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 realtime 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 realtime 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  PierreYves Boelle, Thomas Obadia 
Date of publication  20150521 19:34:12 
Maintainer  Thomas Obadia <thomas.obadia@iplesp.upmc.fr> 
License  GPL (>= 2) 
Version  1.26 
Package repository  View on CRAN 
Installation  Install the latest version of this package by entering the following in R:



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 bestfitting 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 XAxis 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...  
R0package: Estimation of R0 and RealTime 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: Influenzalike illness simulation (individualbased model)  
smooth.Rt: Smooth realtime 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 
R0package  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/R0package.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 
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