MCMC_fit_1.2: Second level wrapper for the MCMC fitting procedure. HIGHEST,...
In jameshay218/mcmcJH: Generic random walk MCMC algorithm for parameter inference

Description Usage Arguments Value See Also

This is the highest level wrapper function for the MCMC algorithm that can be applied to any generic model, data and likelihood function. Calls another function, MCMC_fit_single to carry out the random walk. This function takes care of formatting the results and carrying out some MCMC diagnostics and plots.

MCMC_fit_1.2(temp_dat, param_table, iterations = 1000, opt_freq = 50,
  thin = 1, burnin = 100, adaptive_period = 1, nchain = 1,
  popt = 0.44, filename, LIKELIHOOD_FUNCTION, MODEL_FUNCTION,
  VERBOSE = FALSE, PARALLEL = FALSE, OPTIM_PARAMS = FALSE,
  topdir = paste(getwd(), "/tmp/", sep = ""))

`temp_dat`	the data over which to calculate likelihoods
`param_table`	table of parameter data as specified in `load_param_table`
`iterations`	number of iterations for the MCMC algorithm
`opt_freq`	how frequently the acceptance rate is adapted. Defaults to 50
`thin`	thinning value for the MCMC chain. Default is 1
`burnin`	the length of the burn in period. Defaults to 100
`adaptive_period`	length of the adaptive period. Defaults to 1
`nchain`	number of chains to run
`popt`	the desired acceptance rate. Defaults to 0.44
`filename`	the generic file name/location at which to save plots and diagnostics. Note that the file extension will be appended to this string
`LIKELIHOOD_FUNCTION`	a valid pointer to an R function which returns a single, log likelihood of the data given the current parameters
`MODEL_FUNCTION`	a valid pointer to an R function which is used to evaluate the model for the current set of parameters
`VERBOSE`	boolean flag for additional output. Defaults to FALSE
`PARALLEL`	OPTIONAL boolean flag indicating if each MCMC chain should be run in parallel using doPar. Defaults to FALSE
`OPTIM_PARAMS`	OPTIONAL boolean flag indicating if optim should be used to find the "best fit" parameters. Otherwise the maximum likelihood parameters from the MCMC chain will be used. Defaults to FALSE
`topdir`	the top level directory where the MCMC chains will be saved. By default, a tmp folder will be created in the home folder