Run the main rmaverick MCMC. Model parameters are taken from the current active parameter set, and MCMC parameters are passed in as arguments. All output is stored within the project.

run_mcmc(
  project,
  K = 3,
  burnin = 100,
  samples = 1000,
  rungs = 10,
  GTI_pow = 2,
  auto_converge = TRUE,
  converge_test = ceiling(burnin/10),
  solve_label_switching_on = TRUE,
  coupling_on = TRUE,
  cluster = NULL,
  pb_markdown = FALSE,
  silent = FALSE
)

Arguments

project

an rmaverick project, as produced by the function mavproject()

K

the values of K that the MCMC will explore

burnin

the number of burn-in iterations

samples

the number of sampling iterations

rungs

the number of temperature rungs

GTI_pow

the power used in the generalised thermodynamic integration method. Must be greater than 1.1

auto_converge

whether convergence should be assessed automatically every converge_test iterations, leading to termination of the burn-in phase. If FALSE then the full burnin iterations are used

converge_test

test for convergence every convergence_test iterations if auto_converge is being used

solve_label_switching_on

whether to implement the Stevens' solution to the label-switching problem. If turned off then Q-matrix output will no longer be correct, although evidence estimates will be unaffected.

coupling_on

whether to implement Metropolis-coupling over temperature rungs

cluster

option to pass in a cluster environment (see package "parallel")

pb_markdown

whether to run progress bars in markdown mode, in which case they are updated once at the end to avoid large amounts of output.

silent

whether to suppress all console output