Function reference
Estimation + Reporting
Functions that faciliate end-to-end analysis including imputing cases by infection, estimating Rt and reporting results.
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epinow()
- Real-time Rt Estimation, Forecasting and Reporting
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plot(<epinow>)
- Plot method for epinow
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regional_epinow()
- Real-time Rt Estimation, Forecasting and Reporting by Region
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summary(<epinow>)
- Summary output from epinow
Estimate, Simulate, and Forecast Parameters
Function to estimate, simulate and forecast parameters of interest.
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estimate_infections()
- Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth
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simulate_infections()
- Simulate infections using a given trajectory of the time-varying reproduction number
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estimate_secondary()
- Estimate a Secondary Observation from a Primary Observation
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forecast_secondary()
- Forecast Secondary Observations Given a Fit from estimate_secondary
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estimate_delay()
- Estimate a Delay Distribution
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estimate_truncation()
- Estimate Truncation of Observed Data
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update_horizon()
- Updates Forecast Horizon Based on Input Data and Target
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save_estimate_infections()
- Save Estimated Infections
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save_input()
- Save Observed Data
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estimates_by_report_date()
- Estimate Cases by Report Date
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copy_results_to_latest()
- Copy Results From Dated Folder to Latest
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construct_output()
- Construct Output
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backcalc_opts()
- Back Calculation Options
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delay_opts()
- Delay Distribution Options
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filter_opts()
- Filter Options for a Target Region
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generation_time_opts()
- Generation Time Distribution Options
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gp_opts()
- Approximate Gaussian Process Settings
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obs_opts()
- Observation Model Options
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rstan_opts()
- Rstan Options
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rstan_sampling_opts()
- Rstan Sampling Options
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rstan_vb_opts()
- Rstan Variational Bayes Options
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rt_opts()
- Time-Varying Reproduction Number Options
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secondary_opts()
- Secondary Reports Options
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stan_opts()
- Stan Options
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trunc_opts()
- Truncation Distribution Options
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opts_list()
- Return an _opts List per Region
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create_backcalc_data()
- Create Back Calculation Data
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create_clean_reported_cases()
- Create Clean Reported Cases
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create_future_rt()
- Construct the Required Future Rt assumption
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create_gp_data()
- Create Gaussian Process Data
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create_initial_conditions()
- Create Initial Conditions Generating Function
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create_obs_model()
- Create Observation Model Settings
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create_rt_data()
- Create Time-varying Reproduction Number Data
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create_shifted_cases()
- Create Delay Shifted Cases
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create_stan_args()
- Create a List of Stan Arguments
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create_stan_data()
- Create Stan Data Required for estimate_infections
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create_stan_delays()
- Create delay variables for stan
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allocate_delays()
- Allocate Delays into Required Stan Format
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allocate_empty()
- Allocate Empty Parameters to a List
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fit_model_with_nuts()
- Fit a Stan Model using the NUTs sampler
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fit_model_with_vb()
- Fit a Stan Model using Variational Inference
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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)
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regional_summary()
- Regional Summary Output
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regional_runtimes()
- Summarise Regional Runtimes
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summary(<epinow>)
- Summary output from epinow
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summary(<estimate_infections>)
- Summary output from estimate_infections
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summarise_key_measures()
- Summarise rt and cases
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summarise_results()
- Summarise Real-time Results
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backcalc_opts()
- Back Calculation Options
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calc_CrI()
- Calculate Credible Interval
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calc_CrIs()
- Calculate Credible Intervals
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calc_summary_measures()
- Calculate All Summary Measures
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calc_summary_stats()
- Calculate Summary Statistics
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create_backcalc_data()
- Create Back Calculation Data
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process_region()
- Process regional estimate
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process_regions()
- Process all Region Estimates
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format_fit()
- Format Posterior Samples
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make_conf()
- Format Credible Intervals
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map_prob_change()
- Categorise the Probability of Change for Rt
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plot(<dist_spec>)
- Plot PMF and CDF for a dist_spec object
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plot(<epinow>)
- Plot method for epinow
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plot(<estimate_infections>)
- Plot method for estimate_infections
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plot(<estimate_secondary>)
- Plot method for estimate_secondary
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plot(<estimate_truncation>)
- Plot method for estimate_truncation
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plot_CrIs()
- Plot EpiNow2 Credible Intervals
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plot_estimates()
- Plot Estimates
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plot_summary()
- Plot a Summary of the Latest Results
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report_plots()
- Report plots
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report_cases()
- Report case counts by date of report
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report_plots()
- Report plots
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report_summary()
- Provide Summary Statistics for Estimated Infections and Rt
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bootstrapped_dist_fit()
- Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters
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c(<dist_spec>)
- Combines multiple delay distributions for further processing
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dist_fit()
- Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions
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dist_skel()
- Distribution Skeleton
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dist_spec()
- Specify a distribution.
