mcmc | R Documentation |
Run a mcmc sampler
mcmc(pars, n_steps, compare = NULL, progress = FALSE, n_chains = 1)
pars |
A ['mcmc_parameters'] object containing information about parameters ( parameter ranges, priors, proposal kernel, observation functions). |
n_steps |
Number of MCMC steps to run |
compare |
likelihood function to compare data to epidemic trajectory should return a single value representing the log-likelihood. Default is compare_basic() |
progress |
Logical, indicating if a progress bar should be displayed, using ['progress::progress_bar']. |
n_chains |
Optional integer, indicating the number of chains to run. If more than one then we run a series of chains and merge them with [mcmc_combine()]. Chains are run in series, with the same model. |
This is a basic Metropolis-Hastings MCMC sampler. The 'model' is run with a set of parameters to evaluate the likelihood. A new set of parameters is proposed, and these likelihoods are compared, jumping with probability equal to their ratio. This is repeated for 'n_steps' proposals.
This function is adapted from the 'pmcmc' in the mcstate package https://github.com/mrc-ide/mcstate
A 'gonovax_mcmc' object containing 'pars' (sampled parameters) and 'probabilities' (log prior, log likelihood and log posterior values for these probabilities).
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