fit.epid.optim

An objective function, wrapped around <code>fit.epid()</code>, that will be passed to
<code><a href="/link/stats%3A%3Aoptim()?package=R0&version=1.3-1" data-mini-rdoc="R0::stats::optim()">stats::optim()</a></code> to jointly estimate the best-fitting R and GT distributions
in the context of the Maximum-Likelihood method from <code>est.R0.ML()</code>.

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.optim function

<dl><dt>par</dt>
<dd>A vector of three numerical values to be optimized, in the order <code>c(log.R, GT$mean, GT$sd)</code>.</dd>
<dt>...</dt>
<dd>Parameters passed to inner functions.</dd></dl>

Arguments

Author

An objective function, wrapped around <code>fit.epid()</code>, that will be passed to
<code><a href='https://rdrr.io/r/stats/optim.html'>stats::optim()</a></code> to jointly estimate the best-fitting R and GT distributions
in the context of the Maximum-Likelihood method from <code>est.R0.ML()</code>.

Joint estimation of R and generation time distribution for the ML method — fit.epid.optim

<dl>

<dt>par</dt>
<dd>A vector of three numerical values to be optimized, in the order <code>c(log.R, GT$mean, GT$sd)</code>.</dd>


<dt>...</dt>
<dd>Parameters passed to inner functions.</dd>

</dl>

fit.epid.optim: Joint estimation of R and generation time distribution for the ML method

Description

Usage

Value

Arguments

Author

Details