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:	1.5.2
Depends:	R (≥ 3.5.0)
Imports:	checkmate, data.table, futile.logger (≥ 1.4), future, future.apply, ggplot2, lifecycle, lubridate, methods, patchwork, posterior, 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:	cmdstanr, covr, here, knitr, precommit, rmarkdown, spelling, testthat, usethis, withr
Published:	2024-05-16
DOI:	10.32614/CRAN.package.EpiNow2
Author:	Sam Abbott [aut], Joel Hellewell [aut], Katharine Sherratt [aut], Katelyn Gostic [aut], Joe Hickson [aut], Hamada S. Badr [aut], Michael DeWitt [aut], James M. Azam [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], EpiForecasts [aut], Sebastian Funk [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://mc-stan.org/r-packages/
Language:	en-GB
Materials:	README NEWS
In views:	Epidemiology
CRAN checks:	EpiNow2 results

Documentation:

Reference manual:	EpiNow2.pdf
Vignettes:	Getting started with EpiNow2 Case studies and use in the literature Using epinow() for running in production mode Model definition: estimate_infections() Examples: estimate_infections() Workflow for Rt estimation and forecasting Model definition: estimate_secondary() Model definition: estimate_truncation() Gaussian Process implementation details

Downloads:

Package source:	EpiNow2_1.5.2.tar.gz
Windows binaries:	r-devel: EpiNow2_1.5.2.zip, r-release: EpiNow2_1.5.2.zip, r-oldrel: EpiNow2_1.5.2.zip
macOS binaries:	r-release (arm64): EpiNow2_1.5.2.tgz, r-oldrel (arm64): EpiNow2_1.5.2.tgz, r-release (x86_64): EpiNow2_1.5.2.tgz, r-oldrel (x86_64): EpiNow2_1.5.2.tgz
Old sources:	EpiNow2 archive

Linking:

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