fit.epid

Computes the Poisson log-likelihood of an observed epidemic, compared to the
expected incidence values for a given R and generation time distirbution.

internal

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

fit.epid function

<dl><dt>log.R</dt>
<dd>The log-reproduction ratio.</dd>
<dt>epid</dt>
<dd>An epidemic curve, in the sense of passing <code>check.incid()</code> validations. It must have at least an incidence vector in an <code>incid</code> component.</dd>
<dt>GT</dt>
<dd>Generation time distribution from <code>generation.time()</code>.</dd>
<dt>import</dt>
<dd>Vector of imported cases</dd>
<dt>pred</dt>
<dd>Boolean. By default (<code>FALSE</code>), the function returns the corresponding log-likelihood. When set to <code>TRUE</code>, the function will return the Poisson-predicted incidence series instead.</dd>
<dt>offset</dt>
<dd>Offset value for the log-likelihood (used to calculate confidence intervals).</dd></dl>

Arguments

Author

Poisson log-likelihood for an observed epidemic — fit.epid

<dl>

<dt>log.R</dt>
<dd>The log-reproduction ratio.</dd>


<dt>epid</dt>
<dd>An epidemic curve, in the sense of passing <code>check.incid()</code> validations. It must have at least an incidence vector in an <code>incid</code> component.</dd>


<dt>GT</dt>
<dd>Generation time distribution from <code>generation.time()</code>.</dd>


<dt>import</dt>
<dd>Vector of imported cases</dd>


<dt>pred</dt>
<dd>Boolean. By default (<code>FALSE</code>), the function returns the corresponding log-likelihood. When set to <code>TRUE</code>, the function will return the Poisson-predicted incidence series instead.</dd>


<dt>offset</dt>
<dd>Offset value for the log-likelihood (used to calculate confidence intervals).</dd>

</dl>

fit.epid: Poisson log-likelihood for an observed epidemic

Description

Usage

Value

Arguments

Author

Details