ern: An <math xmlns="http://www.w3.org/1998/Math/MathML"> <mi mathvariant="sans-serif">R</mi> </math> package to estimate the effective reproduction number using clinical and wastewater surveillance data.

Abstract

The effective reproduction number, <math xmlns="http://www.w3.org/1998/Math/MathML"> <msub> <mi mathvariant="script">R</mi> <mi>t</mi> </msub> </math>, 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 <math xmlns="http://www.w3.org/1998/Math/MathML"> <msub> <mi mathvariant="script">R</mi> <mi>t</mi> </msub> </math> is above one, it indicates that new infections are increasing, and thus the epidemic is growing, while an <math xmlns="http://www.w3.org/1998/Math/MathML"> <msub> <mi mathvariant="script">R</mi> <mi>t</mi> </msub> </math> 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 <math xmlns="http://www.w3.org/1998/Math/MathML"> <msub> <mi mathvariant="script">R</mi> <mi>t</mi> </msub> </math> using clinical surveillance data. However, there are comparatively few accessible tools for estimating <math xmlns="http://www.w3.org/1998/Math/MathML"> <msub> <mi mathvariant="script">R</mi> <mi>t</mi> </msub> </math> from pathogen wastewater concentration, a surveillance data stream that cemented its utility during the COVID-19 pandemic. We present the <math xmlns="http://www.w3.org/1998/Math/MathML"> <mi mathvariant="sans-serif">R</mi> </math> 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.