EpiNow2-package: EpiNow2: Estimate and Forecast Real-Time Infection Dynamics
In EpiNow2: Estimate and Forecast Real-Time Infection Dynamics
EpiNow2-package R Documentation
EpiNow2: Estimate and Forecast Real-Time Infection Dynamics
Description
Estimates the time-varying reproduction number, rate of spread, and doubling time using a renewal equation approach combined with Bayesian inference via Stan. Supports Gaussian process and random walk priors for modelling changes in transmission over time. Accounts for delays between infection and observation (incubation period, reporting delays), right-truncation in recent data, day-of-week effects, and observation overdispersion. Can estimate relationships between primary and secondary outcomes (e.g., cases to hospitalisations or deaths) and forecast both. Runs across multiple regions in parallel. Based on Abbott et al. (2020) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.12688/wellcomeopenres.16006.1")} and Gostic et al. (2020) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/2020.06.18.20134858")}.
Author(s)
Maintainer: Sebastian Funk sebastian.funk@lshtm.ac.uk (ORCID)
Authors:
Sebastian Funk sebastian.funk@lshtm.ac.uk (ORCID)
Sam Abbott sam.abbott@lshtm.ac.uk (ORCID)
Joel Hellewell joel.hellewell@lshtm.ac.uk (ORCID)
Katharine Sherratt katharine.sherratt@lshtm.ac.uk
Katelyn Gostic kgostic@uchicago.edu
Joe Hickson joseph.hickson@metoffice.gov.uk
Hamada S. Badr badr@jhu.edu (ORCID)
Michael DeWitt me.dewitt.jr@gmail.com (ORCID)
James M. Azam james.azam@lshtm.ac.uk (ORCID)
Adrian Lison adrian.lison@bsse.ethz.ch (ORCID)
Other contributors:
Robin Thompson robin.thompson@lshtm.ac.uk [contributor]
Sophie Meakin sophie.meakin@lshtm.ac.uk [contributor]
James Munday james.munday@lshtm.ac.uk [contributor]
Nikos Bosse [contributor]
Paul Mee paul.mee@lshtm.ac.uk [contributor]
Peter Ellis peter.ellis2013nz@gmail.com [contributor]
Pietro Monticone pietro.monticone@edu.unito.it [contributor]
Lloyd Chapman lloyd.chapman1@lshtm.ac.uk [contributor]
Andrew Johnson andrew.johnson@arjohnsonau.com [contributor]
Kaitlyn Johnson johnsonkaitlyne9@gmail.com (ORCID) [contributor]
Adam Howes adamthowes@gmail.com (ORCID) [contributor]
See Also
Useful links:
EpiNow2 documentation built on June 17, 2026, 1:07 a.m.
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| EpiNow2-package | R Documentation |
EpiNow2: Estimate and Forecast Real-Time Infection Dynamics
Description
Estimates the time-varying reproduction number, rate of spread, and doubling time using a renewal equation approach combined with Bayesian inference via Stan. Supports Gaussian process and random walk priors for modelling changes in transmission over time. Accounts for delays between infection and observation (incubation period, reporting delays), right-truncation in recent data, day-of-week effects, and observation overdispersion. Can estimate relationships between primary and secondary outcomes (e.g., cases to hospitalisations or deaths) and forecast both. Runs across multiple regions in parallel. Based on Abbott et al. (2020) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.12688/wellcomeopenres.16006.1")} and Gostic et al. (2020) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/2020.06.18.20134858")}.
Author(s)
Maintainer: Sebastian Funk sebastian.funk@lshtm.ac.uk (ORCID)
Authors:
Sebastian Funk sebastian.funk@lshtm.ac.uk (ORCID)
Sam Abbott sam.abbott@lshtm.ac.uk (ORCID)
Joel Hellewell joel.hellewell@lshtm.ac.uk (ORCID)
Katharine Sherratt katharine.sherratt@lshtm.ac.uk
Katelyn Gostic kgostic@uchicago.edu
Joe Hickson joseph.hickson@metoffice.gov.uk
Hamada S. Badr badr@jhu.edu (ORCID)
Michael DeWitt me.dewitt.jr@gmail.com (ORCID)
James M. Azam james.azam@lshtm.ac.uk (ORCID)
Adrian Lison adrian.lison@bsse.ethz.ch (ORCID)
Other contributors:
Robin Thompson robin.thompson@lshtm.ac.uk [contributor]
Sophie Meakin sophie.meakin@lshtm.ac.uk [contributor]
James Munday james.munday@lshtm.ac.uk [contributor]
Nikos Bosse [contributor]
Paul Mee paul.mee@lshtm.ac.uk [contributor]
Peter Ellis peter.ellis2013nz@gmail.com [contributor]
Pietro Monticone pietro.monticone@edu.unito.it [contributor]
Lloyd Chapman lloyd.chapman1@lshtm.ac.uk [contributor]
Andrew Johnson andrew.johnson@arjohnsonau.com [contributor]
Kaitlyn Johnson johnsonkaitlyne9@gmail.com (ORCID) [contributor]
Adam Howes adamthowes@gmail.com (ORCID) [contributor]
See Also
Useful links:
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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