runSyntheticSingle: Driver Routine Uncoupled Spatial Model - Synthetic Data

In predsci/DICE: DICE: Dynamics of Interacting Community Epidemics

Description

A spatailly uncoupled MCMC fit of synthetic data. The code first fits the model data directly and then fits each of the sub-regions sequentially - minimizing the likelihood of each one. The final indirect model fit is obtained as a weighted sum of these individual fits with the weights given by the relative population of each region. The data is synthetic (although it has the dataType 'cdc'). This synthetic example has been set up for the case of fit_level = 3 and mod_level = 2, that is fit the national data using the ten uncoupled HHS regions

Usage

runSyntheticSingle(mydata = NULL, opt.list = NULL, run.list = NULL,
  ireal = 1, iseed = NULL)

Arguments

mydata	A complex list with all the data for a single season. Everything except the number of cases and %ILI is from the 'cdc' dataType and will not be replaced. Only the number of cases and the %ILI will be replaced by syntehtic profiles
opt.list	A Logical list with TRUE or FALSE values for all the parameters supported by DICE. The synthetic example has been set-up for model = 4
run.list	A list with parameters needed for the MCMC procedure #' @param iseed An integer used to set the random-number-generator seed. When not specified, the seed is generated randomly. Setting the seed to a known integer allows an MCMC chain to be reproducible.

Value

A list with the following arguments:

model_rtn

The best result of the MCMC procedure for the model synthetic data

model_profile

Randomly selected results from the MCMC procedure of directly fitting the model synthetic data

tab.model

The MCMC history of the direct fit to the model synthetic data

fit_rtn

The best result for indirectly fitting the model synthetic data using the synthetic fit regions

fit_profile

Randomly selected results from the MCMC procedure of indirectly fitting the model data using the fit regions

tab.fit

The MCMC history of indirectly fitting the model data using the fit regions

Examples

runSyntheticSingle{mydata = mydata, opt.list = opt.list, run.list = run.list, ireal = 1}

predsci/DICE documentation built on Aug. 9, 2019, 9:41 a.m.