CRAN/E | EpiNow2

EpiNow2

Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

Installation

About

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.

Citation EpiNow2 citation info
epiforecasts.io/EpiNow2/
epiforecasts.io/EpiNow2/dev/
github.com/epiforecasts/EpiNow2
System requirements GNU make C++17
Bug report File report

Key Metrics

Version 1.4.0
R ≥ 3.5.0
Published 2023-09-26 210 days ago
Needs compilation? yes
License MIT
License File
CRAN checks EpiNow2 results
Language en-GB

Downloads

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Last 7 days 137 -21%
Last 30 days 628 -6%
Last 90 days 2.308 -2%
Last 365 days 8.755 +85%

Maintainer

Maintainer

Sam Abbott

sam.abbott@lshtm.ac.uk

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

ctb

Sophie Meakin

ctb

James Munday

ctb

Nikos Bosse

ctb

Paul Mee

ctb

Peter Ellis

ctb

Pietro Monticone

ctb

Lloyd Chapman

ctb

James M. Azam

ctb

Andrew Johnson

ctb

EpiForecasts

aut

Sebastian Funk

aut

Material

README
NEWS
Reference manual
Package source

In Views

Epidemiology

Vignettes

Case studies and use in the literature
Model definition: estimate_infections()
Model definition: estimate_secondary()
Model definition: estimate_truncation()
Gaussian Process implementation details

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

EpiNow2 archive

Depends

R ≥ 3.5.0

Imports

data.table
futile.logger ≥ 1.4
future
future.apply
ggplot2
lifecycle
lubridate
methods
patchwork
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

Suggests

covr
dplyr
here
kableExtra
knitr
magrittr
precommit
rmarkdown
spelling
styler
testthat
tidyr
withr

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