ern: An R package to estimate the effective reproduction number using clinical and wastewater surveillance data
David Champredon, Irena Papst, Warsame Yusuf
Abstract
The effective reproduction number, <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="M1"><mml:msub><mml:mi mathvariant="script">R</mml:mi> <mml:mi>t</mml:mi></mml:msub></mml: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 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="M2"><mml:msub><mml:mi mathvariant="script">R</mml:mi> <mml:mi>t</mml:mi></mml:msub></mml:math> is above one, it indicates that new infections are increasing, and thus the epidemic is growing, while an <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="M3"><mml:msub><mml:mi mathvariant="script">R</mml:mi> <mml:mi>t</mml:mi></mml:msub></mml: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 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="M4"><mml:msub><mml:mi mathvariant="script">R</mml:mi> <mml:mi>t</mml:mi></mml:msub></mml:math> using clinical surveillance data. However, there are comparatively few accessible tools for estimating <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="M5"><mml:msub><mml:mi mathvariant="script">R</mml:mi> <mml:mi>t</mml:mi></mml:msub></mml:math> from pathogen wastewater concentration, a surveillance data stream that cemented its utility during the COVID-19 pandemic. We present the <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="M6"><mml:mi mathvariant="sans-serif">R</mml:mi></mml: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.