Data on the 1972 smallpox epidemic in Kosovo
Function to ensure compatibility with EpiEstim versions <2.0
Function to ensure compatibility with EpiEstim versions <2.0
Data on the 1918 H1N1 influenza pandemic in Baltimore.
Function to ensure compatibility with EpiEstim versions <2.0
Data on the 1861 measles epidemic in Hagelloch, Germany.
Data on the 2009 H1N1 influenza pandemic in a school in Pennsylvania.
Function to ensure compatibility with EpiEstim versions <2.0
Data on the 2003 SARS epidemic in Hong Kong.
Mock data on a rotavirus epidemic.
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 from the posterior R distribution
Estimation of the case reproduction number using the Wallinga and Teunis
method
Wrapper for plot.estimate_R
Data on the 2009 H1N1 influenza pandemic in a school in New York city
Discretized Generation Time Distribution Assuming A Shifted Gamma
Distribution
Estimated Instantaneous Reproduction Number
estimate_R estimates the reproduction number of an epidemic, given the
incidence time series and the serial interval distribution.
Set and check parameter settings of estimate_R
Link coarseDataTools and EpiEstim
check_cdt_samples_convergence
Checking convergence of an MCMC chain by using the Gelman-Rubin algorithm
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").
Data on Middle East Respiratory Syndrome (MERS) in Saudi Arabia.
Plot outputs of estimate_r
Overall Infectivity Due To Previously Infected Individuals