Estimation of R0 and Real-Time Reproduction Number from Epidemics

censored.deviation | Impute censored cases to rebuild longer epidemic vector |

check.incid | Check incid in the input |

est.GT | Find the best-fitting GT distribution for a series of serial... |

estimate.R | Estimate R0 for one incidence dataset using several methods |

est.R0.AR | Estimate R0 from attack rate of an epidemic |

est.R0.EG | Estimate R from exponential growth rate |

est.R0.ML | Estimate the reproduction number by maximum likelihood |

est.R0.SB | Estimate the time dependent reproduction number using a... |

est.R0.TD | Estimate the time dependent reproduction number |

fit.epid | Compute the Poisson log - likelihood between epid and... |

fit.epid.optim | Joint estimation of GT distribution and R |

generation.time | Generation Time distribution |

Germany.1918 | Germany.1918 exemple dataset |

get.scale | Internal scaling function to display proper X-Axis labels |

GT.chld.hsld | 2009 A/H1N1 observed Generation Time distribution |

H1N1.serial.interval | H1N1 serial interval sample |

impute.incid | Optimiziation routine for incidence imputation |

integrity.checks | Input parameters integrity checks |

plotfit | Generic S3 method to plot either "R0.R" and "R0.sR" objects |

plotfit.R0.R | Plot the fit of a model to epidemic data |

plotfit.R0.sR | Plot the fit of all requested models to epidemic data |

plotfitRAR | Internal plotfit method for AR estimates |

plotfitRSB | Internal plot method for SB estimates |

plotfitRxx | Internal plotfit method for EG, ML and TD estimates |

plot.R0.GT | Print the characteristics of the generation time distribution |

plot.R0.R | Plot the R0/Rt value along with confidence interval |

plot.R0.S | Plot objects from sensitivity.analysis |

plot.R0.sR | Plot the R0/Rt value along with confidence interval of all... |

plotRAR | Internal plot method for AR estimates |

plotREG | Internal plot method for EG estimates |

plotRML | Internal plot method for ML estimates |

plotRSB | Internal plot method for SB estimates |

plotRTD | Internal plot method for TD estimates |

print.R0.GT | Print the characteristics of the generation time distribution |

print.R0.R | Print the R estimate |

print.R0.sR | Plot the R0/Rt value along with confidence interval of all... |

R0-package | Estimation of R0 and Real-Time Reproduction Number from... |

R.from.r | Compute the discretized Laplace Transform using a discretized... |

sa.GT | Sensitivity analysis of reproduction ratio with varying GT... |

sa.time | Sensitivity analysis of basic reproduction ratio to begin/end... |

sensitivity.analysis | Sensitivity analysis of basic reproduction ratio to begin/end... |

sim.epid | Epidemic outbreak simulation |

sim.epid.indiv | Influenza-like illness simulation (individual-based model) |

smooth.Rt | Smooth real-time reproduction number over larger time period |

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