Estimate Time Varying Reproduction Numbers from Epidemic Curves

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Documentation for package ‘EpiEstim’ version 2.2-4

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check_cdt_samples_convergence Checking convergence of an MCMC chain by using the Gelman-Rubin algorithm
coarse2estim Link coarseDataTools and EpiEstim
DiscrSI Function to ensure compatibility with EpiEstim versions <2.0
discr_si Discretized Generation Time Distribution Assuming A Shifted Gamma Distribution
EstimateR Function to ensure compatibility with EpiEstim versions <2.0
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.
estimate_R_plots Wrapper for plot.estimate_R
Flu1918 Data on the 1918 H1N1 influenza pandemic in Baltimore.
Flu2009 Data on the 2009 H1N1 influenza pandemic in a school in Pennsylvania.
flu_2009_NYC_school Data on the 2009 H1N1 influenza pandemic in a school in New York city
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'
make_config Set and check parameter settings of estimate_R
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").
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.
OverallInfectivity Function to ensure compatibility with EpiEstim versions <2.0
overall_infectivity Overall Infectivity Due To Previously Infected Individuals
plot.estimate_R Plot outputs of estimate_r
sample_posterior_R sample from the posterior R distribution
SARS2003 Data on the 2003 SARS epidemic in Hong Kong.
Smallpox1972 Data on the 1972 smallpox epidemic in Kosovo
wallinga_teunis Estimation of the case reproduction number using the Wallinga and Teunis method
WT Function to ensure compatibility with EpiEstim versions <2.0