sim.epid.indiv

Generates several epidemic curves with an individual-based model.

Estimation of reproduction numbers for disease outbreak, based on
incidence data. The R0 package implements several documented methods. It is
therefore possible to compare estimations according to the methods used.
Depending on the methods requested by user, basic reproduction number
(commonly denoted as R0) or real-time reproduction number (referred to as
R(t)) is computed, along with a 95% Confidence Interval. Plotting outputs
will give different graphs depending on the methods requested : basic
reproductive number estimations will only show the epidemic curve
(collected data) and an adjusted model, whereas real-time methods will also
show the R(t) variations throughout the outbreak time period. Sensitivity
analysis tools are also provided, and allow for investigating effects of
varying Generation Time distribution or time window on estimates.

Thomas Obadia

Estimation of R0 and Real-Time Reproduction Number from
Epidemics

sim.epid.indiv function

<dl><dt>beta</dt>
<dd>Contact rate in the SEIR model.</dd>
<dt>Tmax</dt>
<dd>Maximum length of the epidemic (cases infected after this length will be truncated).</dd>
<dt>n</dt>
<dd>Number of epidemics to be simulated (defaults to 1)</dd>
<dt>family</dt>
<dd>Distribution of offspring. Can be either <code>"poisson"</code> (default) or <code>"negbin"</code>.</dd>
<dt>negbin.size</dt>
<dd>If family is set to "negbin", sets the size parameter of the negative binomial distribution.</dd></dl>

Arguments

Author

Influenza-like illness simulation (individual-based model) — sim.epid.indiv

<dl>

<dt>beta</dt>
<dd>Contact rate in the SEIR model.</dd>


<dt>Tmax</dt>
<dd>Maximum length of the epidemic (cases infected after this length will be truncated).</dd>


<dt>n</dt>
<dd>Number of epidemics to be simulated (defaults to 1)</dd>


<dt>family</dt>
<dd>Distribution of offspring. Can be either <code>"poisson"</code> (default) or <code>"negbin"</code>.</dd>


<dt>negbin.size</dt>
<dd>If family is set to "negbin", sets the size parameter of the negative binomial distribution.</dd>

</dl>

sim.epid.indiv: Influenza-like illness simulation (individual-based model)

Description

Usage

Value

Arguments

Author

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