Function reference • EpiNow2

Estimation + Reporting Functions that faciliate end-to-end analysis including imputing cases by infection, estimating Rt and reporting results.
`epinow()`	Real-time Rt Estimation, Forecasting and Reporting
`plot(<epinow>)`	Plot method for epinow
`regional_epinow()`	Real-time Rt Estimation, Forecasting and Reporting by Region
`summary(<epinow>)`	Summary output from epinow
Estimate Parameters Function to estimate parameters of interest.
`estimate_infections()`	Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth
`forecast_infections()`	Forecast Infections and the Time-Varying Reproduction Number
`estimate_delay()`	Estimate a Delay Distribution
`estimate_truncation()`	Estimate Truncation of Observed Data
`estimate_secondary()`	Estimate a Secondary Observation from a Primary Observation
`forecast_secondary()`	Forecast Secondary Observations Given a Fit from estimate_secondary
Internal epinow Functions Functions used internally by epinow
`update_horizon()`	Updates Forecast Horizon Based on Input Data and Target
`save_estimate_infections()`	Save Estimated Infections
`save_forecast_infections()`	Save Forecast Infections
`save_input()`	Save Observed Data
`estimates_by_report_date()`	Estimate Cases by Report Date
`copy_results_to_latest()`	Copy Results From Dated Folder to Latest
`construct_output()`	Construct Output
Internal estimate_infections Functions Functions used by estimate_infections
`backcalc_opts()`	Back Calculation Options
`delay_opts()`	Delay Distribution Options
`filter_opts()`	Filter Options for a Target Region
`gp_opts()`	Approximate Gaussian Process Settings
`obs_opts()`	Observation Model Options
`rstan_opts()`	Rstan Options
`rstan_sampling_opts()`	Rstan Sampling Options
`rstan_vb_opts()`	Rstan Variational Bayes Options
`rt_opts()`	Time-Varying Reproduction Number Options
`secondary_opts()`	Secondary Reports Options
`stan_opts()`	Stan Options
`trunc_opts()`	Truncation Distribution Options
`opts_list()`	Return an _opts List per Region
`create_backcalc_data()`	Create Back Calculation Data
`create_clean_reported_cases()`	Create Clean Reported Cases
`create_future_rt()`	Construct the Required Future Rt assumption
`create_gp_data()`	Create Gaussian Process Data
`create_initial_conditions()`	Create Initial Conditions Generating Function
`create_obs_model()`	Create Observation Model Settings
`create_rt_data()`	Create Time-varying Reproduction Number Data
`create_shifted_cases()`	Create Delay Shifted Cases
`create_stan_args()`	Create a List of Stan Arguments
`create_stan_data()`	Create Stan Data Required for estimate_infections
`allocate_delays()`	Allocate Delays into Required Stan Format
`allocate_empty()`	Allocate Empty Parameters to a List
Model Fitting Functions for model fitting
`fit_model_with_nuts()`	Fit a Stan Model using the NUTs sampler
`fit_model_with_vb()`	Fit a Stan Model using Variational Inference
`init_cumulative_fit()`	Generate initial conditions by fitting to cumulative cases
Summarise Across Regions Functions used for summarising across regions (designed for use with regional_epinow)
`regional_summary()`	Regional Summary Output
`regional_runtimes()`	Summarise Regional Runtimes
Summarise results Functions from summarising results
`summary(<epinow>)`	Summary output from epinow
`summary(<estimate_infections>)`	Summary output from estimate_infections
`summarise_key_measures()`	Summarise rt and cases
`summarise_results()`	Summarise Real-time Results
`backcalc_opts()`	Back Calculation Options
`calc_CrI()`	Calculate Credible Interval
`calc_CrIs()`	Calculate Credible Intervals
`calc_summary_measures()`	Calculate All Summary Measures
`calc_summary_stats()`	Calculate Summary Statistics
`create_backcalc_data()`	Create Back Calculation Data
`process_region()`	Process regional estimate
`process_regions()`	Process all Region Estimates
`format_fit()`	Format Posterior Samples
`make_conf()`	Format Credible Intervals
`map_prob_change()`	Categorise the Probability of Change for Rt
Plot Results Plot generated results
`plot(<epinow>)`	Plot method for epinow
`plot(<estimate_infections>)`	Plot method for estimate_infections
`plot(<estimate_secondary>)`	Plot method for estimate_secondary
`plot(<estimate_truncation>)`	Plot method for estimate_truncation
