Package: epinowcast Title: A Bayesian Framework for Real-time Infectious Disease Surveillance Version: 0.6.0 Authors@R: c(person(given = "Sam Abbott", role = c("aut", "cre"), email = "contact@samabbott.co.uk", comment = c(ORCID = "0000-0001-8057-8037")), person(given = "Adrian", family = "Lison", role = "aut", email = "adrian.lison@bsse.ethz.ch", comment = c(ORCID = "0000-0002-6822-8437")), person(given = "Sebastian", family = "Funk", role = "aut", email = "sebastian.funk@lshtm.ac.uk"), person(given = "Carl", family = "Pearson", role = "aut", email = "carl.ab.pearson@gmail.com", comment = c(ORCID = "0000-0003-0701-7860")), person(given = "Hugo", family = "Gruson", role = "aut", email = "hugo.gruson@normalesup.org", comment = c(ORCID = "0000-0002-4094-1476")), person(given = "Felix", family = "Guenther", role = "aut", email = "felixguenther1@gmx.de", comment = c(ORCID = "0000-0001-6582-1174")), person(given = "Michael", family = "DeWitt", role = "aut", email = "me.dewitt.jr@gmail.com", comment = c(ORCID = "0000-0001-8940-1967")), person(given = "James Mba", family = "Azam", role = "aut", email = "james.azam@lshtm.ac.uk", comment = c(ORCID = "0000-0001-5782-7330")), person(given = "Jessalyn", family = "Sebastian", role = "aut", email = "jessalynsebastian@gmail.com", comment = c(ORCID = "0000-0002-1768-3229")), person(given = "Hannah", family = "Choi", role = "ctb", email = "hannah.choi1@lshtm.ac.uk"), person(given = "Pratik", family = "Gupte", role = "ctb", email = "pratik.gupte@lshtm.ac.uk", comment = c(ORCID = "0000-0001-5294-7819")), person(given = "Joel", family = "Hellewell", role = "ctb", email = "joel@ebi.ac.uk", comment = c(ORCID = "0000-0003-2683-0849")), person(given = "Luis", family = "Rivas", role = "ctb", email = "luisnicolasrivas@gmail.com"), person(given = "Sang Woo", family = "Park", role = "ctb", email = "swp2@princeton.edu", comment = c(ORCID = "0000-0003-2202-3361")), person(given = "Nathan", family = "McIntosh", role = "ctb", email = "natemcintosh@gmail.com"), person(given = "Kath", family = "Sherratt", role = "ctb", email = "katharine.sherratt@lshtm.ac.uk", comment = c(ORCID = "0000-0003-2049-3423")), person(given = "Nikos", family = "Bosse", role = "ctb", email = "nikos.bosse@lshtm.ac.uk", comment = c(ORCID = "0000-0002-7750-5280")), person(given = "Adam", family = "Howes", role = "ctb", email = "adamthowes@gmail.com", comment = c(ORCID = "0000-0003-2386-4031")), person(given = "Kaitlyn", family = "Johnson", role = "ctb", email = "johnsonkaitlyne9@gmail.com", comment = c(ORCID = "0000-0001-8011-0012")), person(given = "Barbora", family = "Nemcova", role = "ctb", email = "barbora.nemcova@kit.edu", comment = c(ORCID = "0009-0004-7565-4145"))) Description: A modular Bayesian framework for real-time infectious disease surveillance. Provides tools for nowcasting, reproduction number estimation, delay estimation, and forecasting from data subject to reporting delays, right-truncation, missing data, and incomplete ascertainment. Users can build models suited to their setting using a flexible formula interface supporting fixed effects, random effects, random walks, and time-varying parameters, with options including parametric and non-parametric delay distributions with optional modifiers (via discrete-time hazard models), renewal processes, observation models, missing data imputation, and stratified analyses with partial pooling. By jointly estimating disease dynamics and reporting patterns, our framework enables earlier and more reliable detection of trends. While designed with epidemiological applications in mind, the framework can be applied to any right-truncated time series count data. License: MIT + file LICENSE URL: https://package.epinowcast.org, https://github.com/epinowcast/epinowcast/ BugReports: https://github.com/epinowcast/epinowcast/issues/ Depends: R (>= 4.4.0) Imports: cli, data.table, reformulas, ggplot2, posterior, purrr, rlang, scales, lifecycle Suggests: bookdown, scoringutils, cmdstanr, cyclocomp, dplyr, lme4, loo (>= 2.4.1), primarycensored, knitr, RcppEigen, rmarkdown, spelling, testthat (>= 3.1.9), usethis, vdiffr, withr VignetteBuilder: knitr Additional_repositories: https://stan-dev.r-universe.dev Config/Needs/website: r-lib/pkgdown, epinowcast/enwtheme Config/Needs/hexsticker: hexSticker, sysfonts Config/testthat/edition: 3 Encoding: UTF-8 Language: en-GB LazyData: true Roxygen: list(markdown = TRUE) RoxygenNote: 7.3.3 Repository: https://epinowcast.r-universe.dev Date/Publication: 2026-04-22 11:19:25 UTC RemoteUrl: https://github.com/epinowcast/epinowcast RemoteRef: v0.6.0 RemoteSha: f95e55371ac3905fc91d7bae1491e8aa6bd059da NeedsCompilation: no Packaged: 2026-06-21 08:54:40 UTC; root Author: Sam Abbott [aut, cre] (ORCID: ), Adrian Lison [aut] (ORCID: ), Sebastian Funk [aut], Carl Pearson [aut] (ORCID: ), Hugo Gruson [aut] (ORCID: ), Felix Guenther [aut] (ORCID: ), Michael DeWitt [aut] (ORCID: ), James Mba Azam [aut] (ORCID: ), Jessalyn Sebastian [aut] (ORCID: ), Hannah Choi [ctb], Pratik Gupte [ctb] (ORCID: ), Joel Hellewell [ctb] (ORCID: ), Luis Rivas [ctb], Sang Woo Park [ctb] (ORCID: ), Nathan McIntosh [ctb], Kath Sherratt [ctb] (ORCID: ), Nikos Bosse [ctb] (ORCID: ), Adam Howes [ctb] (ORCID: ), Kaitlyn Johnson [ctb] (ORCID: ), Barbora Nemcova [ctb] (ORCID: ) Maintainer: Sam Abbott