run_mcmc: Run main MCMC

In bobverity/MALECOT: Joint estimation of COI and population structure for malaria genetic data

Description

Run the main MALECOT 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.

Usage

run_mcmc(project, K = NULL, precision = 0.01, burnin = 1000,
  samples = 1000, rungs = 1, GTI_pow = 3, auto_converge = TRUE,
  converge_test = 100, solve_label_switching_on = TRUE,
  coupling_on = TRUE, cluster = NULL, pb_markdown = FALSE,
  store_acceptance = TRUE, store_raw = TRUE, silent = FALSE)

Arguments

project	a MALECOT project, as produced by the function malecot_project()
K	the values of K that the MCMC will explore
precision	the level of precision at which allele frequencies are represented in the bi-allelic case. This allows the use of look-up tables for the likelihood, which significantly speeds up the MCMC. Set to 0 to use exact values (up to C++ "double" precision) rather than using look-up tables
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
store_acceptance	whether to store acceptance rates for all parameters updated by Metropolis-Hastings. Proposal distributions are tuned adaptively with a target acceptance rate of 23%
store_raw	whether to store raw MCMC output in addition to summary output. Setting to FALSE can considerably reduce output size in memory
silent	whether to suppress all console output

Examples

# TODO

bobverity/MALECOT documentation built on May 13, 2019, 4:01 a.m.