Man pages for R0
Estimation of R0 and Real-Time Reproduction Number from Epidemics

censored.deviationDeviation between theorietical incidence and observed data.
check.incidCheck incidence vector in the input
est.GTEstimate generation time distribution
estimate.REstimate reproduction number (R0 or Rt) for one incidence...
est.R0.AREstimate R0 from attack rate of an epidemic
est.R0.EGEstimate R0 from exponential growth rate of an epidemic
est.R0.MLEstimate R0 by Maximum Likelihood
est.R0.SBEstimate the time dependent R using a Bayesian method
est.R0.TDEstimate the Time-Dependent reproduction number
fit.epidPoisson log-likelihood for an observed epidemic
fit.epid.optimJoint estimation of R and generation time distribution for...
generation.timeGeneration Time distribution
Germany.1918Germany 1918 dataset
get.scaleScaling of x-axis
GT.chld.hsld2009 A/H1N1 observed generation time distribution
H1N1.serial.intervalH1N1 serial interval
impute.incidImpute censored cases to rebuild longer epidemic vector
inspect.dataAudit input data for common issues
integrity.checksIntegrity checks for input parameters
plotfitS3 method for objects of class 'R0.R' or 'R0.sR'
plotfit.R0.RPlot a model fit for 'R0.R' objects
plotfit.R0.sRPlot a model fit for 'R0.sR' objects
plotfitRARInternal plotfit method for AR estimates
plotfitRSBInternal plotfit method for AR estimates
plotfitRxxInternal plotfit method for EG, ML and TD estimates
plot.R0.GTPlot a generation time distribution
plot.R0.RPlot the R0/Rt value along with confidence interval
plot.R0.SPlot of sensitivity analyses.
plot.R0.sRPlot the R0/Rt value along with confidence interval
plotRARPlot R0 for Attack Rate method
plotREGPlot R0 for Exponential Growth method
plotRMLPlot R0 for Maximum Likelihood method
plotRSBPlot R0 for Sequential Bayesian method
plotRTDPlot R0 for Time-Dependent method
print.R0.GTPrint method for objects of class 'R0.GT'
print.R0.RPrint method for objects of class 'R0.R'
print.R0.sRPrint method for objects of class 'R0.sR'
R.from.rEstimate reproduction number from exponential growth rate
sa.GTSensitivity of R0 to varying generation time distributions
sa.timeSensitivity of R0 to time estimation windows
sensitivity.analysisSensitivity analysis of basic reproduction ratio to begin/end...
sim.epidEpidemic outbreak simulation
sim.epid.indivInfluenza-like illness simulation (individual-based model)
smooth.RtSmooth real-time reproduction number over larger time periods
R0 documentation built on Sept. 26, 2023, 5:10 p.m.