make_parameters_X_hMoI

MoI stands for Multiplicity of Infection, and refers to malarial superinfection.

Provides tools to set up modular ordinary and delay differential equation
models for mosquito-borne pathogens, focusing on malaria. Modular design is achieved
by S3 dispatch on parameter lists for each component which is used to compute
the full set of differential equations which may be solved using
any of the packages for numerical simulation of differential equations in R. The
methods implemented by this package are described in Wu et al. (2022) <doi:10.1101/2022.11.07.22282044>.

Sean L. Wu

exDE

Extensible Differential Equations for Mosquito-Borne Pathogen
Modeling

David L. Smith

make_parameters_X_hMoI function

<dl><dt>pars</dt>
<dd>an <a href="/link/environment?package=exDE&version=1.0.0" data-mini-rdoc="exDE::environment">environment</a></dd>
<dt>b</dt>
<dd>transmission probability (efficiency) from mosquito to human</dd>
<dt>c1</dt>
<dd>transmission probability (efficiency) from inapparent human infections to mosquito</dd>
<dt>c2</dt>
<dd>transmission probability (efficiency) from patent human infections to mosquito</dd>
<dt>r1</dt>
<dd>recovery rate from inapparent infections</dd>
<dt>r2</dt>
<dd>recovery rate from patent infections</dd>
<dt>Psi</dt>
<dd>a <a href="/link/matrix?package=exDE&version=1.0.0" data-mini-rdoc="exDE::matrix">matrix</a> of dimensions <code>nPatches</code> by <code>nStrata</code></dd>
<dt>wf</dt>
<dd>vector of biting weights of length <code>nStrata</code></dd>
<dt>m10</dt>
<dd>mean MoI among inapparent human infections</dd>
<dt>m20</dt>
<dd>mean MoI among patent human infections</dd>
<dt>H</dt>
<dd>size of human population in each strata</dd></dl>

Arguments

Make parameters for hybrid MoI human model — make_parameters_X_hMoI

<dl>

<dt>pars</dt>
<dd>an <a href='https://rdrr.io/r/base/environment.html'>environment</a></dd>


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


<dt>c1</dt>
<dd>transmission probability (efficiency) from inapparent human infections to mosquito</dd>


<dt>c2</dt>
<dd>transmission probability (efficiency) from patent human infections to mosquito</dd>


<dt>r1</dt>
<dd>recovery rate from inapparent infections</dd>


<dt>r2</dt>
<dd>recovery rate from patent infections</dd>


<dt>Psi</dt>
<dd>a <a href='https://rdrr.io/r/base/matrix.html'>matrix</a> of dimensions <code>nPatches</code> by <code>nStrata</code></dd>


<dt>wf</dt>
<dd>vector of biting weights of length <code>nStrata</code></dd>


<dt>m10</dt>
<dd>mean MoI among inapparent human infections</dd>


<dt>m20</dt>
<dd>mean MoI among patent human infections</dd>


<dt>H</dt>
<dd>size of human population in each strata</dd>

</dl>

make_parameters_X_hMoI: Make parameters for hybrid MoI human model

Description

Usage

Value

Arguments