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

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

View on CRAN

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

Files in this package

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