metric_calR

Computes a <code>n</code> by <code>n</code> matrix describing parasite dispersal from infecteds (columns)
to infectees (rows).
$$\mathcal{R} = b \beta \cdot {\cal V} \cdot \mbox{diag}\left(W \right) \cdot \beta^T \cdot \mbox{diag}\left(DH\right)$$

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

metric_calR function

<dl><dt>b</dt>
<dd>transmission efficiency from mosquitoes to humans</dd>
<dt>beta</dt>
<dd>the biting distribution matrix</dd>
<dt>calV</dt>
<dd>parasite dispersal by mosquitoes matrix (see metric_calV)</dd>
<dt>W</dt>
<dd>ambient human population at each patch</dd>
<dt>D</dt>
<dd>human transmitting capacity</dd>
<dt>H</dt>
<dd>human population size of each strata</dd></dl>

Arguments

Parasite Dispersal through one Parasite Generation (Humans) — metric_calR

<dl>

<dt>b</dt>
<dd>transmission efficiency from mosquitoes to humans</dd>


<dt>beta</dt>
<dd>the biting distribution matrix</dd>


<dt>calV</dt>
<dd>parasite dispersal by mosquitoes matrix (see metric_calV)</dd>


<dt>W</dt>
<dd>ambient human population at each patch</dd>


<dt>D</dt>
<dd>human transmitting capacity</dd>


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

</dl>

metric_calR: Parasite Dispersal through one Parasite Generation (Humans)

Description

Usage

Value

Arguments