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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()
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enw_assign_group()
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enw_extend_date()
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enw_latest_data()
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enw_metadata()
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enw_new_reports()
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enw_preprocess_data()
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enw_reporting_triangle()
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enw_reporting_triangle_to_long()
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enw_retrospective_data()
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Model design tools

Functions that assist with designing models.

enw_add_cumulative_membership()
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enw_add_pooling_effect()
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enw_dates_to_factors()
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enw_design()
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enw_effects_metadata()
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enw_formula()
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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()
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enw_priors_as_data_list()
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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()
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enw_sample()
Fit a CmdStan model using NUTS

Postprocess

Functions for postprocessing model output.

enw_add_latest_obs_to_nowcast()
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enw_nowcast_samples()
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enw_nowcast_summary()
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enw_posterior()
Summarise the posterior
enw_pp_summary()
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enw_quantiles_to_long()
Convert summarised quantiles from wide to long format
enw_summarise_samples()
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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()
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Generate data

Functions for generating simulated data.

Define and generate scenarios

Functions for defining and generating data scenarios.

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()
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is.Date()
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