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Combined MCMC Multi-Region - series of MCMC iterations for one or more regions

Usage

MCMC(
  params_data = data.frame(name = "FOI_var1", initial = 1, max = Inf, min = -Inf, mean =
    0, sd = 1, estimate = TRUE),
  input_data = list(),
  obs_sero_data = NULL,
  obs_case_data = NULL,
  filename_prefix = "Chain",
  Niter = 1,
  mode_start = 1,
  time_inc = 1,
  n_reps = 1,
  enviro_data_const = list(),
  enviro_data_var = list(),
  deterministic = FALSE,
  mode_time = 1,
  mode_parallel = FALSE,
  cluster = NULL
)

Arguments

params_data

#Data frame of parameter information containing names, initial values, maximum and minimum values, mean and standard deviation (for prior calculation) and flag indicating whether parameter estimated or fixed
Parameters to include: coefficients of environmental covariates to calculate FOI_spillover and R0, reported vaccination effectiveness, probability of severe case reporting, probability of fatal case reporting, Brazil FOI_spillover multiplier, FOI_spillover and R0 (latter two never estimated, included only for priors)
TBA - instructions

input_data

List of population and vaccination data for multiple regions (created using data input creation code and usually loaded from RDS file)

obs_sero_data

Seroprevalence data for comparison, by region, year & age group, in format no. samples/no. positives (TBA - instructions)

obs_case_data

Annual reported case/death data for comparison, by region and year, in format no. cases/no. deaths (TBA - instructions)

filename_prefix

Prefix of output RDS file name, e.g. "Chain.Rds"

Niter

Total number of iterations to run

mode_start

Flag indicating how to set initial population immunity level in addition to vaccination
If mode_start = 0, only vaccinated individuals
If mode_start = 1, shift some non-vaccinated individuals into recovered to give herd immunity (stratified by age)
If mode_start = 2, use SEIRV input in list from previous run(s)

time_inc

time increment in days (must be 1 or 5)

n_reps

Number of times to repeat calculations to get average likelihood at each iteration

enviro_data_const

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

enviro_data_var

List containing time-varying environmental covariate data:
regions: Vector of region labels
env_vars: Vector of covariate names
values: Array of covariate values with dimensions (number of covariates, number of regions, number of time points). Number of time points must be correct for mode_time setting.

deterministic

TRUE/FALSE - set model to run in deterministic mode if TRUE

mode_time

Type of time dependence of FOI_spillover and R0 to be used:
If mode_time = 0, no time variation (constant values)
If mode_time = 1, FOI/R0 vary annually without seasonality (number of values = number of years to consider)
If mode_time = 2, FOI/R0 vary with monthly seasonality without inter-annual variation (number of values = 12)
If mode_time = 3, FOI/R0 vary with daily seasonality without inter-annual variation (number of values = 365/dt)
If mode_time = 4, FOI/R0 vary annually with monthly seasonality (number of values = 12*number of years to consider)
If mode_time = 5, FOI/R0 vary annually with daily seasonality (number of values = (365/dt)*number of years to consider)

mode_parallel

TRUE/FALSE - indicate whether to use parallel processing on supplied cluster for speed

cluster

Cluster of threads to use if mode_parallel = TRUE '

Details

This is the master function for running a Markov chain to optimize the parameters of the yellow fever model based on the calculated likelihood of observing supplied data given a particular set of parameters.