Man pages for EpiNow2
Estimate and Forecast Real-Time Infection Dynamics
| add_breakpoints | Add breakpoints to certain dates in a data set. |
| add_day_of_week | Adds a day of the week vector |
| add_horizon | Add missing values for future dates |
| allocate_delays | Allocate Delays into Required Stan Format |
| allocate_empty | Allocate Empty Parameters to a List |
| apply_default_cdf_cutoff | Apply default CDF cutoff to a <dist_spec> if it is... |
| apply_zero_threshold | Convert zero case counts to 'NA' (missing) if the 7-day... |
| as_forecast_sample | Convert EpiNow2 model output to a 'forecast_sample' object |
| backcalc_opts | Back Calculation Options |
| bootstrapped_dist_fit | Fit a Subsampled Bootstrap to Integer Values and Summarise... |
| bound_dist | Define bounds of a <dist_spec> |
| build_np_est_data | Build Stan data for estimated nonparametric delays |
| calc_CrI | Calculate Credible Interval |
| calc_CrIs | Calculate Credible Intervals |
| calc_summary_measures | Calculate All Summary Measures |
| calc_summary_stats | Calculate Summary Statistics |
| cash-.epinow | Extract elements from epinow objects with deprecation errors |
| cash-.estimate_infections | Extract elements from estimate_infections objects with... |
| cash-.estimate_secondary | Extract elements from estimate_secondary objects with... |
| c.dist_spec | Combines multiple delay distributions for further processing |
| check_generation_time | Validate probability distribution for using as generation... |
| check_reports_valid | Validate data input |
| check_simulation_input | Validate simulation input data frame |
| check_sparse_pmf_tail | Check that PMF tail is not sparse |
| check_stan_delay | Validate probability distribution for passing to stan |
| check_truncation_length | Check and warn if truncation distribution is longer than... |
| check_truncation_obs_opts | Check that obs_opts settings unused by estimate_truncation... |
| clean_nowcasts | Clean Nowcasts for a Supplied Date |
| clean_regions | Clean Regions |
| collapse | Collapse nonparametric distributions in a <dist_spec> |
| combine_tv_and_static_params | Combine time-varying and static parameters |
| 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... |
| convert_to_natural | Internal function for converting parameters to natural... |
| convolve_and_scale | Convolve and scale a time series |
| copy_results_to_latest | Copy Results From Dated Folder to Latest |
| create_backcalc_data | Create Back Calculation Data |
| create_delay_inits | Create initial conditions for delays |
| create_future_rt | Construct the Required Future Rt assumption |
| create_gp_data | Create Gaussian Process Data |
| create_infection_summary | Create summary output from infection estimation objects |
| 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_sampling_log_message | Create sampling log message |
| 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 |
| create_stan_delays | Create delay variables for stan |
| create_stan_params | Create parameters for stan |
| delay_opts | Delay Distribution Options |
| discrete_pmf | Discretised probability mass function |
| discretise | Discretise a <dist_spec> |
| dist_fit | Fit an Integer Adjusted Exponential, Gamma or Lognormal... |
| dist_id_to_name | Get distribution name from primarycensored Stan dist_id |
| Distributions | Probability distributions |
| dot-extract_to_dist_spec | Extract parameters and convert to dist_spec |
| dot-get_dist_id | Map distribution name to primarycensored ID |
| dot-get_param_names | Map distribution name to parameter names |
| dot-prepare_linelist_data | Prepare linelist data for delay estimation |
| epinow | Real-time Rt Estimation, Forecasting and Reporting |
| epinow2_cmdstan_model | Load and compile an EpiNow2 cmdstanr model |
| EpiNow2-package | EpiNow2: Estimate and Forecast Real-Time Infection Dynamics |
| epinow2_rstan_model | Load an EpiNow2 rstan model. |
| epinow2_stan_model | Return a stan model object for the appropriate backend |
| equals-.dist_spec | Compares two delay distributions |
| estimate_delay | Estimate a Delay Distribution |
| estimate_dist | Estimate a delay distribution using primarycensored |
| estimate_infections | Estimate Infections, the Time-Varying Reproduction Number and... |
| estimates_by_report_date | Estimate Cases by Report Date |
| estimate_secondary | Estimate a Secondary Observation from a Primary Observation |
| estimate_truncation | Estimate truncation of observed data |
| example_confirmed | Example Confirmed Case Data Set |
| example_generation_time | Example generation time |
| example_incubation_period | Example incubation period |
| example_reporting_delay | Example reporting delay |
| example_truncated | Example Case Data Set with Truncation |
| expose_stan_fns | Expose internal package stan functions in R |
| extract_CrIs | Extract Credible Intervals Present |
| extract_delay_params | Extract delay distributions from a fitted model |
| extract_delays | Extract samples from all delay parameters |
| extract_inits | Generate initial conditions from a Stan fit |
| extract_latent_state | Extract samples for a latent state from a Stan model |
| extract_parameters | Extract samples from all parameters |
| extract_params | Extract parameter names |
| extract_samples | Extract all samples from a stan fit |
| extract_scalar_params | Extract scalar parameters from a fitted model |
| extract_single_dist | Extract a single element of a composite <dist_spec> |
| extract_stan_param | Extract a parameter summary from a Stan object |
| fill_missing | Fill missing data in a data set to prepare it for use within... |
| filter_leading_zeros | Filter leading zeros from a data set. |
| filter_opts | Filter Options for a Target Region |
| fit_model | Fit a model using the chosen backend. |
| fit_model_approximate | Fit a Stan Model using an approximate method |
| fit_model_with_nuts | Fit a Stan Model using the NUTs sampler |
| fix_parameters | Fix the parameters of a <dist_spec> |
| forecast_infections | Forecast infections from a given fit and trajectory of the... |
