Package: EpiEstim 3.0.0

Anne Cori

EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves

Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.

Authors:Anne Cori [aut, cre], Simon Cauchemez [ctb], Neil M. Ferguson [ctb], Christophe Fraser [ctb], Elisabeth Dahlqwist [ctb], P. Alex Demarsh [ctb], Thibaut Jombart [ctb], Zhian N. Kamvar [ctb], Justin Lessler [ctb], Shikun Li [ctb], Jonathan A. Polonsky [ctb], Jake Stockwin [ctb], Robin Thompson [ctb], Rolina van Gaalen [ctb], Rebecca Nash [ctb], Sangeeta Bhatia [ctb], Jack Wardle [ctb], Andrea Brizzi [ctb]

EpiEstim_3.0.0.tar.gz
EpiEstim_3.0.0.zip(r-4.7)EpiEstim_3.0.0.zip(r-4.6)EpiEstim_3.0.0.zip(r-4.5)
EpiEstim_3.0.0.tgz(r-4.6-any)EpiEstim_3.0.0.tgz(r-4.5-any)
EpiEstim_3.0.0.tar.gz(r-4.7-any)EpiEstim_3.0.0.tar.gz(r-4.6-any)
EpiEstim_3.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
EpiEstim/json (API)
NEWS

# Install 'EpiEstim' in R:

install.packages('EpiEstim', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrc-ide/epiestim/issues

Datasets:

covid_deaths_2020_uk - Data on the 2020-2022 SARS-CoV-2 epidemic in the UK.
flu_2009_NYC_school - Data on the 2009 H1N1 influenza pandemic in a school in New York city
Flu1918 - Data on the 1918 H1N1 influenza pandemic in Baltimore.
Flu2009 - Data on the 2009 H1N1 influenza pandemic in a school in Pennsylvania.
Measles1861 - Data on the 1861 measles epidemic in Hagelloch, Germany.
mers_2014_15 - Data on Middle East Respiratory Syndrome (MERS) in Saudi Arabia.
MockRotavirus - Mock data on a rotavirus epidemic.
SARS2003 - Data on the 2003 SARS epidemic in Hong Kong.
Smallpox1972 - Data on the 1972 smallpox epidemic in Kosovo

On CRAN:

12.74 score 103 stars 7 packages 1.2k scripts 1.1k downloads 60 mentions 31 exports 56 dependencies

Last updated from:8ae0cfb2c1 (on main). Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	139
source / vignettes	OK	279
linux-release-x86_64	ERROR	132
macos-release-arm64	ERROR	85
macos-oldrel-arm64	ERROR	82
windows-devel	ERROR	78
windows-release	ERROR	76
windows-oldrel	ERROR	79
wasm-release	OK	144

Exports:aggregate_inc backimpute_I check_cdt_samples_convergence coarse2estim compute_lambda compute_si_cutoff compute_t_min default_mcmc_controls default_priors discr_si DiscrSI draw_epsilon draw_R estimate_advantage estimate_R estimate_R_agg estimate_R_plots EstimateR first_nonzero_incid get_shape_epsilon get_shape_R_flat init_mcmc_params make_config make_mcmc_control overall_infectivity OverallInfectivity process_I_multivariant sample_posterior_R si_from_data_valid_distrs wallinga_teunis WT

Dependencies:abind aweek cli coarseDataTools coda cpp11 data.table distcrete dplyr epitrix farver fastymd fitdistrplus generics ggplot2 glue grates gtable incidence incidence2 isoband labeling lattice lifecycle magrittr MASS Matrix MatrixModels mcmc MCMCpack patchwork pillar pkgconfig plyr purrr quantreg R6 RColorBrewer Rcpp reshape2 rlang S7 scales sodium SparseM stringi stringr survival tibble tidyr tidyselect utf8 vctrs viridisLite withr ympes

Alternative software for estimating the reproduction number

Rendered fromalternative_software.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2023-04-20
Started: 2022-04-01

