plot_effective_reproduction_number

Computes and visualizes the effective reproduction number (Rt) over time
using incidence data and generation time distribution. Optionally overlays
a smoothed spline curve.

Provides various functions for parameter estimation of one-dimensional
stable distributions and their mixtures. It implements a diverse set of
estimation methods, including quantile-based approaches, regression methods
based on the empirical characteristic function (empirical, kernel, and
recursive), and maximum likelihood estimation. For mixture models, it provides
stochastic expectation–maximization (SEM) algorithms and Bayesian estimation
methods using sampling and importance sampling to overcome the long burn-in
period of Markov Chain Monte Carlo (MCMC) strategies. The package also includes
tools and statistical tests for analyzing whether a dataset follows a stable
distribution. Some of the implemented methods are described in
Hajjaji, O., Manou-Abi, S. M., and Slaoui, Y. (2024) <doi:10.1080/02664763.2024.2434627>.

Solym Manou-Abi

MixStable

Parameter Estimation for Stable Distributions and Their Mixtures

Adam Najib

Yousri Slaoui

plot_effective_reproduction_number function

<dl><dt>GT</dt>
<dd>Numeric vector. Generation time distribution.</dd>
<dt>S</dt>
<dd>Numeric vector. Secondary cases.</dd>
<dt>inc</dt>
<dd>Numeric vector. Incidence time series.</dd>
<dt>dates</dt>
<dd>Date vector corresponding to observations.</dd>
<dt>est_r0_ml</dt>
<dd>Function to estimate R0.</dd>
<dt>RT</dt>
<dd>Function to compute Rt.</dd>
<dt>output_file</dt>
<dd>Output PDF filename.</dd></dl>

Arguments

Plot effective reproduction number (Re) over time — plot_effective_reproduction_number

<dl>

<dt>GT</dt>
<dd>Numeric vector. Generation time distribution.</dd>


<dt>S</dt>
<dd>Numeric vector. Secondary cases.</dd>


<dt>inc</dt>
<dd>Numeric vector. Incidence time series.</dd>


<dt>dates</dt>
<dd>Date vector corresponding to observations.</dd>


<dt>est_r0_ml</dt>
<dd>Function to estimate R0.</dd>


<dt>RT</dt>
<dd>Function to compute Rt.</dd>


<dt>output_file</dt>
<dd>Output PDF filename.</dd>

</dl>

plot_effective_reproduction_number: Plot effective reproduction number (Re) over time

Description

Usage

Value

Arguments