make_parameters_X_SIP

Make parameters for SIP human model

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_SIP 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>c</dt>
<dd>transmission probability (efficiency) from human to mosquito</dd>
<dt>r</dt>
<dd>recovery rate</dd>
<dt>rho</dt>
<dd>probability of successful treatment upon infection</dd>
<dt>eta</dt>
<dd>prophylaxis waning rate</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>X0</dt>
<dd>size of infected population in each strata</dd>
<dt>P0</dt>
<dd>size of population protected by prophylaxis in each strata</dd>
<dt>H</dt>
<dd>size of human population in each strata</dd></dl>

Arguments

Make parameters for SIP human model — make_parameters_X_SIP

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


<dt>r</dt>
<dd>recovery rate</dd>


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


<dt>eta</dt>
<dd>prophylaxis waning rate</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>X0</dt>
<dd>size of infected population in each strata</dd>


<dt>P0</dt>
<dd>size of population protected by prophylaxis in each strata</dd>


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

</dl>

make_parameters_X_SIP: Make parameters for SIP human model

Description

Usage

Value

Arguments