Type: Package
Package: EpiNow2
Title: Estimate and Forecast Real-Time Infection Dynamics
Version: 1.8.0
Authors@R: 
    c(person(given = "Sam",
             family = "Abbott",
             role = c("aut"),
             email = "sam.abbott@lshtm.ac.uk",
             comment = c(ORCID = "0000-0001-8057-8037")),
      person(given = "Joel",
             family = "Hellewell",
             role = "aut",
             email = "joel.hellewell@lshtm.ac.uk",
             comment = c(ORCID = "0000-0003-2683-0849")),
      person(given = "Katharine",
             family = "Sherratt",
             role = "aut",
             email = "katharine.sherratt@lshtm.ac.uk"),
      person(given = "Katelyn",
             family = "Gostic",
             role = "aut",
             email = "kgostic@uchicago.edu"),
      person(given = "Joe",
             family = "Hickson",
             role = "aut",
             email = "joseph.hickson@metoffice.gov.uk"),
      person(given = "Hamada S.",
             family = "Badr",
             role = "aut",
             email = "badr@jhu.edu",
             comment = c(ORCID = "0000-0002-9808-2344")),
      person(given = "Michael",
             family = "DeWitt",
             role = "aut",
             email = "me.dewitt.jr@gmail.com",
             comment = c(ORCID = "0000-0001-8940-1967")),
      person(given = "James M.",
             family = "Azam",
             role = "aut",
             email = "james.azam@lshtm.ac.uk",
             comment = c(ORCID = "0000-0001-5782-7330")),
      person(given = "Adrian",
             family = "Lison",
             role = "aut",
             email = "adrian.lison@bsse.ethz.ch",
             comment = c(ORCID = "0000-0002-6822-8437")),
      person(given = "Robin",
             family = "Thompson",
             role = "ctb",
             email = "robin.thompson@lshtm.ac.uk"),
      person(given = "Sophie",
             family = "Meakin",
             role = "ctb",
             email = "sophie.meakin@lshtm.ac.uk"),
      person(given = "James",
             family = "Munday",
             role = "ctb",
             email = "james.munday@lshtm.ac.uk"),
      person(given = "Nikos",
             family = "Bosse",
             role = "ctb"),
      person(given = "Paul",
             family = "Mee",
             role = "ctb",
             email = "paul.mee@lshtm.ac.uk"),
      person(given = "Peter",
             family = "Ellis",
             role = "ctb",
             email = "peter.ellis2013nz@gmail.com"),
      person(given = "Pietro",
             family = "Monticone",
             role = "ctb",
             email = "pietro.monticone@edu.unito.it"),
      person(given = "Lloyd",
             family = "Chapman",
             role = "ctb",
             email = "lloyd.chapman1@lshtm.ac.uk"),
      person(given = "Andrew",
             family = "Johnson",
             role = "ctb",
             email = "andrew.johnson@arjohnsonau.com"),
      person(given = "Kaitlyn",
             family = "Johnson",
             role = "ctb",
             email = "johnsonkaitlyne9@gmail.com",
             comment = c(ORCID = "0000-0001-8011-0012")),
      person(given = "Adam",
             family = "Howes",
             role = "ctb",
             email = "adamthowes@gmail.com",
             comment = c(ORCID = "0000-0003-2386-4031")),
      person(given = "Sebastian",
             family = "Funk",
             role = c("aut", "cre"),
             email = "sebastian.funk@lshtm.ac.uk",
             comment = c(ORCID = "0000-0002-2842-3406"))
    )
Description: 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>.
License: MIT + file LICENSE
URL: https://epiforecasts.io/EpiNow2/,
        https://epiforecasts.io/EpiNow2/dev/,
        https://github.com/epiforecasts/EpiNow2
BugReports: https://github.com/epiforecasts/EpiNow2/issues
Depends: R (>= 3.5.0)
Imports: checkmate, cli, data.table (>= 1.15.0), futile.logger (>=
        1.4), ggplot2, lifecycle, lubridate, methods, patchwork,
        posterior, primarycensored, 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
Suggests: cmdstanr, future, future.apply, knitr, parallelly, progressr,
        rmarkdown, scoringutils, spelling, testthat, withr
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)
Additional_repositories: https://production.r-multiverse.org/2025-12-15
Biarch: true
Config/testthat/edition: 3
Config/Needs/dev: covr, here, hexSticker, lintr, magick, pkgdown,
        precommit, styler, usethis
Encoding: UTF-8
Language: en-GB
LazyData: true
RoxygenNote: 7.3.3
SystemRequirements: GNU make C++17
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2026-02-04 22:49:39 UTC; eidesfun
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>
Repository: CRAN
Date/Publication: 2026-02-04 23:30:02 UTC
Built: R 4.5.3; x86_64-w64-mingw32; 2026-03-27 05:20:51 UTC; windows
Archs: x64
