setup_humans_SIR

A simple SIR (Susceptible-Infected-Recovered) model

Provides a framework based on S3 dispatch for constructing models
of mosquito-borne pathogen transmission which are constructed from submodels of various
components (i.e. immature and adult mosquitoes, human populations). A consistent mathematical
expression for the distribution of bites on hosts means that different models
(stochastic, deterministic, etc.) can be coherently incorporated and updated
over a discrete time step.

Sean L. Wu

MicroMoB

Discrete Time Simulation of Mosquito-Borne Pathogen Transmission

David L. Smith

Sophie Libkind

setup_humans_SIR function

<dl><dt>model</dt>
<dd>an object from make_MicroMoB</dd>
<dt>stochastic</dt>
<dd>should the model update deterministically or stochastically?</dd>
<dt>theta</dt>
<dd>a time spent matrix</dd>
<dt>wf</dt>
<dd>biting weights</dd>
<dt>H</dt>
<dd>vector of strata population sizes</dd>
<dt>SIR</dt>
<dd>a matrix giving S, I, R counts (columns) for each strata (rows)</dd>
<dt>b</dt>
<dd>transmission efficiency (mosquito to human)</dd>
<dt>c</dt>
<dd>transmission efficiency (human to mosquito)</dd>
<dt>gamma</dt>
<dd>rate of recovery</dd></dl>

Arguments

Setup humans with SIR infection model — setup_humans_SIR

<dl>

<dt>model</dt>
<dd>an object from make_MicroMoB</dd>


<dt>stochastic</dt>
<dd>should the model update deterministically or stochastically?</dd>


<dt>theta</dt>
<dd>a time spent matrix</dd>


<dt>wf</dt>
<dd>biting weights</dd>


<dt>H</dt>
<dd>vector of strata population sizes</dd>


<dt>SIR</dt>
<dd>a matrix giving S, I, R counts (columns) for each strata (rows)</dd>


<dt>b</dt>
<dd>transmission efficiency (mosquito to human)</dd>


<dt>c</dt>
<dd>transmission efficiency (human to mosquito)</dd>


<dt>gamma</dt>
<dd>rate of recovery</dd>

</dl>

setup_humans_SIR: Setup humans with SIR infection model

Description

Usage

Value

Arguments