Dealing with missed generations of infections with EpiEstim

Andrea Brizzi

Rendered fromEpiEstim_backimputation.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2026-03-27
Started: 2024-08-30

EpiEstim: a demonstration

Anne Cori

Rendered fromshort_demo.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2026-03-25
Started: 2021-04-09

EpiEstim for aggregated incidence data

Rebecca Nash

Rendered fromEpiEstim_aggregated_data.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2026-03-25
Started: 2022-12-07

EpiEstim Vignette

Rebecca Nash

Rendered fromfull_EpiEstim_vignette.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2026-03-27
Started: 2021-04-09

MV-EpiEstim

Rendered fromMV_EpiEstim_vignette.Rmdusingknitr::rmarkdownon May 15 2026.

Last update: 2026-03-27
Started: 2021-11-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Aggregating daily incidence to longer time windows	aggregate_inc
Impute unobserved generations of infection	backimpute_I
Check MCMC chain convergence using the Gelman-Rubin algorithm	check_cdt_samples_convergence
Link coarseDataTools and EpiEstim	coarse2estim
Compute the overall infectivity	compute_lambda
Index before which at most a given probability mass is captured	compute_si_cutoff
Compute the smallest index at which joint estimation should start	compute_t_min
Data on the 2020-2022 SARS-CoV-2 epidemic in the UK.	covid_deaths_2020_uk
Set default for MCMC control	default_mcmc_controls
Set default for Gamma priors	default_priors
Compute discretized generation time distribution	discr_si
Function to ensure compatibility with EpiEstim versions <2.0	DiscrSI
Draw epsilon from marginal posterior distribution	draw_epsilon
Draw R from marginal posterior distribution	draw_R
Estimate instantaneous reproduction number	estimate_advantage
Estimate the instantaneous reproduction number	estimate_R
Estimate instantaneous reproduction number from coarsely aggregated data	estimate_R_agg
Wrapper for plot.estimate_R	estimate_R_plots
Function to ensure compatibility with EpiEstim versions <2.0	EstimateR
First day of non-zero incidence	first_nonzero_incid
Data on the 2009 H1N1 influenza pandemic in a school in New York city	flu_2009_NYC_school
Data on the 1918 H1N1 influenza pandemic in Baltimore.	Flu1918
Data on the 2009 H1N1 influenza pandemic in a school in Pennsylvania.	Flu2009
Precompute shape of posterior distribution for epsilon	get_shape_epsilon
Precompute shape of posterior distribution for R	get_shape_R_flat
Find clever starting points for MCMC estimation	init_mcmc_params
Set and check parameter settings for 'estimate_R()'	make_config
Create list of MCMC control parameters	make_mcmc_control
Data on the 1861 measles epidemic in Hagelloch, Germany.	Measles1861
Data on Middle East Respiratory Syndrome (MERS) in Saudi Arabia.	mers_2014_15
Mock data on a rotavirus epidemic.	MockRotavirus
Overall Infectivity Due To Previously Infected Individuals	overall_infectivity
Function to ensure compatibility with EpiEstim versions <2.0	OverallInfectivity
Plot outputs of 'estimate_R()'	plot.estimate_R plot.wallinga_teunis
Process incidence input for multivariant analyses	process_I_multivariant
Sample from the posterior R distribution	sample_posterior_R
Data on the 2003 SARS epidemic in Hong Kong.	SARS2003
Distribution names valid when using MCMC to estimate SI from data	si_from_data_valid_distrs
Data on the 1972 smallpox epidemic in Kosovo	Smallpox1972
Estimate case reproduction number using the Wallinga and Teunis method	wallinga_teunis wallinga_teunis.data.frame wallinga_teunis.default wallinga_teunis.incidence wallinga_teunis.incidence2 wallinga_teunis.integer wallinga_teunis.numeric
Function to ensure compatibility with EpiEstim versions <2.0	WT