Package: EpiEstim 2.4

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_2.4.tar.gz
EpiEstim_2.4.zip(r-4.5)EpiEstim_2.4.zip(r-4.4)EpiEstim_2.4.zip(r-4.3)
EpiEstim_2.4.tgz(r-4.4-any)EpiEstim_2.4.tgz(r-4.3-any)
EpiEstim_2.4.tar.gz(r-4.5-noble)EpiEstim_2.4.tar.gz(r-4.4-noble)
EpiEstim_2.4.tgz(r-4.4-emscripten)EpiEstim_2.4.tgz(r-4.3-emscripten)
EpiEstim.pdf |EpiEstim.html✨
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:

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.
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
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
mers_2014_15 - Data on Middle East Respiratory Syndrome (MERS) in Saudi Arabia.

On CRAN:

10.98 score 94 stars 7 packages 1.2k scripts 1.1k downloads 30 exports 56 dependencies

Last updated 3 months agofrom:238d43548d (on master). Checks:OK: 3 NOTE: 3 ERROR: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 29 2024
R-4.5-win	ERROR	Oct 29 2024
R-4.5-linux	NOTE	Oct 29 2024
R-4.4-win	NOTE	Oct 29 2024
R-4.4-mac	NOTE	Oct 29 2024
R-4.3-win	OK	Oct 29 2024
R-4.3-mac	OK	Oct 29 2024

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 wallinga_teunis WT

Dependencies:abind aweek cli coarseDataTools coda colorspace cpp11 distcrete dplyr epitrix fansi farver fitdistrplus generics ggplot2 glue gridExtra gtable incidence isoband labeling lattice lifecycle magrittr MASS Matrix MatrixModels mcmc MCMCpack mgcv munsell nlme patchwork pillar pkgconfig plyr purrr quantreg R6 RColorBrewer Rcpp reshape2 rlang scales sodium SparseM stringi stringr survival tibble tidyr tidyselect utf8 vctrs viridisLite withr

Alternative software for estimating the reproduction number

Rendered fromalternative_software.Rmdusingknitr::rmarkdownon Oct 29 2024.

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

Dealing with missed generations of infections with EpiEstim

Andrea Brizzi

Rendered fromEpiEstim_backimputation.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-08-30
Started: 2024-08-30

EpiEstim: a demonstration

Anne Cori

Rendered fromshort_demo.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-08-30
Started: 2021-04-09

EpiEstim for aggregated incidence data

Rebecca Nash

Rendered fromEpiEstim_aggregated_data.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2023-07-03
Started: 2022-12-07

EpiEstim Vignette

Rebecca Nash

Rendered fromfull_EpiEstim_vignette.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-08-30
Started: 2021-04-09

MV-EpiEstim

Rendered fromMV_EpiEstim_vignette.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2024-08-30
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
Checking convergence of an MCMC chain by 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
Discretized Generation Time Distribution Assuming A Shifted Gamma 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
Jointly estimate the instantaneous reproduction number for a reference pathogen/strain/variant and the relative transmissibility of a "new" pathogen/strain/variant	estimate_advantage
Estimated Instantaneous Reproduction Number	estimate_R
Estimated 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
Get the first day of non-zero incidence across all variants and locations.	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
init_mcmc_params Finds clever starting points for the MCMC to be used to estimate the serial interval, e.g. when using option 'si_from_data' in 'estimate_R'	init_mcmc_params
Set and check parameter settings of estimate_R	make_config
make_mcmc_control Creates a list of mcmc control parameters to be used in 'config$mcmc_control', where 'config' is an argument of the 'estimate_R' function. This is used to configure the MCMC chain used to estimate the serial interval within 'estimate_R' (with method "si_from_data").	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
Process incidence input for multivariant analyses with estimate_advantage	process_I_multivariant
sample from the posterior R distribution	sample_posterior_R
Data on the 2003 SARS epidemic in Hong Kong.	SARS2003
Data on the 1972 smallpox epidemic in Kosovo	Smallpox1972
Estimation of the case reproduction number using the Wallinga and Teunis method	wallinga_teunis
Function to ensure compatibility with EpiEstim versions <2.0	WT