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) ), and current best practices (Gostic et al. (2020) ). 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.


Reference manual

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1.3.1 by Sam Abbott, 3 days ago

Browse source code at

Authors: Sam Abbott [aut, cre] , Joel Hellewell [aut] , Robin Thompson [aut] , Katelyn Gostic [aut] , Katharine Sherratt [aut] , Hamada S. Badr [aut] , Michael DeWitt [aut] , Sophie Meakin [aut] , James Munday [aut] , Nikos Bosse [aut] , Joe Hickson [aut] , Paul Mee [ctb] , Peter Ellis [ctb] , EpiForecasts [aut] , Sebastian Funk [aut]

Documentation:   PDF Manual  

MIT + file LICENSE license

Imports cowplot, data.table, futile.logger, future, future.apply, ggplot2, lubridate, methods, patchwork, progressr, purrr, R.utils, Rcpp, rlang, rstan, scales, stats, truncnorm, lifecycle

Suggests countrycode, dplyr, EpiSoon, forecastHybrid, here, kableExtra, knitr, magrittr, rmarkdown, rnaturalearth, rstantools, spelling, tidyr, testthat, covr

Linking to BH, Rcpp, RcppEigen, rstan, StanHeaders

See at CRAN