sim_trajectory_base_R_decoupled_SIS

This is an internal function to <code>sim_trajectory_R</code>. It does the
actual sampling once all of the functions have been checked and setup.

A simulation modeling framework which significantly extends capabilities from the
'MGDrivE' simulation package via a new mathematical and computational framework based on stochastic Petri nets.
For more information about 'MGDrivE', see our publication: Sánchez et al. (2019) <doi:10.1111/2041-210X.13318>
Some of the notable capabilities of 'MGDrivE2' include: incorporation of human populations,
epidemiological dynamics, time-varying parameters, and a continuous-time simulation
framework with various sampling algorithms for both deterministic and stochastic interpretations.
'MGDrivE2' relies on the genetic inheritance structures provided in package 'MGDrivE', so we
suggest installing that package initially.

Agastya Mondal

MGDrivE2

Mosquito Gene Drive Explorer 2

Sean L. Wu

Jared B. Bennett

Héctor Manuel Sánchez Castellanos

Tomás M. León

Andrew J. Dolgert

John M. Marshall

sim_trajectory_base_R_decoupled_SIS function

<dl><dt>x0</dt>
<dd>the initial marking of the SPN (initial state)</dd>
<dt>h0</dt>
<dd>initial human state distribution</dd>
<dt>SPN_P</dt>
<dd>stochastic petri net, places</dd>
<dt>theta</dt>
<dd>parameters</dd>
<dt>times</dt>
<dd>sequence of sampling times</dd>
<dt>num_reps</dt>
<dd>number of repetitions to run</dd>
<dt>stepFun</dt>
<dd>a sampling function</dd>
<dt>events</dt>
<dd>a <code>data.frame</code> of events (uses the same format as required in package <code>deSolve</code> for consistency, see <code>events</code> for more information)</dd>
<dt>batch</dt>
<dd>a <code>list</code> of batch migration events, created from <code>batch_migration</code>, may be set to <code>NULL</code> if not used</dd>
<dt>Sout</dt>
<dd>an optional matrix to track event firings</dd>
<dt>verbose</dt>
<dd>print a progress bar?</dd>
<dt>cube</dt>
<dd>inheritance cube</dd></dl>

Arguments

Simulate Trajectory From one SPN Model using Human SIS model — sim_trajectory_base_R_decoupled_SIS

<dl>

<dt>x0</dt>
<dd>the initial marking of the SPN (initial state)</dd>


<dt>h0</dt>
<dd>initial human state distribution</dd>


<dt>SPN_P</dt>
<dd>stochastic petri net, places</dd>


<dt>theta</dt>
<dd>parameters</dd>


<dt>times</dt>
<dd>sequence of sampling times</dd>


<dt>num_reps</dt>
<dd>number of repetitions to run</dd>


<dt>stepFun</dt>
<dd>a sampling function</dd>


<dt>events</dt>
<dd>a <code>data.frame</code> of events (uses the same format as required in package <code>deSolve</code> for consistency, see <code>events</code> for more information)</dd>


<dt>batch</dt>
<dd>a <code>list</code> of batch migration events, created from <code>batch_migration</code>, may be set to <code>NULL</code> if not used</dd>


<dt>Sout</dt>
<dd>an optional matrix to track event firings</dd>


<dt>verbose</dt>
<dd>print a progress bar?</dd>


<dt>cube</dt>
<dd>inheritance cube</dd>

</dl>

sim_trajectory_base_R_decoupled_SIS: Simulate Trajectory From one SPN Model using Human SIS model

Description

Usage

Value

Arguments