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.

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

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

Functions

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

Files

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

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