setup_humans_SIP

A simple SIP (Susceptible-Infected-Protected) 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_SIP 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>SIP</dt>
<dd>matrix of strata (rows) by health states (SIP)</dd>
<dt>b</dt>
<dd>transmission efficiency (mosquito to human)</dd>
<dt>c</dt>
<dd>transmission efficiency (human to mosquito)</dd>
<dt>r</dt>
<dd>recovery rate (inverse of infectious duration)</dd>
<dt>rho</dt>
<dd>probability of treatment upon infection</dd>
<dt>eta</dt>
<dd>rate at which prophylaxis decays</dd></dl>

Arguments

Setup humans with SIP pathogen model — setup_humans_SIP

<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>SIP</dt>
<dd>matrix of strata (rows) by health states (SIP)</dd>


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


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


<dt>r</dt>
<dd>recovery rate (inverse of infectious duration)</dd>


<dt>rho</dt>
<dd>probability of treatment upon infection</dd>


<dt>eta</dt>
<dd>rate at which prophylaxis decays</dd>

</dl>

setup_humans_SIP: Setup humans with SIP pathogen model

Description

Usage

Value

Arguments