%0 Journal Article
%T ern: An [Formula: see text] package to estimate the effective reproduction number using clinical and wastewater surveillance data.
%A Champredon D
%A Papst I
%A Yusuf W
%J PLoS One
%V 19
%N 6
%D 2024
%M 38905266
%F 3.752
%R 10.1371/journal.pone.0305550
%X The effective reproduction number, [Formula: see text], is an important epidemiological metric used to assess the state of an epidemic, as well as the effectiveness of public health interventions undertaken in response. When [Formula: see text] is above one, it indicates that new infections are increasing, and thus the epidemic is growing, while an [Formula: see text] is below one indicates that new infections are decreasing, and so the epidemic is under control. There are several established software packages that are readily available to statistically estimate [Formula: see text] using clinical surveillance data. However, there are comparatively few accessible tools for estimating [Formula: see text] from pathogen wastewater concentration, a surveillance data stream that cemented its utility during the COVID-19 pandemic. We present the [Formula: see text] package ern that aims to perform the estimation of the effective reproduction number from real-world wastewater or aggregated clinical surveillance data in a user-friendly way.