Estimate Time Varying Reproduction Numbers from Epidemic Curves
Checking convergence of an MCMC chain by using the Gelman-Rubin algori...
Link coarseDataTools and EpiEstim
Discretized Generation Time Distribution Assuming A Shifted Gamma Dist...
Function to ensure compatibility with EpiEstim versions <2.0
Estimated Instantaneous Reproduction Numberestimate_R estimates the ...
Wrapper for plot.estimate_R
Function to ensure compatibility with EpiEstim versions <2.0
init_mcmc_params Finds clever starting points for the MCMC to be used ...
Set and check parameter settings of estimate_R
make_mcmc_control Creates a list of mcmc control parameters to be used...
Overall Infectivity Due To Previously Infected Individuals
Function to ensure compatibility with EpiEstim versions <2.0
Plot outputs of estimate_r
sample from the posterior R distribution
Estimation of the case reproduction number using the Wallinga and Teun...
Function to ensure compatibility with EpiEstim versions <2.0
Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.