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EpiEstim

A tool to estimate time varying instantaneous reproduction number during epidemics

This tool is described in the following paper:

A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics Anne Cori, Neil M. Ferguson, Christophe Fraser and Simon Cauchemez American Journal of Epidemiology 2013.

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Version

Install

install.packages('EpiEstim')

Monthly Downloads

1,411

Version

2.2-4

License

GPL (>= 2)

Issues

47

Pull Requests

1

Stars

96

Forks

39

Maintainer

Anne Cori

Last Published

January 7th, 2021

Functions in EpiEstim (2.2-4)

Smallpox1972

Data on the 1972 smallpox epidemic in Kosovo
EstimateR

Function to ensure compatibility with EpiEstim versions <2.0
OverallInfectivity

Function to ensure compatibility with EpiEstim versions <2.0
Flu1918

Data on the 1918 H1N1 influenza pandemic in Baltimore.
DiscrSI

Function to ensure compatibility with EpiEstim versions <2.0
Measles1861

Data on the 1861 measles epidemic in Hagelloch, Germany.
Flu2009

Data on the 2009 H1N1 influenza pandemic in a school in Pennsylvania.
WT

Function to ensure compatibility with EpiEstim versions <2.0
SARS2003

Data on the 2003 SARS epidemic in Hong Kong.
MockRotavirus

Mock data on a rotavirus epidemic.
init_mcmc_params

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
sample_posterior_R

sample from the posterior R distribution
wallinga_teunis

Estimation of the case reproduction number using the Wallinga and Teunis method
estimate_R_plots

Wrapper for plot.estimate_R
flu_2009_NYC_school

Data on the 2009 H1N1 influenza pandemic in a school in New York city
discr_si

Discretized Generation Time Distribution Assuming A Shifted Gamma Distribution
estimate_R

Estimated Instantaneous Reproduction Number estimate_R estimates the reproduction number of an epidemic, given the incidence time series and the serial interval distribution.
make_config

Set and check parameter settings of estimate_R
coarse2estim

Link coarseDataTools and EpiEstim
check_cdt_samples_convergence

Checking convergence of an MCMC chain by using the Gelman-Rubin algorithm
make_mcmc_control

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").
mers_2014_15

Data on Middle East Respiratory Syndrome (MERS) in Saudi Arabia.
plot.estimate_R

Plot outputs of estimate_r
overall_infectivity

Overall Infectivity Due To Previously Infected Individuals