R0: Estimation of R0 and Real-Time Reproduction Number from Epidemics
Version 1.2-6

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.

AuthorPierre-Yves Boelle, Thomas Obadia
Date of publication2015-05-21 19:34:12
MaintainerThomas Obadia <thomas.obadia@iplesp.upmc.fr>
LicenseGPL (>= 2)
Version1.2-6
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("R0")

Getting started

Package overview

Popular man pages

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.TD: Estimate the time dependent reproduction number
generation.time: Generation Time distribution
get.scale: Internal scaling function to display proper X-Axis labels
plotfit.R0.R: Plot the fit of a model to epidemic data
See all...

All man pages Function index File listing

Man pages

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

Functions

GT.chld.hsld Man page
Germany.1918 Man page
H1N1.serial.interval Man page
R.from.r Man page Source code
R0 Man page
R0-package Man page
censored.deviation Man page Source code
check.incid Man page Source code
est.GT Man page Source code
est.R0.AR Man page Source code
est.R0.EG Man page Source code
est.R0.ML Man page Source code
est.R0.SB Man page Source code
est.R0.TD Man page Source code
estimate.R Man page Source code
fit.epid Man page Source code
fit.epid.optim Man page Source code
generation.time Man page Source code
get.scale Man page Source code
impute.incid Man page Source code
integrity.checks Man page Source code
plot.R0.GT Man page Source code
plot.R0.R Man page Source code
plot.R0.S Man page Source code
plot.R0.sR Man page Source code
plotRAR Man page Source code
plotREG Man page Source code
plotRML Man page Source code
plotRSB Man page Source code
plotRTD Man page Source code
plotfit Man page Source code
plotfit.R0.R Man page Source code
plotfit.R0.sR Man page Source code
plotfitRAR Man page Source code
plotfitRSB Man page Source code
plotfitRxx Man page Source code
print.R0.GT Man page Source code
print.R0.R Man page Source code
print.R0.sR Man page Source code
sa.GT Man page Source code
sa.time Man page Source code
sensitivity.analysis Man page Source code
sim.epid Man page Source code
sim.epid.indiv Man page Source code
smooth.Rt Man page Source code

Files

tests
tests/est.R0.ML.R
tests/est.R0.TD.R
tests/check.incid.R
tests/estimate.R.R
tests/est.R0.SB.R
tests/est.R0.AR.R
tests/est.GT.R
tests/est.R0.EG.R
tests/smooth.Rt.R
tests/sensitivity.analysis.R
tests/sim.epid.R
tests/generation.time.R
NAMESPACE
demo
demo/00Index
demo/epid.demo.R
data
data/GT.chld.hsld.rda
data/H1N1.serial.interval.rda
data/Germany.1918.rda
R
R/plotfit.R0.sR.R
R/plot.R0.R.R
R/print.R0.sR.R
R/impute.incid.R
R/plotfit.R0.R.R
R/plot.R0.GT.R
R/integrity.checks.R
R/sa.time.R
R/sim.epid.indiv.R
R/plotfit.R
R/est.R0.ML.R
R/plot.R0.sR.R
R/est.R0.TD.R
R/check.incid.R
R/estimate.R.R
R/print.R0.R.R
R/est.R0.SB.R
R/est.R0.AR.R
R/plot.R0.S.R
R/est.GT.R
R/censored.deviation.R
R/sa.GT.R
R/est.R0.EG.R
R/smooth.Rt.R
R/sensitivity.analysis.R
R/fit.epid.R
R/R.from.r.R
R/sim.epid.R
R/print.R0.GT.R
R/generation.time.R
MD5
DESCRIPTION
man
man/est.R0.SB.Rd
man/censored.deviation.Rd
man/GT.chld.hsld.Rd
man/est.R0.TD.Rd
man/integrity.checks.Rd
man/plotfitRxx.Rd
man/print.R0.GT.Rd
man/plotfit.Rd
man/sa.GT.Rd
man/smooth.Rt.Rd
man/sim.epid.Rd
man/fit.epid.optim.Rd
man/est.R0.ML.Rd
man/est.R0.EG.Rd
man/fit.epid.Rd
man/plotfitRSB.Rd
man/generation.time.Rd
man/plotRAR.Rd
man/plotREG.Rd
man/sim.epid.indiv.Rd
man/sa.time.Rd
man/sensitivity.analysis.Rd
man/print.R0.sR.Rd
man/plotfitRAR.Rd
man/plotRTD.Rd
man/plotRML.Rd
man/H1N1.serial.interval.Rd
man/plot.R0.GT.Rd
man/impute.incid.Rd
man/plot.R0.S.Rd
man/R.from.r.Rd
man/est.GT.Rd
man/plot.R0.sR.Rd
man/plot.R0.R.Rd
man/print.R0.R.Rd
man/R0-package.Rd
man/est.R0.AR.Rd
man/Germany.1918.Rd
man/check.incid.Rd
man/plotRSB.Rd
man/plotfit.R0.sR.Rd
man/plotfit.R0.R.Rd
man/get.scale.Rd
man/estimate.R.Rd
R0 documentation built on May 19, 2017, 8:38 p.m.

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