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CoriEstimator
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CoriEstimator |
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GrowthRateEstimator
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GrowthRateEstimator |
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InfectivityProfile
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InfectivityProfile |
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JavaApi
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Java Epidemic |
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Serialiser
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Serialiser |
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addBinomialRate()
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Calculate a simulated set of expected proportions based on imports, growth rates and a baseline total |
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addBootstrappedObservations()
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Generate a random set of observations from a poisson rate |
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addImportations()
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Add importations to the simulation. Without importations there will be no growth so some cases must be imported. |
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addObservedRate()
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Add in a simulated rate of observed cases based on the underlying growth rate and imports with a weekly variation |
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addPoissonRate()
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Calculate a simulated set of expected incidences based on imports and growth rate |
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discreteGammaInfectivityProfile()
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Generates one or more discrete infectivity profiles based on discretised gamma distributions. |
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doublingTimeFromGrowthRate()
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Calucualte a doubling time with quantiles for any timeseries with Growth rate estimates |
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epiestimRtEstimate()
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Minimal epiestim wrapper to execute a time series R_t using a discrete infectivity profile matrix, and format the result to be consistent with the rest of this.. |
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generateGrowthRate()
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Generate a growth timeseries simulation based on a small set of fixed time points. |
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generateRt()
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Generate an R_t timeseries simulation based on a small set of fixed time points. |
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getGrowthRateBasedDataset()
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Convenience method to generate a random growth rate simulation |
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getTwoAlternativesDataset()
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Convenience wrapper to generate a 2 strain type comparison. strain 1 will have suffix .s1 and strain 2 will have .s2 |
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jepidemic-package
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jepidemic: Java Epidemic |
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locfitGrowthEstimate()
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Generate a smoothed estimate of the absolute growth rate of cases using a poisson model. |
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locfitPoissonRateEstimate()
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Generate a smoothed estimate of the absolute growth rate of cases using a poisson model. |
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locfitProportionEstimate()
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Generate a smoothed estimate of the proportion of cases compared to some total. |
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locfitProportionalGrowthEstimate()
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Generate a smoothed estimate of the relative growth rate of cases compared to some baseline using proportions. |
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periodicGrowthRate()
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Generate a periodic growth timeseries simulation |
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pointPoissonEstimate()
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Calculate a slightly more robust estimate of growth rate and poisson rate based on a single model |
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pointProportionEstimate()
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Calculate a slightly more robust estimate of growth rate and proportion based on a single model at a range of |
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renameResult()
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Rename a growth rate estimate by placing a prefix in front o |
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rtFromGrowthRate()
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Calculate a reproduction number estimate using the Wallinga 2007 estimation using empirical generation time distribution. This uses resampling to transmit uncertainty in growth rate estimates |
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uncertainGammaInfectivityProfiles()
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Generate a set of infectivity profiles based on uncertain |
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weekendEffect()
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Calculates a weighting to apply to each day of week |