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: 1.4.0
Depends: R (≥ 3.5.0)
Imports: data.table, futile.logger (≥ 1.4), future, future.apply, ggplot2, lifecycle, lubridate, methods, patchwork, progressr, 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: covr, dplyr, here, kableExtra, knitr, magrittr, precommit, rmarkdown, spelling, styler, testthat, tidyr, withr
Published: 2023-09-26
Author: Sam Abbott ORCID iD [aut, cre], 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], Robin Thompson [ctb], Sophie Meakin [ctb], James Munday [ctb], Nikos Bosse [ctb], Paul Mee [ctb], Peter Ellis [ctb], Pietro Monticone [ctb], Lloyd Chapman [ctb], James M. Azam ORCID iD [ctb], Andrew Johnson [ctb], EpiForecasts [aut], Sebastian Funk ORCID iD [aut]
Maintainer: Sam Abbott <sam.abbott 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
Language: en-GB
Citation: EpiNow2 citation info
Materials: README NEWS
In views: Epidemiology
CRAN checks: EpiNow2 results

Documentation:

Reference manual: EpiNow2.pdf
Vignettes: Case studies and use in the literature
Model definition: estimate_infections()
Model definition: estimate_secondary()
Model definition: estimate_truncation()
Gaussian Process implementation details

Downloads:

Package source: EpiNow2_1.4.0.tar.gz
Windows binaries: r-devel: EpiNow2_1.4.0.zip, r-release: EpiNow2_1.3.5.zip, r-oldrel: EpiNow2_1.4.0.zip
macOS binaries: r-release (arm64): EpiNow2_1.4.0.tgz, r-oldrel (arm64): EpiNow2_1.4.0.tgz, r-release (x86_64): EpiNow2_1.4.0.tgz, r-oldrel (x86_64): EpiNow2_1.3.5.tgz
Old sources: EpiNow2 archive

Linking:

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