setup_humans_MOI

This is a queueing model (M/M/inf) of superinfection in humans.

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_MOI 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>MOI</dt>
<dd>a matrix giving the distribution of persons across strata (columns) and
multiplicity of infection (rows).</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>sigma</dt>
<dd>control non-independence of pathogen clearance; <code>sigma &gt; 1</code> indicates competition
(clearance is faster than independent) and <code>sigma &lt; 1</code> indicates facilitation (clearance is slower than independent).</dd></dl>

Arguments

Setup humans with MOI (multiplicity of infection) pathogen model — setup_humans_MOI

<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>MOI</dt>
<dd>a matrix giving the distribution of persons across strata (columns) and
multiplicity of infection (rows).</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>sigma</dt>
<dd>control non-independence of pathogen clearance; <code>sigma &gt; 1</code> indicates competition
(clearance is faster than independent) and <code>sigma &lt; 1</code> indicates facilitation (clearance is slower than independent).</dd>

</dl>

setup_humans_MOI: Setup humans with MOI (multiplicity of infection) pathogen model

Description

Usage

Value

Arguments