EpiEstim

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.

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.

Function to ensure compatibility with EpiEstim versions <2.0

Data on the 2003 SARS epidemic in Hong Kong.

Data on the 1972 smallpox epidemic in Kosovo

Function to ensure compatibility with EpiEstim versions <2.0

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

Link coarseDataTools and EpiEstim

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.

Wrapper for plot.estimate_R

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

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

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.

Overall Infectivity Due To Previously Infected Individuals

Plot outputs of estimate_r

sample from the posterior R distribution

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