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EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters
Estimates the time-varying reproduction number, rate of spread, and doubling time using a range of open-source tools (Abbott et al. (2020) <doi:10.12688/wellcomeopenres.16006.1>), and current best practices (Gostic et al. (2020) <doi:10.1101/2020.06.18.20134858>). It aims to help users avoid some of the limitations of naive implementations in a framework that is informed by community feedback and is actively supported.
Getting started
Package overview
README.md
Case studies and use in the literature
Examples: estimate_infections()
Gaussian Process implementation details
Getting started with EpiNow2
Model definition: estimate_infections()
Model definition: estimate_secondary()
Model definition: estimate_truncation()
Using epinow() for running in production mode
Workflow for Rt estimation and forecasting
Browse package contents
Package details |
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| Author | Sam Abbott [aut] (<https://orcid.org/0000-0001-8057-8037>), Joel Hellewell [aut] (<https://orcid.org/0000-0003-2683-0849>), Katharine Sherratt [aut], Katelyn Gostic [aut], Joe Hickson [aut], Hamada S. Badr [aut] (<https://orcid.org/0000-0002-9808-2344>), Michael DeWitt [aut] (<https://orcid.org/0000-0001-8940-1967>), James M. Azam [aut] (<https://orcid.org/0000-0001-5782-7330>), 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] (<https://orcid.org/0000-0001-8011-0012>), EpiForecasts [aut], Sebastian Funk [aut, cre] (<https://orcid.org/0000-0002-2842-3406>) |
| Maintainer | Sebastian Funk <sebastian.funk@lshtm.ac.uk> |
| License | MIT + file LICENSE |
| Version | 1.6.1 |
| URL | https://epiforecasts.io/EpiNow2/ https://epiforecasts.io/EpiNow2/dev/ https://github.com/epiforecasts/EpiNow2 |
| Package repository | View on CRAN |
| Installation |
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