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