R: Estimate Time Varying Reproduction Numbers from Epidemic Curves

# Estimate Time Varying Reproduction Numbers from Epidemic Curves

## Documentation for package ‘EpiEstim’ version 2.2-5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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_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