Estimate Epidemiological Delay Distributions with 'brms'

Documentation for package ‘epidist’ version 1.0.0

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-- A --

add_delay_parameter_draws	Posterior draws of the delay distribution parameters
add_summaries	Add natural scale summaries of the delay distribution
assert_epidist	Validation for epidist objects
assert_epidist.epidist_aggregate_data	Assert validity of 'epidist_aggregate_data' objects
assert_epidist.epidist_estimates_data	Assert validity of 'epidist_estimates_data' objects
assert_epidist.epidist_linelist_data	Assert validity of 'epidist_linelist_data' objects
assert_epidist.epidist_meta_model	Assert validity of 'epidist_meta_model' objects
assert_epidist.epidist_multivariate	Assert validity of 'epidist_multivariate' objects
as_dist_spec.epidist_fit	Export a fitted delay distribution as a 'distspec' distribution
as_epidist_aggregate_data	Create an epidist_aggregate_data object
as_epidist_aggregate_data.data.frame	Create an epidist_aggregate_data object from a data.frame
as_epidist_aggregate_data.default	Create an epidist_aggregate_data object from vectors of event times
as_epidist_aggregate_data.epidist_linelist_data	Convert linelist data to aggregate format
as_epidist_estimates_data	Create an 'epidist_estimates_data' object
as_epidist_estimates_data.data.frame	Create an 'epidist_estimates_data' object from a data frame
as_epidist_estimates_data.epidist_estimates_data	Return an 'epidist_estimates_data' object unchanged
as_epidist_estimates_data.epidist_multivariate	Create an 'epidist_estimates_data' object from a multivariate representation
as_epidist_estimates_data.list	Combine 'epidist_estimates_data' objects from several studies
as_epidist_latent_model	Convert an object to an 'epidist_latent_model' object
as_epidist_latent_model.epidist_aggregate_data	The latent model method for 'epidist_aggregate_data' objects
as_epidist_latent_model.epidist_linelist_data	The latent model method for 'epidist_linelist_data' objects
as_epidist_linelist_data	Create an epidist_linelist_data object
as_epidist_linelist_data.data.frame	Create an epidist_linelist_data object from a data frame with event dates
as_epidist_linelist_data.default	Create an epidist_linelist_data object from vectors of event times
as_epidist_linelist_data.epidist_aggregate_data	Convert aggregate data to linelist format
as_epidist_marginal_model	Convert an object to an 'epidist_marginal_model' object
as_epidist_marginal_model.epidist_aggregate_data	The marginal model method for 'epidist_aggregate_data' objects
as_epidist_marginal_model.epidist_linelist_data	The marginal model method for 'epidist_linelist_data' objects
as_epidist_meta_model	Convert an object to an 'epidist_meta_model' object
as_epidist_meta_model.epidist_aggregate_data	The meta model method for 'epidist_aggregate_data' objects
as_epidist_meta_model.epidist_estimates_data	The meta model method for 'epidist_estimates_data' objects
as_epidist_meta_model.epidist_linelist_data	The meta model method for 'epidist_linelist_data' objects
as_epidist_meta_model.NULL	The meta model method for summary estimates only
as_epidist_multivariate	Create an 'epidist_multivariate' object
as_epidist_multivariate.data.frame	Create an 'epidist_multivariate' object from a data frame of draws
as_epidist_multivariate.matrix	Create an 'epidist_multivariate' object from a matrix of draws
as_epidist_naive_model	Convert an object to an 'epidist_naive_model' object
as_epidist_naive_model.epidist_aggregate_data	The naive model method for 'epidist_aggregate_data' objects
as_epidist_naive_model.epidist_linelist_data	The naive model method for 'epidist_linelist_data' objects
autoplot.epidist_delay_draws	Plot posterior draws of the delay distribution

