Package index
-
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
-
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
-
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()
-
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
-
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
-
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
-
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
-
sierra_leone_ebola_data
- Ebola linelist data from Fang et al. (2016)
-
epidist_diagnostics()
- Diagnostics for
epidist_fit
models