Function reference • epinowcast

Nowcast

Functions for nowcasting.

epinowcast(): Nowcast right censored data

plot(<epinowcast>): Plot method for epinowcast

summary(<epinowcast>): Summary method for epinowcast

Preprocess

Functions for preprocessing observations.

enw_add_metaobs_features(): FUNCTION_TITLE

enw_assign_group(): FUNCTION_TITLE

enw_extend_date(): FUNCTION_TITLE

enw_latest_data(): FUNCTION_TITLE

enw_metadata(): FUNCTION_TITLE

enw_new_reports(): FUNCTION_TITLE

enw_preprocess_data(): FUNCTION_TITLE

enw_reporting_triangle(): FUNCTION_TITLE

enw_reporting_triangle_to_long(): FUNCTION_TITLE

enw_retrospective_data(): FUNCTION_TITLE

Model design tools

Functions that assist with designing models.

enw_add_cumulative_membership(): FUNCTION_TITLE

enw_add_pooling_effect(): FUNCTION_TITLE

enw_dates_to_factors(): FUNCTION_TITLE

enw_design(): FUNCTION_TITLE

enw_effects_metadata(): FUNCTION_TITLE

enw_formula(): FUNCTION_TITLE

Model tools

Functions that assist with interpreting models for stan.

enw_formula_as_data_list(): Format formula data for use with stan

enw_opts_as_data_list(): Format model options for use with stan

enw_posterior_as_prior(): FUNCTION_TITLE

enw_priors_as_data_list(): FUNCTION_TITLE

remove_profiling(): Remove profiling statements from a character vector representing stan code

write_stan_files_no_profile(): Write copies of the .stan files of a Stan model and its #include files with all profiling statements removed.

Model

Functions for fitting the nowcasting model.

enw_as_data_list(): Format data for use with stan

enw_inits(): Set up initial conditions for model

enw_model(): Load and compile the nowcasting model

enw_obs_as_data_list(): Format observed data for use with stan

enw_priors(): FUNCTION_TITLE

enw_sample(): Fit a CmdStan model using NUTS

Postprocess

Functions for postprocessing model output.

enw_add_latest_obs_to_nowcast(): FUNCTION_TITLE

enw_nowcast_samples(): FUNCTION_TITLE

enw_nowcast_summary(): FUNCTION_TITLE

enw_posterior(): Summarise the posterior

enw_pp_summary(): FUNCTION_TITLE

enw_quantiles_to_long(): Convert summarised quantiles from wide to long format

enw_summarise_samples(): FUNCTION_TITLE

Plot

Functions for plotting postprocessed nowcast model output.

enw_plot_nowcast_quantiles(): Plot nowcast quantiles

enw_plot_obs(): Generic quantile plot

enw_plot_pp_quantiles(): Plot posterior prediction quantiles

enw_plot_quantiles(): Generic quantile plot

enw_plot_theme(): Package plot theme

plot(<epinowcast>): Plot method for epinowcast

Model validation

Functions for validating model fits.

enw_score_nowcast(): FUNCTION_TITLE

Generate data

Functions for generating simulated data.

enw_apply_truncation_to_cases(): FUNCTION_TITLE

enw_dist_cmf(): FUNCTION_TITLE

enw_simulate_lnorm_trunc_obs(): FUNCTION_TITLE

Define and generate scenarios

Functions for defining and generating data scenarios.

enw_random_intercept_scenario(): FUNCTION_TITLE

Datasets

Package datasets used in examples and by users to explore the package functionality.

germany_covid19_hosp: Hospitalisations in Germany by date of report and reference

Check inputs

Functions to check the structure of user inputs.

check_quantiles(): Check Quantiles Required are Present

Utilities

Utility functions

expose_stan_fns(): FUNCTION_TITLE

is.Date(): FUNCTION_TITLE