Type: Package Package: EpiNow2 Title: Estimate and Forecast Real-Time Infection Dynamics Version: 1.9.0.9000 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) and Gostic et al. (2020) . 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/2026-06-15 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 Roxygen: list(markdown = TRUE) SystemRequirements: GNU make C++17 VignetteBuilder: knitr Config/roxygen2/version: 8.0.0 Config/pak/sysreqs: make Repository: https://epiforecasts.r-universe.dev Date/Publication: 2026-07-01 12:00:23 UTC RemoteUrl: https://github.com/epiforecasts/EpiNow2 RemoteRef: HEAD RemoteSha: 9e8374599431fd633fceecbfa357f64b047e660e NeedsCompilation: no Packaged: 2026-07-01 15:51:44 UTC; root Author: Sam Abbott [aut] (ORCID: ), Joel Hellewell [aut] (ORCID: ), Katharine Sherratt [aut], Katelyn Gostic [aut], Joe Hickson [aut], Hamada S. Badr [aut] (ORCID: ), Michael DeWitt [aut] (ORCID: ), James M. Azam [aut] (ORCID: ), Adrian Lison [aut] (ORCID: ), 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: ), Adam Howes [ctb] (ORCID: ), Sebastian Funk [aut, cre] (ORCID: ) Maintainer: Sebastian Funk