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 under active development.

Version: 1.2.1
Depends: R (≥ 3.4.0)
Imports: cowplot, data.table, futile.logger (≥ 1.4), future, future.apply, ggplot2, lubridate, methods, patchwork, progressr, purrr, R.utils (≥ 2.0.0), Rcpp (≥ 0.12.0), rlang (≥ 0.4.7), rstan (≥ 2.18.1), scales, stats, truncnorm
LinkingTo: BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), rstan (≥ 2.21.1), StanHeaders (≥ 2.21.0-5)
Suggests: countrycode, dplyr, EpiSoon, forecastHybrid, here, kableExtra, knitr, magrittr, rmarkdown, rnaturalearth, rstantools, spelling, tidyr, testthat
Published: 2020-10-20
Author: Sam Abbott ORCID iD [aut, cre], Joel Hellewell ORCID iD [aut], Robin Thompson [aut], Katelyn Gostic [aut], Katharine Sherratt [aut], Sophie Meakin [aut], James Munday [aut], Nikos Bosse [aut], Joe Hickson [aut], Paul Mee [ctb], Peter Ellis [ctb], Hamada S. Badr ORCID iD [ctb], Michael DeWitt ORCID iD [ctb], EpiForecasts [aut], Sebastian Funk [aut]
Maintainer: Sam Abbott <sam.abbott at lshtm.ac.uk>
License: MIT + file LICENSE
NeedsCompilation: yes
Language: en-GB
Citation: EpiNow2 citation info
Materials: README NEWS
CRAN checks: EpiNow2 results

Downloads:

Reference manual: EpiNow2.pdf
Package source: EpiNow2_1.2.1.tar.gz
Windows binaries: r-devel: EpiNow2_1.2.1.zip, r-release: EpiNow2_1.2.1.zip, r-oldrel: EpiNow2_1.2.1.zip
macOS binaries: r-release: EpiNow2_1.2.1.tgz, r-oldrel: EpiNow2_1.1.0.tgz
Old sources: EpiNow2 archive

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