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.

Version: 1.7.1
Depends: R (≥ 3.5.0)
Imports: checkmate, cli, data.table, futile.logger (≥ 1.4), ggplot2, lifecycle, lubridate, methods, patchwork, posterior, purrr, R.utils (≥ 2.0.0), Rcpp (≥ 0.12.0), rlang (≥ 0.4.7), rstan (≥ 2.26.0), rstantools (≥ 2.2.0), runner, scales, stats, truncnorm, utils
LinkingTo: BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.26.0), StanHeaders (≥ 2.26.0)
Suggests: cmdstanr, covr, future, future.apply, here, knitr, precommit, progressr, rmarkdown, spelling, testthat, usethis, withr
Published: 2025-02-19
DOI: 10.32614/CRAN.package.EpiNow2
Author: Sam Abbott ORCID iD [aut], Joel Hellewell ORCID iD [aut], Katharine Sherratt [aut], Katelyn Gostic [aut], Joe Hickson [aut], Hamada S. Badr ORCID iD [aut], Michael DeWitt ORCID iD [aut], James M. Azam ORCID iD [aut], 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 ORCID iD [ctb], EpiForecasts [aut], Sebastian Funk ORCID iD [aut, cre]
Maintainer: Sebastian Funk <sebastian.funk at lshtm.ac.uk>
BugReports: https://github.com/epiforecasts/EpiNow2/issues
License: MIT + file LICENSE
URL: https://epiforecasts.io/EpiNow2/, https://epiforecasts.io/EpiNow2/dev/, https://github.com/epiforecasts/EpiNow2
NeedsCompilation: yes
SystemRequirements: GNU make C++17
Additional_repositories: https://stan-dev.r-universe.dev
Language: en-GB
Materials: README, NEWS
In views: Epidemiology
CRAN checks: EpiNow2 results

Documentation:

Reference manual: EpiNow2.html , EpiNow2.pdf
Vignettes: Getting started with EpiNow2 (source)
Case studies and use in the literature (source, R code)
Using epinow() for running in production mode (source)
Model definition: estimate_infections() (source, R code)
Examples: estimate_infections() (source)
Workflow for Rt estimation and forecasting (source)
Model definition: estimate_secondary() (source, R code)
Model definition: estimate_truncation() (source, R code)
Gaussian Process implementation details (source, R code)

Downloads:

Package source: EpiNow2_1.7.1.tar.gz
Windows binaries: r-devel: EpiNow2_1.7.1.zip, r-release: EpiNow2_1.7.1.zip, r-oldrel: EpiNow2_1.7.1.zip
macOS binaries: r-release (arm64): EpiNow2_1.7.1.tgz, r-oldrel (arm64): EpiNow2_1.7.1.tgz, r-release (x86_64): EpiNow2_1.7.1.tgz, r-oldrel (x86_64): EpiNow2_1.7.1.tgz
Old sources: EpiNow2 archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=EpiNow2 to link to this page.