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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.

Version: 1.6.1
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: 2024-10-31
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.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_1.6.1.tar.gz
Windows binaries: r-devel: EpiNow2_1.6.1.zip, r-release: EpiNow2_1.6.1.zip, r-oldrel: EpiNow2_1.6.1.zip
macOS binaries: r-release (arm64): EpiNow2_1.6.1.tgz, r-oldrel (arm64): EpiNow2_1.6.1.tgz, r-release (x86_64): EpiNow2_1.6.1.tgz, r-oldrel (x86_64): EpiNow2_1.6.1.tgz
Old sources: EpiNow2 archive

Linking:

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

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.