Package index
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aggregate_inc() - Aggregating daily incidence to longer time windows
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backimpute_I() - Impute unobserved generations of infection
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compute_si_cutoff() - Index before which at most a given probability mass is captured
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compute_t_min() - Compute the smallest index at which joint estimation should start
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discr_si() - Compute discretized generation time distribution
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first_nonzero_incid() - First day of non-zero incidence
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get_shape_R_flat() - Precompute shape of posterior distribution for R
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get_shape_epsilon() - Precompute shape of posterior distribution for epsilon
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si_from_data_valid_distrs() - Distribution names valid when using MCMC to estimate SI from data
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estimate_R() - Estimate the instantaneous reproduction number
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estimate_R_agg() - Estimate instantaneous reproduction number from coarsely aggregated data
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estimate_advantage() - Estimate instantaneous reproduction number
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compute_lambda() - Compute the overall infectivity
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overall_infectivity() - Overall Infectivity Due To Previously Infected Individuals
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process_I_multivariant() - Process incidence input for multivariant analyses
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wallinga_teunis() - Estimate case reproduction number using the Wallinga and Teunis method
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check_cdt_samples_convergence() - Check MCMC chain convergence using the Gelman-Rubin algorithm
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draw_R() - Draw R from marginal posterior distribution
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draw_epsilon() - Draw epsilon from marginal posterior distribution
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sample_posterior_R() - Sample from the posterior R distribution
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default_mcmc_controls() - Set default for MCMC control
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default_priors() - Set default for Gamma priors
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init_mcmc_params() - Find clever starting points for MCMC estimation
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make_config() - Set and check parameter settings for
estimate_R() -
make_mcmc_control() - Create list of MCMC control parameters
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plot(<estimate_R>)plot(<wallinga_teunis>) - Plot outputs of
estimate_R() -
estimate_R_plots() - Wrapper for plot.estimate_R
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DiscrSI() - Function to ensure compatibility with EpiEstim versions <2.0
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EstimateR() - Function to ensure compatibility with EpiEstim versions <2.0
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OverallInfectivity() - Function to ensure compatibility with EpiEstim versions <2.0
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WT() - Function to ensure compatibility with EpiEstim versions <2.0
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coarse2estim() - Link coarseDataTools and EpiEstim
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Flu1918 - Data on the 1918 H1N1 influenza pandemic in Baltimore.
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Flu2009 - Data on the 2009 H1N1 influenza pandemic in a school in Pennsylvania.
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Measles1861 - Data on the 1861 measles epidemic in Hagelloch, Germany.
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MockRotavirus - Mock data on a rotavirus epidemic.
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SARS2003 - Data on the 2003 SARS epidemic in Hong Kong.
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Smallpox1972 - Data on the 1972 smallpox epidemic in Kosovo
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covid_deaths_2020_uk - Data on the 2020-2022 SARS-CoV-2 epidemic in the UK.
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flu_2009_NYC_school - Data on the 2009 H1N1 influenza pandemic in a school in New York city
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mers_2014_15 - Data on Middle East Respiratory Syndrome (MERS) in Saudi Arabia.