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mcmc_checks

mcmc_checks.Rd

Perform checks on MCMC inputs

Usage

mcmc_checks(
  log_params_ini = c(),
  n_regions = 1,
  prior_settings = list(type = "zero"),
  enviro_data = list(),
  add_values = list(vaccine_efficacy = 1, p_rep_severe = 1, p_rep_death = 1, m_FOI_Brazil
    = 1),
  extra_estimated_params = list()
)

Arguments

log_params_ini

Initial values of parameters to be estimated (natural logarithm of actual parameters; see documentation for MCMC() function for more details)

n_regions

Number of regions

prior_settings

List containing settings for priors; see documentation for MCMC() function for more details)

enviro_data

Data frame of values of environmental covariates (columns) by region (rows)

add_values

List of parameters in addition to those governing FOI/R0, either giving a fixed value or giving NA to indicate that they are part of the parameter set to be estimated
vaccine_efficacy Vaccine efficacy (proportion of reported vaccinations causing immunity) (must be present)
p_rep_severe Probability of observation of severe infection
p_rep_death Probability of observation of death
m_FOI_Brazil Multiplier of spillover FOI for Brazil regions (only relevant if regions in Brazil to be considered)

extra_estimated_params

Vector of names of parameters to be estimated in addition to those governing FOI and R0; see add_values

Details

This function, which is called by MCMC(), performs a number of checks on data to be used in fitting to ensure proper functionality. It verifies that the number of parameters being estimated is consistent with other settings and that certain values are not outwith sensible boundaries (e.g. probabilities must be between 0 and 1).