make_parameters_MYZ_RM_ode

Make parameters for generalized RM ODE adult mosquito 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_MYZ_RM_ode 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>g</dt>
<dd>mosquito mortality rate</dd>
<dt>sigma</dt>
<dd>emigration rate</dd>
<dt>calK</dt>
<dd>mosquito dispersal matrix of dimensions <code>nPatches</code> by <code>nPatches</code></dd>
<dt>f</dt>
<dd>feeding rate</dd>
<dt>q</dt>
<dd>human blood fraction</dd>
<dt>nu</dt>
<dd>oviposition rate of gravid mosquitoes</dd>
<dt>eggsPerBatch</dt>
<dd>eggs laid per oviposition</dd>
<dt>tau</dt>
<dd>length of extrinsic incubation period</dd>
<dt>M0</dt>
<dd>total mosquito density at each patch</dd>
<dt>G0</dt>
<dd>gravid mosquito density at each patch</dd>
<dt>Y0</dt>
<dd>infected mosquito density at each patch</dd>
<dt>Z0</dt>
<dd>infectious mosquito density at each patch</dd></dl>

Arguments

Make parameters for generalized RM ODE adult mosquito model — make_parameters_MYZ_RM_ode

<dl>

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


<dt>g</dt>
<dd>mosquito mortality rate</dd>


<dt>sigma</dt>
<dd>emigration rate</dd>


<dt>calK</dt>
<dd>mosquito dispersal matrix of dimensions <code>nPatches</code> by <code>nPatches</code></dd>


<dt>f</dt>
<dd>feeding rate</dd>


<dt>q</dt>
<dd>human blood fraction</dd>


<dt>nu</dt>
<dd>oviposition rate of gravid mosquitoes</dd>


<dt>eggsPerBatch</dt>
<dd>eggs laid per oviposition</dd>


<dt>tau</dt>
<dd>length of extrinsic incubation period</dd>


<dt>M0</dt>
<dd>total mosquito density at each patch</dd>


<dt>G0</dt>
<dd>gravid mosquito density at each patch</dd>


<dt>Y0</dt>
<dd>infected mosquito density at each patch</dd>


<dt>Z0</dt>
<dd>infectious mosquito density at each patch</dd>

</dl>

make_parameters_MYZ_RM_ode: Make parameters for generalized RM ODE adult mosquito model

Description

Usage

Value

Arguments