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

Abstract

The effective reproduction number, R t, 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 R t is above one, it indicates that new infections are increasing, and thus the epidemic is growing, while an R t 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 R t using clinical surveillance data. However, there are comparatively few accessible tools for estimating R t 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.