Reference

Pre-processing

aggregate_inc()

Aggregating daily incidence to longer time windows

backimpute_I()

Impute unobserved generations of infection

compute_si_cutoff()

Index before which at most a given probability mass is captured

compute_t_min()

Compute the smallest index at which joint estimation should start

discr_si()

Compute discretized generation time distribution

first_nonzero_incid()

First day of non-zero incidence

get_shape_R_flat()

Precompute shape of posterior distribution for R

get_shape_epsilon()

Precompute shape of posterior distribution for epsilon

si_from_data_valid_distrs()

Distribution names valid when using MCMC to estimate SI from data

Estimation

estimate_R()

Estimate the instantaneous reproduction number

estimate_R_agg()

Estimate instantaneous reproduction number from coarsely aggregated data

estimate_advantage()

Estimate instantaneous reproduction number

compute_lambda()

Compute the overall infectivity

overall_infectivity()

Overall Infectivity Due To Previously Infected Individuals

process_I_multivariant()

Process incidence input for multivariant analyses

wallinga_teunis()

Estimate case reproduction number using the Wallinga and Teunis method

Post-processing

MCMC diagnostics

check_cdt_samples_convergence()

Check MCMC chain convergence using the Gelman-Rubin algorithm

Draw from posterior

draw_R()

Draw R from marginal posterior distribution

draw_epsilon()

Draw epsilon from marginal posterior distribution

sample_posterior_R()

Sample from the posterior R distribution

Helpers

Default settings

default_mcmc_controls()

Set default for MCMC control

default_priors()

Set default for Gamma priors

init_mcmc_params()

Find clever starting points for MCMC estimation

make_config()

Set and check parameter settings for estimate_R()

make_mcmc_control()

Create list of MCMC control parameters

Plotting functions

plot(<estimate_R>) plot(<wallinga_teunis>)

Plot outputs of estimate_R()

estimate_R_plots()

Wrapper for plot.estimate_R

Backwards-compatibility functions

DiscrSI()

Function to ensure compatibility with EpiEstim versions <2.0

EstimateR()

Function to ensure compatibility with EpiEstim versions <2.0

OverallInfectivity()

Function to ensure compatibility with EpiEstim versions <2.0

WT()

Function to ensure compatibility with EpiEstim versions <2.0

External package compatibility functions

coarse2estim()

Link coarseDataTools and EpiEstim

Datasets

Flu1918

Data on the 1918 H1N1 influenza pandemic in Baltimore.

Flu2009

Data on the 2009 H1N1 influenza pandemic in a school in Pennsylvania.

Measles1861

Data on the 1861 measles epidemic in Hagelloch, Germany.

MockRotavirus

Mock data on a rotavirus epidemic.

SARS2003

Data on the 2003 SARS epidemic in Hong Kong.

Smallpox1972

Data on the 1972 smallpox epidemic in Kosovo

covid_deaths_2020_uk

Data on the 2020-2022 SARS-CoV-2 epidemic in the UK.

flu_2009_NYC_school

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

mers_2014_15

Data on Middle East Respiratory Syndrome (MERS) in Saudi Arabia.