-- D --

delay_parameter_draws	Posterior draws of the delay distribution parameters
delay_summary_draws	Posterior draws of the delay distribution, summarised
dplyr_col_modify.epidist_data	Keep 'epidist' objects in their class
dplyr_col_modify.epidist_delay_draws	Keep the 'epidist_delay_draws' class through 'dplyr' verbs
dplyr_reconstruct.epidist_data	Keep 'epidist' objects in their class
dplyr_reconstruct.epidist_delay_draws	Keep the 'epidist_delay_draws' class through 'dplyr' verbs
dplyr_row_slice.epidist_data	Keep 'epidist' objects in their class
dplyr_row_slice.epidist_delay_draws	Keep the 'epidist_delay_draws' class through 'dplyr' verbs

-- E --

epidist	Fit epidemiological delay distributions using a 'brms' interface
epidist_data	Keep 'epidist' objects in their class
epidist_delay_draws	Keep the 'epidist_delay_draws' class through 'dplyr' verbs
epidist_diagnostics	Diagnostics for 'epidist_fit' models
epidist_estimates_epireview	Report studies from an 'epireview' parameter table
epidist_estimates_parameters	Report a study that published the parameters of a distribution it fitted
epidist_estimates_summaries	Report a study that published summaries of its delays
epidist_family	Define 'epidist' family
epidist_family_model	The model-specific parts of an 'epidist_family()' call
epidist_family_model.default	Default method for defining a model specific family
epidist_family_model.epidist_latent_model	Create the model-specific component of an 'epidist' custom family
epidist_family_model.epidist_marginal_model	Create the model-specific component of an 'epidist' custom family
epidist_family_model.epidist_meta_model	Create the model-specific component of an 'epidist' custom family
epidist_family_param.default	Default method for families which do not require a reparameterisation
epidist_family_param.gengamma	Method for the 'gengamma()' family
epidist_family_prior	Family specific prior distributions
epidist_family_prior.default	Default family specific prior distributions
epidist_family_prior.gengamma	Family specific prior distributions for the generalised gamma family
epidist_family_prior.lognormal	Family specific prior distributions for the lognormal family
epidist_formula	Define a model specific formula
epidist_formula_model	The model-specific parts of an 'epidist_formula()' call
epidist_formula_model.default	Default method for defining a model specific formula
epidist_formula_model.epidist_latent_model	Define the model-specific component of an 'epidist' custom formula for the latent model
epidist_formula_model.epidist_marginal_model	Define the model-specific component of an 'epidist' custom formula for the marginal model
epidist_formula_model.epidist_meta_model	Define the model-specific component of an 'epidist' custom formula for the meta model
epidist_formula_model.epidist_naive_model	Define the model-specific component of an 'epidist' custom formula for the naive model
epidist_gen_log_lik	Create a function to calculate the marginalised log likelihood for double censored and truncated delay distributions
epidist_gen_meta_log_lik	Create a function to calculate the meta model log likelihood
epidist_gen_meta_predict	Create a function to draw from the meta model posterior predictive distribution
epidist_gen_posterior_epred	Create a function to draw from the expected value of the posterior predictive distribution for a model
epidist_gen_posterior_predict	Create a function to draw from the posterior predictive distribution for a double censored and truncated delay distribution
epidist_meta_leave_one_out	Refit a meta model leaving each study out in turn
epidist_model_prior	Model specific prior distributions
epidist_model_prior.default	Default model specific prior distributions
epidist_model_prior.epidist_latent_model	Model specific prior distributions for latent models
epidist_model_prior.epidist_meta_model	Model specific prior distributions for the meta model
epidist_newdata	Build 'newdata' for prediction from an 'epidist' data object
epidist_newdata.default	Default method for building 'newdata'
epidist_newdata.epidist_latent_model	Build 'newdata' for the latent model
epidist_newdata.epidist_marginal_model	Build 'newdata' for the marginal model
epidist_newdata.epidist_meta_model	Build 'newdata' for the meta model
epidist_newdata.epidist_naive_model	Build 'newdata' for the naive model
epidist_prior	Define custom prior distributions for epidist models
epidist_stancode	Define model specific Stan code
epidist_stancode.default	Default method for defining model specific Stan code
epidist_stancode.epidist_naive_model	Define the Stan code of the naive model
epidist_strata	Unique combinations of the predictors in a model
epidist_transform_data_model	The model-specific parts of an 'epidist_transform_data()' call
epidist_transform_data_model.default	Default method for transforming data for a model
epidist_transform_data_model.epidist_marginal_model	Transform data for the marginal model
epidist_transform_data_model.epidist_meta_model	Transform data for the meta model
epidist_transform_data_model.epidist_naive_model	Transform data for the naive model