| forecast_opts | Forecast options |
| forecast_secondary | Forecast Secondary Observations Given a Fit from... |
| format_fit | Format Posterior Samples |
| format_quantile_predictions | Format quantile predictions |
| format_sample_predictions | Format sample predictions |
| format_samples_with_dates | Format raw Stan samples with dates and metadata |
| format_simulation_output | Format Simulation Output from Stan |
| generation_time_opts | Generation Time Distribution Options |
| get_accumulate | Get accumulation flags from data |
| get_distribution | Get the distribution of a <dist_spec> |
| get_element | Extracts an element of a <dist_spec> |
| get_parameters | Get parameters from distributions or fitted models |
| get_pmf | Get the probability mass function of a nonparametric... |
| get_predictions | Get predictions from a fitted model |
| 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 |
| get_samples | Get posterior samples from a fitted model |
| get_seeding_time | Estimate seeding time from delays and generation time |
| gp_opts | Approximate Gaussian Process Settings |
| growth_to_R | Convert Growth Rates to Reproduction numbers. |
| is_constrained | Check if a <dist_spec> is constrained, i.e. has a finite... |
| lapply_func | Choose a parallel or sequential apply function |
| lower_bounds | Get the lower bounds of the parameters of a distribution |
| make_conf | Format Credible Intervals |
| make_init_priors | Build the stan-side init-prior data block from a list of... |
| make_param | Internal function to create a parameter list |
| map_prob_change | Categorise the Probability of Change for Rt |
| match_output_arguments | Match User Supplied Arguments with Supported Options |
| max.dist_spec | Returns the maximum of one or more delay distribution |
| mean.dist_spec | Returns the mean of one or more delay distribution |
| merge_trunc_pred_obs | Merge truncation predictions with observations for display |
| natural_params | Get the names of the natural parameters of a distribution |
| ndist | Calculate the number of distributions in a <dist_spec> |
| new_dist_spec | Internal function for generating a 'dist_spec' given... |
| nonparametric_pmf_data | Build PMF data for the nonparametric branch of... |
| obs_opts | Observation Model Options |
| opts_list | Forecast optiong |
| pack_init_prior | Pack a dist_spec into stan-side init-prior fields |
| pad_reported_cases | Pads reported cases with daily initial zeros |
| plot_CrIs | Plot EpiNow2 Credible Intervals |
| plot.dist_spec | Plot PMF and CDF for a dist_spec object |
| plot.estimate_infections | Plot method for estimate_infections |
| plot_estimates | Plot Estimates |
| plot.estimate_secondary | Plot method for estimate_secondary |
| plot.estimate_truncation | Plot method for estimate_truncation |
| plot.forecast_infections | Plot method for forecast_infections |
| plot.forecast_secondary | Plot method for forecast_secondary objects |
| plot_summary | Plot a Summary of the Latest Results |
| plus-.dist_spec | Creates a delay distribution as the sum of two other delay... |
| posterior_to_normal | Create a Normal distribution from posterior samples |
| prepare_truncation_obs | Prepare truncation observations for Stan |
| print.dist_spec | Prints the parameters of one or more delay distributions |
| print.epinowfit | Print information about an object that has resulted from a... |
| process_region | Process regional estimate |
| process_regions | Process all Region Estimates |
| rdirichlet | Draw a single sample from a Dirichlet |
| reconstruct_delay | Reconstruct a dist_spec from stored stan data and posterior |
| reconstruct_nonparametric | Reconstruct a nonparametric delay distribution |
| reconstruct_parametric | Reconstruct a parametric delay distribution |
| regional_epinow | Real-time Rt Estimation, Forecasting and Reporting by Region |
| regional_runtimes | Summarise Regional Runtimes |
| regional_summary | Regional Summary Output |
| report_plots | Report plots |
| report_summary | Provide Summary Statistics for Estimated Infections and Rt |
| R_to_growth | Convert Reproduction Numbers to Growth Rates |
| rt_opts | Time-Varying Reproduction Number Options |
| run_region | Run epinow with Regional Processing Code |
| save_estimate_infections | Save Estimated Infections |
| save_input | Save Observed Data |
| sd | Returns the standard deviation of one or more delay... |
| secondary_opts | Secondary Reports Options |
| select_plots | Internal helper function to select plots from those created... |
| set_dt_single_thread | Set to Single Threading |
| 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_infections | Simulate infections using the renewal equation |
| simulate_secondary | Simulate secondary observations from primary observations |
| stable_convolve | Numerically stable convolution function for two pmf vectors |
| stan_laplace_opts | Stan Laplace algorithm Options |
| stan_opts | Stan Options |
| stan_pathfinder_opts | Stan pathfinder algorithm Options |
| stan_sampling_opts | Stan Sampling Options |
| stan_vb_opts | Stan Variational Bayes Options |
| sub-sub-.epinow | Extract elements from epinow objects with bracket notation |
| sub-sub-.estimate_infections | Extract elements from estimate_infections objects with... |
| sub-sub-.estimate_secondary | Extract elements from estimate_secondary objects with bracket... |
| summarise_key_measures | Summarise rt and cases |
| summarise_results | Summarise Real-time Results |
| summary.epinow | Summary output from epinow |
| summary.estimate_dist | Summarise results from estimate_dist |
| summary.estimate_infections | Summary output from estimate_infections |
| summary.estimate_secondary | Summarise results from estimate_secondary |
| summary.estimate_truncation | Summarise results from estimate_truncation |
| summary.forecast_infections | Summary output from forecast_infections |
| trunc_opts | Truncation Distribution Options |
| update_horizon | Updates Forecast Horizon Based on Input Data and Target |
| update_secondary_args | Update estimate_secondary default priors |
