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EpiNow2: Estimate Real-Time Case Counts and Time-Varying EpidemiologicalParameters

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:	1.7.1
Depends:	R (≥ 3.5.0)
Imports:	checkmate,cli,data.table,futile.logger (≥ 1.4),ggplot2,lifecycle,lubridate, methods,patchwork,posterior,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,future,future.apply,here,knitr,precommit,progressr,rmarkdown,spelling,testthat,usethis,withr
Published:	2025-02-19
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], Kaitlyn 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 + fileLICENSE
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://stan-dev.r-universe.dev
Language:	en-GB
Materials:	README,NEWS
In views:	Epidemiology
CRAN checks:	EpiNow2 results

Documentation:

Reference manual:

EpiNow2.html ,EpiNow2.pdf

Vignettes:

Getting started with EpiNow2 (source)
Case studies and use in the literature (source,R code)
Using epinow() for running in production mode (source)
Model definition: estimate_infections() (source,R code)
Examples: estimate_infections() (source)
Workflow for Rt estimation and forecasting (source)
Model definition: estimate_secondary() (source,R code)
Model definition: estimate_truncation() (source,R code)
Gaussian Process implementation details (source,R code)

Downloads:

Package source:	EpiNow2_1.7.1.tar.gz
Windows binaries:	r-devel:EpiNow2_1.7.1.zip, r-release:EpiNow2_1.7.1.zip, r-oldrel:EpiNow2_1.7.1.zip
macOS binaries:	r-release (arm64):EpiNow2_1.7.1.tgz, r-oldrel (arm64):EpiNow2_1.7.1.tgz, r-release (x86_64):EpiNow2_1.7.1.tgz, r-oldrel (x86_64):EpiNow2_1.7.1.tgz
Old sources:	EpiNow2 archive

Linking:

Please use the canonical formhttps://CRAN.R-project.org/package=EpiNow2to link to this page.