fitSARS: Driver Routine - Fitting a Single Plague Incidence Profile

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

Description

A driver for fitting a single cholera incidence profile of a region/patch. The R code calls a Fortran routine which uses an MCMC procedure to maximize the likelihood of the solution using and seir mode.

Usage

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

Arguments

mydata	A list containing all available information for the region: incidence, specific-humidity, school schedule, population etc.
opt.list	A Logical list with TRUE or FALSE values for all the parameters supported by DICE. These values are set based on the user chosen model for the compartmental model and the force of infection.
run.list	A list with parameters needed for the MCMC procedure
ireal	Integer - the MCMC chain number. Default is 1.
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 data

model_profile

Randomly selected results from the MCMC procedure of fitting the data

tab.model

The MCMC history of fitting the data

Examples

fitPlague{mydata = mydata, opt.list = opt.list, run.list = run.list, ireal = ireal, iseed = iseed}

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