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dist_spec_plus()
- Creates a delay distribution as the sum of two other delay distributions
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fix_dist()
- Fix the parameters of a
<dist_spec>
object
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gamma_dist_def()
- Generate a Gamma Distribution Definition Based on Parameter Estimates
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get_dist()
- Get a Literature Distribution
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lognorm_dist_def()
- Generate a Log Normal Distribution Definition Based on Parameter Estimates
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mean(<dist_spec>)
- Returns the mean of one or more delay distribution
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plot(<dist_spec>)
- Plot PMF and CDF for a dist_spec object
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`+`(<dist_spec>)
- Creates a delay distribution as the sum of two other delay distributions
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print(<dist_spec>)
- Prints the parameters of one or more delay distributions
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sample_approx_dist()
- Approximate Sampling a Distribution using Counts
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simulate_infections()
- Simulate infections using a given trajectory of the time-varying reproduction number
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simulate_secondary()
- Simulate a secondary observation
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adjust_infection_to_report()
- Adjust from Case Counts by Infection Date to Date of Report
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example_generation_time
- Example generation time
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example_incubation_period
- Example incubation period
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example_reporting_delay
- Example reporting delay
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example_confirmed
- Example Confirmed Case Data Set
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generation_times
- Literature Estimates of Generation Times
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incubation_periods
- Literature Estimates of Incubation Periods
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get_dist()
- Get a Literature Distribution
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get_generation_time()
- Get a Literature Distribution for the Generation Time
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get_incubation_period()
- Get a Literature Distribution for the Incubation Period
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get_raw_result()
- Get a Single Raw Result
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get_regional_results()
- Get Combined Regional Results
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get_regions()
- Get Folders with Results
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get_regions_with_most_reports()
- Get Regions with Most Reported Cases
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get_seeding_time()
- Estimate seeding time from delays and generation time
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setup_target_folder()
- Setup Target Folder for Saving
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extract_CrIs()
- Extract Credible Intervals Present
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extract_inits()
- Generate initial conditions from a Stan fit
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extract_parameter()
- Extract Samples for a Parameter from a Stan model
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extract_parameter_samples()
- Extract Parameter Samples from a Stan Model
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extract_stan_param()
- Extract a Parameter Summary from a Stan Object
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extract_static_parameter()
- Extract Samples from a Parameter with a Single Dimension
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clean_nowcasts()
- Clean Nowcasts for a Supplied Date
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clean_regions()
- Clean Regions
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create_clean_reported_cases()
- Create Clean Reported Cases
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setup_default_logging()
- Setup Default Logging
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setup_dt()
- Convert to Data Table
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setup_future()
- Set up Future Backend
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setup_logging()
- Setup Logging
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setup_target_folder()
- Setup Target Folder for Saving
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match_output_arguments()
- Match User Supplied Arguments with Supported Options
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run_region()
- Run epinow with Regional Processing Code
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expose_stan_fns()
- Expose internal package stan functions in R
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convert_to_logmean()
- Convert mean and sd to log mean for a log normal distribution
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convert_to_logsd()
- Convert mean and sd to log standard deviation for a log normal distribution
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growth_to_R()
- Convert Growth Rates to Reproduction numbers.
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R_to_growth()
- Convert Reproduction Numbers to Growth Rates
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add_day_of_week()
- Adds a day of the week vector
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update_secondary_args()
- Update estimate_secondary default priors
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update_list()
- Update a List