returns a list containing the following elements:

• gamma, alpha, theta, sigma - Vectors containing posterior samples for each of the HPY parameters.

• tab - List with table indicators for each population.

• t.c - Table counts (and species corresponding to each table)

• n.tab - Number of tables in each population

• n.s.tab - Number of tables for a given species in each population

kevinmcgregor/hpy documentation built on Feb. 4, 2022, 4:46 a.m.