xDE_diffeqn

Compute derivatives for deSolve::ode or deSolve::dede using
generic methods for each model component. The arguments <code>EIR_delta</code> and <code>kappa_delta</code> are
for adding external forcing to the system from unmodeled sources. This can arise
if humans can acquire infection by traveling outside the spatial domain, and
arises for mosquitoes if traveling outside the spatial domain or are being infected
by unmodeled (non-human) sources. By default these are set to <code>NULL</code> and are
turned off.

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

xDE_diffeqn function

<dl><dt>t</dt>
<dd>current simulation time</dd>
<dt>y</dt>
<dd>state vector</dd>
<dt>pars</dt>
<dd>an <a href="/link/environment?package=exDE&version=1.0.0" data-mini-rdoc="exDE::environment">environment</a></dd>
<dt>EIR_delta</dt>
<dd>a vector of values to be added to the internal <code>EIR</code></dd>
<dt>kappa_delta</dt>
<dd>a vector of values to be added to the internal <code>kappa</code></dd></dl>

Arguments

Generalized spatial differential equation model — xDE_diffeqn

<dl>

<dt>t</dt>
<dd>current simulation time</dd>


<dt>y</dt>
<dd>state vector</dd>


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


<dt>EIR_delta</dt>
<dd>a vector of values to be added to the internal <code>EIR</code></dd>


<dt>kappa_delta</dt>
<dd>a vector of values to be added to the internal <code>kappa</code></dd>

</dl>

xDE_diffeqn: Generalized spatial differential equation model

Description

Usage

Value

Arguments