GibbsSamplingAfterBurnin: Start Gibbs sampling on one chain after burnin

In steverozen/mSigHdp: Mutational signature discovery using HDP (hierarchical Dirichlet process)

Start Gibbs sampling on one chain after burnin

Description

This function might be used to start Gibbs sampling after ExtendBurnin.

Usage

GibbsSamplingAfterBurnin(
  burnin.output,
  post.n,
  post.space,
  post.cpiter = 3,
  post.verbosity = 0,
  seedNumber = NULL
)

Arguments

burnin.output	A path to burnin checkpoint Rdata or to an S4 object from Burnin.
post.n	The number of posterior samples to collect.
post.space	The number of iterations between collected samples.
post.cpiter	The number of iterations of concentration parameter sampling to perform after each main Gibbs-sample iteration. (See Teh et al., "Hierarchical Dirichlet Processes", Journal of the American Statistical Association 2006;101(476):1566-1581 (https://doi.org/10.1198/016214506000000302).)
post.verbosity	Verbosity of debugging statements. No need to change unless for testing or debugging.
seedNumber	A random seed that ensures reproducible results.

Value

An hdpSampleChain S4 object with the salient information from each posterior sample. See hdpSampleChain-class in package hdpx.

steverozen/mSigHdp documentation built on Feb. 6, 2023, 1:36 a.m.