epyestim

Introduction

epyestim estimates the effective reproduction number from time series of reported case numbers of epidemics. It is a Python reimplementation of the method outlined by Huisman et al. [1], making use of the method by Cori et al. [2] to estimate the reproduction number R from infection data, available in the R package EpiEstim [3].

The main steps for estimation of the effective reproduction number are:

• Bootstrapping the series of reported case numbers
• Smoothing using a LOWESS filter
• MLE of the infection incidence time series using an adaptation of the Richardson-Lucy deconvolution algorithm.
• Bayesian estimation of the effective reproduction number using the method of Cori et al. [2]

Aggregate estimates for the reproduction number are obtained by bootstrap aggregation (bagging).

The user can choose to output either time-varying estimates or piecewise constant estimates on fixed arbitrary time intervals.

How to install epyestim

pip install epyestim

How to use epyestim

Basic usage of the epyestim package applied to COVID-19 data is explained in the Jupyter tutorial notebook.

The core functions relevant for users are:

• epyestim.bagging_r for the complete estimation process outlined above
• epyestim.covid19.r_covid for the same function with default parameters for COVID-19
• epyestim.estimate_r.estimate_r for the R estimation from infection numbers, based on the EpiEstim package

Authors

• Lorenz Hilfiker
• Johannes Josi

How to contribute

Error reports and suggestions for improvements via GitHub issues are very welcome.

References

[1] Jana S. Huisman, Jeremie Scire, Daniel Angst, Richard Neher, Sebastian Bonhoeffer, Tanja Stadler: A method to monitor the effective reproductive number of SARS-CoV-2 https://ibz-shiny.ethz.ch/covid-19-re/methods.pdf

[2] Anne Cori, Neil M. Ferguson, Christophe Fraser, Simon Cauchemez: A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics, American Journal of Epidemiology, Volume 178, Issue 9, 1 November 2013, Pages 1505–1512, https://doi.org/10.1093/aje/kwt133

[3] EpiEstim CRAN package: https://cran.r-project.org/web/packages/EpiEstim/index.html