EpiNow2: Estimate and Forecast Real-Time Infection Dynamics

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) <doi:10.12688/wellcomeopenres.16006.1> and Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>.

Package overview README.md Case studies and use in the literature Examples: estimate_infections() Fitting delay distributions with estimate_dist() Forecasting multiple data streams Gaussian Process implementation details Getting started with EpiNow2 Model definition: estimate_dist() Model definition: estimate_infections() Model definition: estimate_secondary() Model definition: estimate_truncation() Model features Model overview Prior choice and specification guide Understanding delay distributions in EpiNow2 Using epinow() for running in production mode Workflow for Rt estimation and forecasting

Vignettes Man pages API and functions Files

Package details
Author	Sam Abbott [aut] (ORCID: <https://orcid.org/0000-0001-8057-8037>), Joel Hellewell [aut] (ORCID: <https://orcid.org/0000-0003-2683-0849>), Katharine Sherratt [aut], Katelyn Gostic [aut], Joe Hickson [aut], Hamada S. Badr [aut] (ORCID: <https://orcid.org/0000-0002-9808-2344>), Michael DeWitt [aut] (ORCID: <https://orcid.org/0000-0001-8940-1967>), James M. Azam [aut] (ORCID: <https://orcid.org/0000-0001-5782-7330>), Adrian Lison [aut] (ORCID: <https://orcid.org/0000-0002-6822-8437>), Robin Thompson [ctb], Sophie Meakin [ctb], James Munday [ctb], Nikos Bosse [ctb], Paul Mee [ctb], Peter Ellis [ctb], Pietro Monticone [ctb], Lloyd Chapman [ctb], Andrew Johnson [ctb], Kaitlyn Johnson [ctb] (ORCID: <https://orcid.org/0000-0001-8011-0012>), Adam Howes [ctb] (ORCID: <https://orcid.org/0000-0003-2386-4031>), Sebastian Funk [aut, cre] (ORCID: <https://orcid.org/0000-0002-2842-3406>)
Maintainer	Sebastian Funk <sebastian.funk@lshtm.ac.uk>
License	MIT + file LICENSE
Version	1.9.0
URL	https://epiforecasts.io/EpiNow2/ https://epiforecasts.io/EpiNow2/dev/ https://github.com/epiforecasts/EpiNow2
Package repository	View on CRAN
Installation	Install the latest version of this package by entering the following in R: `install.packages("EpiNow2")`