-- G --

gengamma	Generalised gamma delay distribution family
group_by.epidist_data	Keep 'epidist' objects in their class
group_by.epidist_delay_draws	Keep the 'epidist_delay_draws' class through 'dplyr' verbs

-- I --

is_epidist_aggregate_data	Check if data has the 'epidist_aggregate_data' class
is_epidist_data	Check if data has the 'epidist_data' class
is_epidist_estimates_data	Check if data has the 'epidist_estimates_data' class
is_epidist_latent_model	Check if data has the 'epidist_latent_model' class
is_epidist_linelist_data	Check if data has the 'epidist_linelist_data' class
is_epidist_marginal_model	Check if data has the 'epidist_marginal_model' class
is_epidist_meta_model	Check if data has the 'epidist_meta_model' class
is_epidist_multivariate	Check if an object has the 'epidist_multivariate' class
is_epidist_naive_model	Check if data has the 'epidist_naive_model' class

-- N --

names<-.epidist_data	Keep 'epidist' objects in their class
names<-.epidist_delay_draws	Keep the 'epidist_delay_draws' class through 'dplyr' verbs
new_epidist_aggregate_data	Class constructor for 'epidist_aggregate_data' objects
new_epidist_estimates_data	Class constructor for 'epidist_estimates_data' objects
new_epidist_latent_model	Class constructor for 'epidist_latent_model' objects
new_epidist_linelist_data	Class constructor for 'epidist_linelist_data' objects
new_epidist_marginal_model	Class constructor for 'epidist_marginal_model' objects
new_epidist_meta_model	Class constructor for 'epidist_meta_model' objects
new_epidist_multivariate	Class constructor for 'epidist_multivariate' objects
new_epidist_naive_model	Class constructor for 'epidist_naive_model' objects

-- P --

plot.epidist_delay_draws	Plot posterior draws of the delay distribution
plot_delays	Plot the observed delay distribution
plot_delays.default	Default method for plotting observed delays
plot_delays.epidist_fit	Plot the delays a fitted model predicts over the delays it was fitted to
plot_delays.epidist_linelist_data	Plot the observed delays of a dataset
plot_delays.list	Compare the observed delays of several datasets
plot_events	Plot the primary and secondary event windows of each case
print.epidist_multivariate	Print an 'epidist_multivariate' object

-- R --

rbind.epidist_data

Keep 'epidist' objects in their class

-- S --

sierra_leone_ebola_data	Ebola linelist data from Fang et al. (2016)
simulate_dates	Convert simulated event times to dates
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_study	Simulate the summaries a published study would have reported
simulate_uniform_cases	Simulate cases from a uniform distribution

-- U --

ungroup.epidist_data	Keep 'epidist' objects in their class
ungroup.epidist_delay_draws	Keep the 'epidist_delay_draws' class through 'dplyr' verbs

-- V --

vcov.epidist_multivariate

The covariance matrix of an 'epidist_multivariate' object

-- misc --

$<-.epidist_data	Keep 'epidist' objects in their class
[.epidist_data	Keep 'epidist' objects in their class
[.epidist_delay_draws	Keep the 'epidist_delay_draws' class through 'dplyr' verbs
[<-.epidist_data	Keep 'epidist' objects in their class
[[<-.epidist_data	Keep 'epidist' objects in their class