R_to_growth             Convert Reproduction Numbers to Growth Rates
adjust_infection_to_report
                        Adjust from Case Counts by Infection Date to
                        Date of Report
allocate_delays         Allocate Delays into Required Stan Format
allocate_empty          Allocate Empty Parameters to a List
backcalc_opts           Back Calculation Options
bootstrapped_dist_fit   Fit a Subsampled Bootstrap to Integer Values
                        and Summarise Distribution Parameters
calc_CrI                Calculate Credible Interval
calc_CrIs               Calculate Credible Intervals
calc_summary_measures   Calculate All Summary Measures
calc_summary_stats      Calculate Summary Statistics
clean_nowcasts          Clean Nowcasts for a Supplied Date
clean_regions           Clean Regions
construct_output        Construct Output
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
copy_results_to_latest
                        Copy Results From Dated Folder to Latest
country_map             Generate a country map for a single variable.
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
delay_opts              Delay Distribution Options
dist_fit                Fit an Integer Adjusted Exponential, Gamma or
                        Lognormal distributions
dist_skel               Distribution Skeleton
epinow                  Real-time Rt Estimation, Forecasting and
                        Reporting
estimate_delay          Estimate a Delay Distribution
estimate_infections     Estimate Infections, the Time-Varying
                        Reproduction Number and the Rate of Growth
estimate_secondary      Estimate a Secondary Observation from a Primary
                        Observation
estimate_truncation     Estimate Truncation of Observed Data
estimates_by_report_date
                        Estimate Cases by Report Date
example_confirmed       Example Confirmed Case Data Set
expose_stan_fns         Expose internal package stan functions in R
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
filter_opts             Filter Options for a Target Region
fit_model_with_nuts     Fit a Stan Model using the NUTs sampler
fit_model_with_vb       Fit a Stan Model using Variational Inference
forecast_infections     Forecast Infections and the Time-Varying
                        Reproduction Number
forecast_secondary      Forecast Secondary Observations Given a Fit
                        from estimate_secondary
format_fit              Format Posterior Samples
gamma_dist_def          Generate a Gamma Distribution Definition Based
                        on Parameter Estimates
generation_times        Literature Estimates of Generation Times
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
global_map              Generate a global map for a single variable.
gp_opts                 Approximate Gaussian Process Settings
growth_to_R             Convert Growth Rates to Reproduction numbers.
incubation_periods      Literature Estimates of Incubation Periods
init_cumulative_fit     Generate initial conditions by fitting to
                        cumulative cases
lognorm_dist_def        Generate a Log Normal Distribution Definition
                        Based on Parameter Estimates
make_conf               Format Credible Intervals
map_prob_change         Categorise the Probability of Change for Rt
match_output_arguments
                        Match User Supplied Arguments with Supported
                        Options
obs_opts                Observation Model Options
opts_list               Return an _opts List per Region
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
process_region          Process regional estimate
process_regions         Process all Region Estimates
regional_epinow         Real-time Rt Estimation, Forecasting and
                        Reporting by Region
regional_runtimes       Summarise Regional Runtimes
regional_summary        Regional Summary Output
report_cases            Report case counts by date of report
report_plots            Report plots
report_summary          Provide Summary Statistics for Estimated
                        Infections and Rt
rstan_opts              Rstan Options
rstan_sampling_opts     Rstan Sampling Options
rstan_vb_opts           Rstan Variational Bayes Options
rt_opts                 Time-Varying Reproduction Number Options
run_region              Run epinow with Regional Processing Code
sample_approx_dist      Approximate Sampling a Distribution using
                        Counts
save_estimate_infections
                        Save Estimated Infections
save_forecast_infections
                        Save Forecast Infections
save_input              Save Observed Data
secondary_opts          Secondary Reports Options
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
simulate_cases          Simulate Cases by Date of Infection, Onset and
                        Report
simulate_infections     Simulate infections using a given trajectory of
                        the time-varying reproduction number
stan_opts               Stan Options
summarise_key_measures
                        Summarise rt and cases
summarise_results       Summarise Real-time Results
summary.epinow          Summary output from epinow
summary.estimate_infections
                        Summary output from estimate_infections
theme_map               Custom Map Theme
trunc_opts              Truncation Distribution Options
tune_inv_gamma          Tune an Inverse Gamma to Achieve the Target
                        Truncation
update_horizon          Updates Forecast Horizon Based on Input Data
                        and Target
update_list             Update a List
