ern: An R package to estimate the effective reproduction number using clinical and wastewater surveillance data

Abstract

The effective reproduction number, Rt, 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 Rt is above one, it indicates that new infections are increasing, and thus the epidemic is growing, while an Rt 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 Rt using clinical surveillance data. However, there are comparatively few accessible tools for estimating Rt from pathogen wastewater concentration, a surveillance data stream that cemented its utility during the COVID-19 pandemic. We present the R 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.