Run main MCMC — run_mcmc • rmaverick

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