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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1.3.2 by Sam Abbott, a year ago

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Authors: Sam Abbott [aut, cre] , Joel Hellewell [aut] , Katharine Sherratt [aut] , Katelyn Gostic [aut] , Joe Hickson [aut] , Hamada S. Badr [aut] , Michael DeWitt [aut] , Robin Thompson [aut] , Sophie Meakin [ctb] , James Munday [ctb] , Nikos Bosse [ctb] , 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, runner, scales, stats, truncnorm, lifecycle, utils

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