Package index • epidist

Simulation

Tools for simulating datasets

simulate_exponential_cases(): Simulate exponential cases

simulate_gillespie(): Simulate cases from a stochastic SIR model

simulate_secondary(): Simulate secondary events based on a delay distribution

simulate_uniform_cases(): Simulate cases from a uniform distribution

Observe

Functions for observing data

filter_obs_by_obs_time(): Filter observations based on a observation time of secondary events

filter_obs_by_ptime(): Filter observations based on the observation time of primary events

observe_process(): Observation process for primary and secondary events

S3 generics

S3 generics for delay modelling

epidist(): Fit epidemiological delay distributions using a brms interface

epidist_family(): Define model specific family

epidist_formula(): Define a model specific formula

epidist_stancode(): Define model specific Stan code

epidist_validate(): Validate a data object for use with epidist()

Method default

Default methods for S3 generics

epidist(<default>): Default method used for interface using brms

epidist_family(<default>): Default method for defining a model specific family

epidist_formula(<default>): Default method for defining a model specific formula

epidist_stancode(<default>): Default method for defining model specific Stan code

epidist_validate(<default>): Default method for data validation

Priors

Functions for specifying prior distributions

epidist_family_prior(): Family specific prior distributions

epidist_family_prior(<default>): Default family specific prior distributions

epidist_family_prior(<lognormal>): Family specific prior distributions for the lognormal family

epidist_model_prior(): Model specific prior distributions

epidist_model_prior(<default>): Default model specific prior distributions

epidist_prior(): Define prior distributions using brms defaults, model specific priors, family specific priors, and user provided priors

Latent individual model

Specific methods for the latent individual model

as_latent_individual(): Prepare latent individual model

epidist_family(<epidist_latent_individual>): Check if data has the epidist_latent_individual class

epidist_formula(<epidist_latent_individual>): Define a formula for the latent_individual model

epidist_validate(<epidist_latent_individual>): Validate latent individual model data

is_latent_individual(): Check if data has the epidist_latent_individual class

Postprocess

Functions for postprocessing model output

add_mean_sd(): Add natural scale mean and standard deviation parameters

add_mean_sd(<default>): Default method for add natural scale parameters

add_mean_sd(<gamma_samples>): Add natural scale mean and standard deviation parameters for a latent gamma model

add_mean_sd(<lognormal_samples>): Add natural scale mean and standard deviation parameters for a latent lognormal model

predict_delay_parameters() predict_dpar(): Extract samples of the delay distribution parameters

Data

Data included with the package

sierra_leone_ebola_data: Ebola linelist data from Fang et al. (2016)

Utility functions

Diagnostic functions

epidist_diagnostics(): Diagnostics for epidist_fit models