Estimation of reproduction numbers for disease outbreak, based on incidence data. The R0 package implements several documented methods. It is therefore possible to compare estimations according to the methods used. Depending on the methods requested by user, basic reproduction number (commonly denoted as R0) or real-time reproduction number (referred to as R(t)) is computed, along with a 95% Confidence Interval. Plotting outputs will give different graphs depending on the methods requested : basic reproductive number estimations will only show the epidemic curve (collected data) and an adjusted model, whereas real-time methods will also show the R(t) variations throughout the outbreak time period. Sensitivity analysis tools are also provided, and allow for investigating effects of varying Generation Time distribution or time window on estimates.

Author | Pierre-Yves Boelle, Thomas Obadia |

Date of publication | 2015-05-21 19:34:12 |

Maintainer | Thomas Obadia <thomas.obadia@iplesp.upmc.fr> |

License | GPL (>= 2) |

Version | 1.2-6 |

**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

censored.deviation | Man page |

check.incid | Man page |

est.GT | Man page |

estimate.R | Man page |

est.R0.AR | Man page |

est.R0.EG | Man page |

est.R0.ML | Man page |

est.R0.SB | Man page |

est.R0.TD | Man page |

fit.epid | Man page |

fit.epid.optim | Man page |

generation.time | Man page |

Germany.1918 | Man page |

get.scale | Man page |

GT.chld.hsld | Man page |

H1N1.serial.interval | Man page |

impute.incid | Man page |

integrity.checks | Man page |

plotfit | Man page |

plotfit.R0.R | Man page |

plotfit.R0.sR | Man page |

plotfitRAR | Man page |

plotfitRSB | Man page |

plotfitRxx | Man page |

plot.R0.GT | Man page |

plot.R0.R | Man page |

plot.R0.S | Man page |

plot.R0.sR | Man page |

plotRAR | Man page |

plotREG | Man page |

plotRML | Man page |

plotRSB | Man page |

plotRTD | Man page |

print.R0.GT | Man page |

print.R0.R | Man page |

print.R0.sR | Man page |

R0 | Man page |

R0-package | Man page |

R.from.r | Man page |

sa.GT | Man page |

sa.time | Man page |

sensitivity.analysis | Man page |

sim.epid | Man page |

sim.epid.indiv | Man page |

smooth.Rt | Man page |

R0

R0/tests

R0/tests/est.R0.ML.R

R0/tests/est.R0.TD.R

R0/tests/check.incid.R

R0/tests/estimate.R.R

R0/tests/est.R0.SB.R

R0/tests/est.R0.AR.R

R0/tests/est.GT.R

R0/tests/est.R0.EG.R

R0/tests/smooth.Rt.R

R0/tests/sensitivity.analysis.R

R0/tests/sim.epid.R

R0/tests/generation.time.R

R0/NAMESPACE

R0/demo

R0/demo/00Index

R0/demo/epid.demo.R

R0/data

R0/data/GT.chld.hsld.rda

R0/data/H1N1.serial.interval.rda

R0/data/Germany.1918.rda

R0/R

R0/R/plotfit.R0.sR.R
R0/R/plot.R0.R.R
R0/R/print.R0.sR.R
R0/R/impute.incid.R
R0/R/plotfit.R0.R.R
R0/R/plot.R0.GT.R
R0/R/integrity.checks.R
R0/R/sa.time.R
R0/R/sim.epid.indiv.R
R0/R/plotfit.R
R0/R/est.R0.ML.R
R0/R/plot.R0.sR.R
R0/R/est.R0.TD.R
R0/R/check.incid.R
R0/R/estimate.R.R
R0/R/print.R0.R.R
R0/R/est.R0.SB.R
R0/R/est.R0.AR.R
R0/R/plot.R0.S.R
R0/R/est.GT.R
R0/R/censored.deviation.R
R0/R/sa.GT.R
R0/R/est.R0.EG.R
R0/R/smooth.Rt.R
R0/R/sensitivity.analysis.R
R0/R/fit.epid.R
R0/R/R.from.r.R
R0/R/sim.epid.R
R0/R/print.R0.GT.R
R0/R/generation.time.R
R0/MD5

R0/DESCRIPTION

R0/man

R0/man/est.R0.SB.Rd
R0/man/censored.deviation.Rd
R0/man/GT.chld.hsld.Rd
R0/man/est.R0.TD.Rd
R0/man/integrity.checks.Rd
R0/man/plotfitRxx.Rd
R0/man/print.R0.GT.Rd
R0/man/plotfit.Rd
R0/man/sa.GT.Rd
R0/man/smooth.Rt.Rd
R0/man/sim.epid.Rd
R0/man/fit.epid.optim.Rd
R0/man/est.R0.ML.Rd
R0/man/est.R0.EG.Rd
R0/man/fit.epid.Rd
R0/man/plotfitRSB.Rd
R0/man/generation.time.Rd
R0/man/plotRAR.Rd
R0/man/plotREG.Rd
R0/man/sim.epid.indiv.Rd
R0/man/sa.time.Rd
R0/man/sensitivity.analysis.Rd
R0/man/print.R0.sR.Rd
R0/man/plotfitRAR.Rd
R0/man/plotRTD.Rd
R0/man/plotRML.Rd
R0/man/H1N1.serial.interval.Rd
R0/man/plot.R0.GT.Rd
R0/man/impute.incid.Rd
R0/man/plot.R0.S.Rd
R0/man/R.from.r.Rd
R0/man/est.GT.Rd
R0/man/plot.R0.sR.Rd
R0/man/plot.R0.R.Rd
R0/man/print.R0.R.Rd
R0/man/R0-package.Rd
R0/man/est.R0.AR.Rd
R0/man/Germany.1918.Rd
R0/man/check.incid.Rd
R0/man/plotRSB.Rd
R0/man/plotfit.R0.sR.Rd
R0/man/plotfit.R0.R.Rd
R0/man/get.scale.Rd
R0/man/estimate.R.Rd
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.