`plot_CrIs()`	Plot EpiNow2 Credible Intervals
`plot_estimates()`	Plot Estimates
`plot_summary()`	Plot a Summary of the Latest Results
`report_plots()`	Report plots
Report results Functions to report results
`report_cases()`	Report case counts by date of report
`report_plots()`	Report plots
`report_summary()`	Provide Summary Statistics for Estimated Infections and Rt
Define, Fit and Parameterise Distributions Functions to define, fit and parameterise distributions
`bootstrapped_dist_fit()`	Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters
`dist_fit()`	Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions
`dist_skel()`	Distribution Skeleton
`gamma_dist_def()`	Generate a Gamma Distribution Definition Based on Parameter Estimates
`get_dist()`	Get a Literature Distribution
`lognorm_dist_def()`	Generate a Log Normal Distribution Definition Based on Parameter Estimates
`sample_approx_dist()`	Approximate Sampling a Distribution using Counts
`tune_inv_gamma()`	Tune an Inverse Gamma to Achieve the Target Truncation
Simulate Functions to help with simulating data or mapping to reported cases
`simulate_infections()`	Simulate infections using a given trajectory of the time-varying reproduction number
`simulate_cases()`	Simulate Cases by Date of Infection, Onset and Report
`adjust_infection_to_report()`	Adjust from Case Counts by Infection Date to Date of Report
Data Package datasets that may be used to parameterise other functions or in examples
`generation_times`	Literature Estimates of Generation Times
`incubation_periods`	Literature Estimates of Incubation Periods
`example_confirmed`	Example Confirmed Case Data Set
Get/Extract Data Functions for extracting data from objects or getting data from sources
`get_dist()`	Get a Literature Distribution
`get_generation_time()`	Get a Literature Distribution for the Generation Time
`get_incubation_period()`	Get a Literature Distribution for the Incubation Period
`get_raw_result()`	Get a Single Raw Result
`get_regional_results()`	Get Combined Regional Results
`get_regions()`	Get Folders with Results
`get_regions_with_most_reports()`	Get Regions with Most Reported Cases
`setup_target_folder()`	Setup Target Folder for Saving
`extract_CrIs()`	Extract Credible Intervals Present
`extract_inits()`	Generate initial conditions from a Stan fit
`extract_parameter()`	Extract Samples for a Parameter from a Stan model
`extract_parameter_samples()`	Extract Parameter Samples from a Stan Model
`extract_stan_param()`	Extract a Parameter Summary from a Stan Object
`extract_static_parameter()`	Extract Samples from a Parameter with a Single Dimension
Clean Data Functions for cleaning data
`clean_nowcasts()`	Clean Nowcasts for a Supplied Date
`clean_regions()`	Clean Regions
`create_clean_reported_cases()`	Create Clean Reported Cases
Map results Optional mapping functions (requires additional dependencies)
`global_map()`	Generate a global map for a single variable.
`country_map()`	Generate a country map for a single variable.
`theme_map()`	Custom Map Theme
Setup Utilities Function used for setting up functionality
`setup_default_logging()`	Setup Default Logging
`setup_dt()`	Convert to Data Table
`setup_future()`	Set up Future Backend
`setup_logging()`	Setup Logging
`setup_target_folder()`	Setup Target Folder for Saving
Utilities Utility functions
`match_output_arguments()`	Match User Supplied Arguments with Supported Options
`run_region()`	Run epinow with Regional Processing Code
`expose_stan_fns()`	Expose internal package stan functions in R
`convert_to_logmean()`	Convert mean and sd to log mean for a log normal distribution
`convert_to_logsd()`	Convert mean and sd to log standard deviation for a log normal distribution
`growth_to_R()`	Convert Growth Rates to Reproduction numbers.
`R_to_growth()`	Convert Reproduction Numbers to Growth Rates
`update_list()`	Update a List
`add_day_of_week()`	Adds a day of the week vector

Reference

Estimation + Reporting

Estimate Parameters

Internal epinow Functions

Internal estimate_infections Functions

Model Fitting

Summarise Across Regions

Summarise results

Plot Results

Report results

Define, Fit and Parameterise Distributions

Simulate

Data

Get/Extract Data

Clean Data

Map results

Setup Utilities

Utilities