| censored.deviation | Impute censored cases to rebuild longer epidemic vector |
| check.incid | Check incidence vector in the input |
| est.GT | Estimate generation time distribution |
| estimate.R | Estimate reproduction number (R0 or Rt) for one incidence... |
| est.R0.AR | Estimate R0 from attack rate of an epidemic |
| est.R0.EG | Estimate R0 from exponential growth rate of an epidemic |
| est.R0.ML | Estimate R0 by Maximum Likelihood |
| est.R0.SB | Estimate the time dependent R using a Bayesian method |
| est.R0.TD | Estimate the Time-Dependent reproduction number |
| fit.epid | Poisson log-likelihood for an observed epidemic |
| fit.epid.optim | Joint estimation of R and generation time distribution for... |
| generation.time | Generation Time distribution |
| Germany.1918 | Germany 1918 dataset |
| get.scale | Scaling of x-axis |
| GT.chld.hsld | 2009 A/H1N1 observed generation time distribution |
| H1N1.serial.interval | H1N1 serial interval |
| impute.incid | Optimiziation routine for incidence imputation |
| inspect.data | Audit input data for common issues |
| integrity.checks | Integrity checks for input parameters |
| plotfit | S3 method for objects of class 'R0.R' or 'R0.sR' |
| plotfit.R0.R | Plot a model fit for 'R0.R' objects |
| plotfit.R0.sR | Plot a model fit for 'R0.sR' objects |
| plotfitRAR | Internal plotfit method for AR estimates |
| plotfitRSB | Internal plotfit method for AR estimates |
| plotfitRxx | Internal plotfit method for EG, ML and TD estimates |
| plot.R0.GT | Plot a generation time distribution |
| plot.R0.R | Plot the R0/Rt value along with confidence interval |
| plot.R0.S | Plot of sensitivity analyses. |
| plot.R0.sR | Plot the R0/Rt value along with confidence interval |
| plotRAR | Plot R0 for Attack Rate method |
| plotREG | Plot R0 for Exponential Growth method |
| plotRML | Plot R0 for Maximum Likelihood method |
| plotRSB | Plot R0 for Sequential Bayesian method |
| plotRTD | Plot R0 for Time-Dependent method |
| print.R0.GT | Print method for objects of class 'R0.GT' |
| print.R0.R | Print method for objects of class 'R0.R' |
| print.R0.sR | Print method for objects of class 'R0.sR' |
| R.from.r | Estimate reproduction number from exponential growth rate |
| sa.GT | Sensitivity of R0 to varying generation time distributions |
| sa.time | Sensitivity of R0 to time estimation windows |
| 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 periods |
