├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── Idist.R ├── KerAdjustPD.R ├── KerCori.R ├── KerDateTicker.R ├── KerIncidCheck.R ├── KerLikelihood.R ├── KerMCMC.R ├── KerPtheta.R ├── KerWT.R ├── RcppExports.R ├── Rmodelpriors.R ├── S3_Idist_plot.R ├── S3_Rt_plot.R ├── S3_Rt_summary.R ├── S3_Rtnow_plot.R ├── S3_incubestim_plot.R ├── S3_nowcast_plot.R ├── cov19incidence2022.R ├── cov19mort2021.R ├── cppsource.R ├── epicurve.R ├── epilps.R ├── episim.R ├── eruptions.R ├── estimIncub.R ├── estimR.R ├── estimRmcmc.R ├── histosmooth.R ├── incubsim.R ├── influenza2009.R ├── influenza2009serial.R ├── nowcasting.R ├── nowcastingR.R ├── perfRestim.R ├── sars2003.R └── zika2015.R ├── README.md ├── README_files └── figure-gfm │ ├── lpsmap-1.png │ ├── performance_check-1.png │ ├── plotepi-1.png │ ├── plotepi2-1.png │ ├── realdata-1.png │ ├── simex1-1.png │ └── unnamed-chunk-1-1.png ├── data ├── cov19incidence2022.rda ├── cov19mort2021.rda ├── eruptions.rda ├── influenza2009.rda ├── influenza2009serial.rda ├── sars2003.rda └── zika2015.rda ├── man ├── Idist.Rd ├── Rmodelpriors.Rd ├── cov19incidence2022.Rd ├── cov19mort2021.Rd ├── epicurve.Rd ├── episim.Rd ├── eruptions.Rd ├── estimIncub.Rd ├── estimR.Rd ├── estimRmcmc.Rd ├── figures │ └── gplv3-or-later.png ├── histosmooth.Rd ├── incubsim.Rd ├── influenza2009.Rd ├── influenza2009serial.Rd ├── nowcasting.Rd ├── nowcastingR.Rd ├── perfRestim.Rd ├── plot.Idist.Rd ├── plot.Rt.Rd ├── plot.Rtnow.Rd ├── plot.incubestim.Rd ├── plot.nowcasted.Rd ├── sars2003.Rd ├── summary.Rt.Rd └── zika2015.Rd └── src ├── .gitignore ├── KerLaplace.cpp ├── KerLaplaceIncub.cpp ├── KerLaplaceNowcast.cpp ├── KerMVN.cpp ├── KerRpostmap.cpp ├── KerRpostmcmc.cpp ├── KercubicBspline.cpp ├── Kerhyperoptim.cpp ├── Makevars ├── Makevars.win └── RcppExports.cpp /.Rbuildignore: -------------------------------------------------------------------------------- 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