haiti3_spatPomp: Build pomp object for model 3.

In zjiang2/haitipkg: R Package for Haiti Article

Build pomp object for model 3.

Description

Generate a ‘spatPomp’ object for fitting to Haiti cholera data. This model is a stochastic compartmental model applied at the level of the ten Haitian departments. It is the stochastic translation of a deterministic SIRB model based on Ordinary Differential Equations (ODEs), and has been implemented as a discrete-state model based on a Partially-Observed Markov Process (POMP), simulating the stochastic transitions between compartments as discrete events.

Usage

haiti3_spatPomp(dt_years = 1/365.25, start_date = "2010-11-20")

Arguments

dt_years	step size, in years, for the Euler approximation.
start_date	Date of the first observation that will be modeled. All prior observations are used to initialize the latent states.

Details

The model subdivides the population of each department into compartments counting the number of individuals at the different stages of the disease: Susceptible individuals (S), Infected symptomatic (I), infected Asymptomatic (A), and Recoverd (R). The main feature of this model is that it contains an environmental compartment describing the bacterial concentration (B) in the local environment, which is used to estimate the force of infection.

This model removes the redundancy in the Recovered compartments found in the original code.

This model was developed by Lemaitre, Joseph, et. al at the Laboratory of Ecohydrology, Ecole Polytechnique Federale de Lausanne (CH).

Value

spatPomp representation of model 3 described in Lee, Elizabeth et. al. and it's accompanying Supplemental Material.

See Also

haiti2 and haiti1 for other models used to fit the cholera epidemic in Haiti.

Examples

## Not run: mod3 <- haiti3_spatPomp()

zjiang2/haitipkg documentation built on March 1, 2024, 11:34 p.m.