create_scenario_list

An EpiModel scenario allows one or multiple set of parameters to be applied
to a model a predefined timesteps. They are usually used by a researcher who
wants to model counterfactuals using a pre calibrated model.

Tools for simulating mathematical models of infectious disease dynamics.
Epidemic model classes include deterministic compartmental models, stochastic
individual-contact models, and stochastic network models. Network models use the
robust statistical methods of exponential-family random graph models (ERGMs)
from the Statnet suite of software packages in R. Standard templates for epidemic
modeling include SI, SIR, and SIS disease types. EpiModel features an API for
extending these templates to address novel scientific research aims. Full
methods for EpiModel are detailed in Jenness et al. (2018, <doi:10.18637/jss.v084.i08>).

Samuel Jenness

EpiModel

Mathematical Modeling of Infectious Disease Dynamics

Steven M. Goodreau

Martina Morris

Adrien Le Guillou

Chad Klumb

Skye Bender-deMoll

create_scenario_list function

<dl><dt>scenarios.df</dt>
<dd>a <code>data.frame</code></dd></dl>

Arguments

The <code>scenarios.df</code> is a <code>data.frame</code> of values to be used as
parameters.
It must contain a ".at" column, specifying when the changes should occur.
It requires the "updater" module of EpiModel. See, vignette. If the ".at"
value of a row is less than two, the changes will be applied to the
parameter list iteself. The second mandatory column is ".scenario.id". It
is used to distinguish the different scenarios. If multiple rows share the
same ".scenario.id", the resulting scenario will contain one updater per row.
This permits modifying parameters at multiple points in time. (e.g. an
intervention limited in time).
The other column names must correspond either to:
the name of one parameter if this parameter is of size 1 or the name of the
parameter with "_1", "_2", "N" with the second part being the position of
the value for a parameter of size &gt; 1. This means that the parameter names
cannot contain any underscore "". (e.g "a.rate", "d.rate_1", "d.rate_2")

scenarios.df

Make a list of EpiModel scenarios from a data.frame of scenarios — create_scenario_list

<dl>

<dt>scenarios.df</dt>
<dd>a <code>data.frame</code></dd>

</dl>

The <code>scenarios.df</code> is a <code>data.frame</code> of values to be used as
parameters.
It must contain a ".at" column, specifying when the changes should occur.
It requires the "updater" module of EpiModel. See, vignette. If the ".at"
value of a row is less than two, the changes will be applied to the
parameter list iteself. The second mandatory column is ".scenario.id". It
is used to distinguish the different scenarios. If multiple rows share the
same ".scenario.id", the resulting scenario will contain one updater per row.
This permits modifying parameters at multiple points in time. (e.g. an
intervention limited in time).
The other column names must correspond either to:
the name of one parameter if this parameter is of size 1 or the name of the
parameter with "_1", "_2", "N" with the second part being the position of
the value for a parameter of size &gt; 1. This means that the parameter names
cannot contain any underscore "". (e.g "a.rate", "d.rate_1", "d.rate_2")

create_scenario_list: Make a list of EpiModel scenarios from a data.frame of scenarios

Description

Usage

Value

Arguments

scenarios.df