Man pages for annecori/EpiEstim
Estimate Time Varying Reproduction Numbers from Epidemic Curves
| aggregate_inc | Aggregating daily incidence to longer time windows |
| backimpute_I | Impute unobserved generations of infection |
| check_cdt_samples_convergence | Checking convergence of an MCMC chain by using the... |
| coarse2estim | Link coarseDataTools and EpiEstim |
| compute_lambda | Compute the overall infectivity |
| compute_si_cutoff | Index before which at most a given probability mass is... |
| compute_t_min | Compute the smallest index at which joint estimation should... |
| covid_deaths_2020_uk | Data on the 2020-2022 SARS-CoV-2 epidemic in the UK. |
| default_mcmc_controls | Set default for MCMC control |
| default_priors | Set default for Gamma priors |
| discr_si | Discretized Generation Time Distribution Assuming A Shifted... |
| DiscrSI | Function to ensure compatibility with EpiEstim versions <2.0 |
| draw_epsilon | Draw epsilon from marginal posterior distribution |
| draw_R | Draw R from marginal posterior distribution |
| estimate_advantage | Jointly estimate the instantaneous reproduction number for a... |
| estimate_R | Estimated Instantaneous Reproduction Number |
| EstimateR | Function to ensure compatibility with EpiEstim versions <2.0 |
| estimate_R_agg | Estimated Instantaneous Reproduction Number from coarsely... |
| estimate_R_plots | Wrapper for plot.estimate_R |
| first_nonzero_incid | Get the first day of non-zero incidence across all variants... |
| Flu1918 | Data on the 1918 H1N1 influenza pandemic in Baltimore. |
| Flu2009 | Data on the 2009 H1N1 influenza pandemic in a school in... |
| flu_2009_NYC_school | Data on the 2009 H1N1 influenza pandemic in a school in New... |
| get_shape_epsilon | Precompute shape of posterior distribution for epsilon |
| get_shape_R_flat | Precompute shape of posterior distribution for R |
| init_mcmc_params | init_mcmc_params Finds clever starting points for the MCMC to... |
| make_config | Set and check parameter settings of estimate_R |
| make_mcmc_control | make_mcmc_control Creates a list of mcmc control parameters... |
| Measles1861 | Data on the 1861 measles epidemic in Hagelloch, Germany. |
| mers_2014_15 | Data on Middle East Respiratory Syndrome (MERS) in Saudi... |
| MockRotavirus | Mock data on a rotavirus epidemic. |
| overall_infectivity | Overall Infectivity Due To Previously Infected Individuals |
| OverallInfectivity | Function to ensure compatibility with EpiEstim versions <2.0 |
| plot.estimate_R | Plot outputs of estimate_r |
| process_I_multivariant | Process incidence input for multivariant analyses with... |
| 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... |
| WT | Function to ensure compatibility with EpiEstim versions <2.0 |
