Estimate Real-Time Case Counts and Time-Varying Epidemiological
Parameters
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Documentation for package ‘EpiNow2’ version 1.5.2
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| +.dist_spec | Creates a delay distribution as the sum of two other delay distributions. |
| apply_tolerance | Applies a threshold to all nonparametric distributions in a <dist_spec> |
| backcalc_opts | Back Calculation Options |
| bootstrapped_dist_fit | Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters |
| c.dist_spec | Combines multiple delay distributions for further processing |
| 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 |
| collapse | Collapse nonparametric distributions in a <dist_spec> |
| 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 |
| convolve_and_scale | Convolve and scale a time series |
| delay_opts | Delay Distribution Options |
| discretise | Discretise a <dist_spec> |
| discretize | Discretise a <dist_spec> |
| Distributions | Probability distributions |
| 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 |
| 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_inits | Generate initial conditions from a Stan fit |
| extract_samples | Extract all samples from a stan fit |
| extract_stan_param | Extract a Parameter Summary from a Stan Object |
| filter_opts | Filter Options for a Target Region |
| Fixed | Probability distributions |
| fix_dist | Fix the parameters of a <dist_spec> |
| forecast_infections | Forecast infections from a given fit and trajectory of the time-varying reproduction number |
| forecast_secondary | Forecast Secondary Observations Given a Fit from estimate_secondary |
| Gamma | Probability distributions |
| generation_times | Literature Estimates of Generation Times |
| generation_time_opts | Generation Time Distribution Options |
| get_distribution | Get the distribution of a 'dist_spec()' |
| get_parameters | Get parameters of a parametric distribution |
| get_pmf | Get the probability mass function of a nonparametric distribution |
| get_regional_results | Get Combined Regional Results |
| gp_opts | Approximate Gaussian Process Settings |
| growth_to_R | Convert Growth Rates to Reproduction numbers. |
| incubation_periods | Literature Estimates of Incubation Periods |
| LogNormal | Probability distributions |
| make_conf | Format Credible Intervals |
| map_prob_change | Categorise the Probability of Change for Rt |
| max.dist_spec | Returns the maximum of one or more delay distribution |
| mean.dist_spec | Returns the mean of one or more delay distribution |
| new_dist_spec | Internal function for generating a 'dist_spec' given parameters and a distribution. |
| NonParametric | Probability distributions |
| Normal | Probability distributions |
| obs_opts | Observation Model Options |
| opts_list | Return an _opts List per Region |
| plot | Plot method for estimate_infections |
| plot.dist_spec | Plot PMF and CDF for a dist_spec object |
| 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 |
| print.dist_spec | Prints the parameters of one or more delay distributions |
| regional_epinow | Real-time Rt Estimation, Forecasting and Reporting by Region |
| regional_summary | Regional Summary Output |
| 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 |
| R_to_growth | Convert Reproduction Numbers to Growth Rates |
| secondary_opts | Secondary Reports Options |
| setup_default_logging | Setup Default Logging |
| setup_future | Set up Future Backend |
| setup_logging | Setup Logging |
| simulate_infections | Simulate infections using the renewal equation |
| simulate_secondary | Simulate secondary observations from primary observations |
| 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 |
| summary | Summary output from epinow |
| summary.epinow | Summary output from epinow |
| summary.estimate_infections | Summary output from estimate_infections |
| trunc_opts | Truncation Distribution Options |
| update_secondary_args | Update estimate_secondary default priors |