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Case studies and use in the literature

Case studies

Estimating reporting delays and nowcasting/forecasting infections with EpiNow2 using HHS COVID-19 hospitalizations by Sam Abbott, Zachary Susswein, and Katie Gostic.
Estimating reporting delays and nowcasting/forecasting infections with EpiNow2 by Sebastian Funk and Sam Abbott.
Forecast Covid-19 reported deaths from Covid-19 reported cases (both observed and forecast) for a country in the ECDC by Sam Abbott.
Explore Covid-19 data truncation in England by Sam Abbott.
Estimate the effective reproduction number of Covid-19 in last 3 months for a country By Sam Abbott.

Public health surveillance

CDC. 2022. “Technical Report 3: Multi-National Monkeypox Outbreak, United States, 2022.” Centers for Disease Control and Prevention. October 3, 2022. https://www.cdc.gov/poxvirus/mpox/cases-data/technical-report/report-3.html.

Literature

By package authors

Abbott, Sam, Joel Hellewell, Robin N. Thompson, Katharine Sherratt, Hamish P. Gibbs, Nikos I. Bosse, James D. Munday, et al. 2020. “Estimating the Time-Varying Reproduction Number of SARS-CoV-2 Using National and Subnational Case Counts.” Wellcome Open Research 5 (December): 112. http://dx.doi.org/10.12688/wellcomeopenres.16006.2
Sherratt, Katharine, Sam Abbott, Sophie R. Meakin, Joel Hellewell, James D. Munday, Nikos Bosse, Null Null, Mark Jit, and Sebastian Funk. 2021. “Exploring Surveillance Data Biases When Estimating the Reproduction Number: With Insights into Subpopulation Transmission of COVID-19 in England.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 376 (1829): 20200283. http://dx.doi.org/10.1098/rstb.2020.0283
Bosse, Nikos I., Sam Abbott, Johannes Bracher, Habakuk Hain, Billy J. Quilty, Mark Jit, Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group, Edwin van Leeuwen, Anne Cori, and Sebastian Funk. 2022. “Comparing Human and Model-Based Forecasts of COVID-19 in Germany and Poland.” PLoS Computational Biology 18 (9): e1010405. http://dx.doi.org/10.1371/journal.pcbi.1010405
Davies, Nicholas G., Sam Abbott, Rosanna C. Barnard, Christopher I. Jarvis, Adam J. Kucharski, James D. Munday, Carl A. B. Pearson, et al. 2021. “Estimated Transmissibility and Impact of SARS-CoV-2 Lineage B.1.1.7 in England.” Science 372 (6538). https://doi.org/10.1126/science.abg3055.
Meakin, Sophie, Sam Abbott, Nikos Bosse, James Munday, Hugo Gruson, Joel Hellewell, Katharine Sherratt, CMMID COVID-19 Working Group, and Sebastian Funk. 2022. “Comparative Assessment of Methods for Short-Term Forecasts of COVID-19 Hospital Admissions in England at the Local Level.” BMC Medicine 20 (1): 86. http://dx.doi.org/10.1186/s12916-022-02271-x

By others

Hay, James A., Lee Kennedy-Shaffer, Sanjat Kanjilal, Niall J. Lennon, Stacey B. Gabriel, Marc Lipsitch, and Michael J. Mina. 2021. “Estimating Epidemiologic Dynamics from Cross-Sectional Viral Load Distributions.” Science 373 (6552). https://doi.org/10.1126/science.abh0635.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.