Estimation + ReportingFunctions that faciliate end-to-end analysis including imputing cases by infection, estimating Rt and reporting results. |
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Real-time Rt Estimation, Forecasting and Reporting |
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Plot method for epinow |
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Real-time Rt Estimation, Forecasting and Reporting by Region |
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Summary output from epinow |
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Estimate ParametersFunction to estimate parameters of interest. |
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Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth |
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Forecast Infections and the Time-Varying Reproduction Number |
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Estimate a Delay Distribution |
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Estimate Truncation of Observed Data |
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Estimate a Secondary Observation from a Primary Observation |
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Forecast Secondary Observations Given a Fit from estimate_secondary |
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Internal epinow FunctionsFunctions used internally by epinow |
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Updates Forecast Horizon Based on Input Data and Target |
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Save Estimated Infections |
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Save Forecast Infections |
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Save Observed Data |
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Estimate Cases by Report Date |
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Copy Results From Dated Folder to Latest |
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Construct Output |
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Internal estimate_infections FunctionsFunctions used by estimate_infections |
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Back Calculation Options |
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Delay Distribution Options |
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Filter Options for a Target Region |
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Approximate Gaussian Process Settings |
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Observation Model Options |
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Rstan Options |
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Rstan Sampling Options |
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Rstan Variational Bayes Options |
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Time-Varying Reproduction Number Options |
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Secondary Reports Options |
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Stan Options |
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Truncation Distribution Options |
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Return an _opts List per Region |
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Create Back Calculation Data |
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Create Clean Reported Cases |
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Construct the Required Future Rt assumption |
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Create Gaussian Process Data |
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Create Initial Conditions Generating Function |
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Create Observation Model Settings |
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Create Time-varying Reproduction Number Data |
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Create Delay Shifted Cases |
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Create a List of Stan Arguments |
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Create Stan Data Required for estimate_infections |
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Allocate Delays into Required Stan Format |
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Allocate Empty Parameters to a List |
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Model FittingFunctions for model fitting |
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Fit a Stan Model using the NUTs sampler |
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Fit a Stan Model using Variational Inference |
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Generate initial conditions by fitting to cumulative cases |
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Summarise Across RegionsFunctions used for summarising across regions (designed for use with regional_epinow) |
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Regional Summary Output |
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Summarise Regional Runtimes |
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Summarise resultsFunctions from summarising results |
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Summary output from epinow |
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Summary output from estimate_infections |
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Summarise rt and cases |
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Summarise Real-time Results |
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Back Calculation Options |
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Calculate Credible Interval |
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Calculate Credible Intervals |
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Calculate All Summary Measures |
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Calculate Summary Statistics |
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Create Back Calculation Data |
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Process regional estimate |
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Process all Region Estimates |
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Format Posterior Samples |
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Format Credible Intervals |
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Categorise the Probability of Change for Rt |
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Plot ResultsPlot generated results |
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Plot method for epinow |
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Plot method for estimate_infections |
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Plot method for estimate_secondary |
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Plot method for estimate_truncation |
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Plot EpiNow2 Credible Intervals |
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Plot Estimates |
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Plot a Summary of the Latest Results |
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Report plots |
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Report resultsFunctions to report results |
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Report case counts by date of report |
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Report plots |
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Provide Summary Statistics for Estimated Infections and Rt |
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Define, Fit and Parameterise DistributionsFunctions to define, fit and parameterise distributions |
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Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters |
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Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions |
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Distribution Skeleton |
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Generate a Gamma Distribution Definition Based on Parameter Estimates |
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Get a Literature Distribution |
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Generate a Log Normal Distribution Definition Based on Parameter Estimates |
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Approximate Sampling a Distribution using Counts |
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Tune an Inverse Gamma to Achieve the Target Truncation |
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SimulateFunctions to help with simulating data or mapping to reported cases |
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Simulate infections using a given trajectory of the time-varying reproduction number |
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Simulate Cases by Date of Infection, Onset and Report |
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Adjust from Case Counts by Infection Date to Date of Report |
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DataPackage datasets that may be used to parameterise other functions or in examples |
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Literature Estimates of Generation Times |
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Literature Estimates of Incubation Periods |
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Example Confirmed Case Data Set |
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Get/Extract DataFunctions for extracting data from objects or getting data from sources |
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Get a Literature Distribution |
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Get a Literature Distribution for the Generation Time |
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Get a Literature Distribution for the Incubation Period |
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Get a Single Raw Result |
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Get Combined Regional Results |
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Get Folders with Results |
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Get Regions with Most Reported Cases |
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Setup Target Folder for Saving |
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Extract Credible Intervals Present |
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Generate initial conditions from a Stan fit |
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Extract Samples for a Parameter from a Stan model |
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Extract Parameter Samples from a Stan Model |
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Extract a Parameter Summary from a Stan Object |
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Extract Samples from a Parameter with a Single Dimension |
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Clean DataFunctions for cleaning data |
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Clean Nowcasts for a Supplied Date |
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Clean Regions |
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Create Clean Reported Cases |
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Map resultsOptional mapping functions (requires additional dependencies) |
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Generate a global map for a single variable. |
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Generate a country map for a single variable. |
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Custom Map Theme |
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Setup UtilitiesFunction used for setting up functionality |
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Setup Default Logging |
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Convert to Data Table |
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Set up Future Backend |
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Setup Logging |
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Setup Target Folder for Saving |
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UtilitiesUtility functions |
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Match User Supplied Arguments with Supported Options |
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Run epinow with Regional Processing Code |
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Expose internal package stan functions in R |
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Convert mean and sd to log mean for a log normal distribution |
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Convert mean and sd to log standard deviation for a log normal distribution |
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Convert Growth Rates to Reproduction numbers. |
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Convert Reproduction Numbers to Growth Rates |
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Update a List |
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Adds a day of the week vector |