Tool box for fitting dynamic infectious disease models to time series.

burnAndThin | Burn and thin MCMC chain |

computeDIC | Compute the DIC |

computeDistanceABC | Compute the distance between a model and data for ABC |

distanceOscillation | Distance weighted by number of oscillations |

dTrajObs | Log-likelihood of a trajectory for a deterministic model |

export2Tracer | Export trace in Tracer format |

fitmodel | Constructor of fitmodel object |

FluTdC1971 | Time-series of the 1971 influenza epidemic in... |

logPosterior | Posterior distribution for a fitmodel |

logPosteriorWrapper | A wrapper for 'logPosterior' |

margLogLikeSto | Marginal log-likelihood for a stochastic model |

mcmcMH | Metropolis-Hasting MCMC |

measles | Time-series of a measles outbreak |

particleFilter | Run a particle filter for fitmodel object |

plotESSBurn | Plot Effective Sample Size (ESS) against burn-in |

plotFit | Plot fit of model to data |

plotHPDregion2D | 2D highest posterior density region |

plotPosteriorDensity | Plot MCMC posterior densities |

plotPosteriorFit | Plot MCMC posterior fit |

plotSMC | Plot result of SMC |

plotTrace | Plot MCMC trace |

plotTraj | Plot model trajectories |

printNamedVector | Print named vector |

rTrajObs | Generate an observation trajectory for a fitmodel |

SEIT2L_deter | The deterministic SEIT2L model with constant population size |

SEIT2L_pomp | The SEIT2L model for pomp |

SEIT2L_pomp_r | The SEIT2L model for pomp, using only R code |

SEIT2L_stoch | The stochastic SEIT2L model with constant population size |

SEIT4L_deter | The deterministic SEIT4L model with constant population size |

SEIT4L_pomp | The SEIT4L model for pomp |

SEIT4L_pomp_r | The SEIT4L model for pomp, using only R code |

SEIT4L_stoch | The stochastic SEIT4L model with constant population size |

SEITL_deter | The deterministic SEITL model with constant population size |

SEITL_distanceOscillation | ABC distance with oscillations |

SEITL_pomp | The SEITL model for pomp |

SEITL_pomp_r | The SEITL model for pomp, using only R code |

SEITL_stoch | The stochastic SEITL model with constant population size |

simulateFinalStateAtExtinction | Simulate model until extinction |

simulateModelReplicates | Simulate several replicate of the model |

simulateModelStochastic | Simulate forward a stochastic model |

SIR | A simple deterministic SIR model with constant population... |

SIR_exp | A simple deterministic SIR model with constant population... |

SIR_reporting | A simple deterministic SIR model with constant population... |

SIR_stoch | A simple stochastic SIR model with constant population size |

testFitmodel | Test a fitmodel |

updateCovmat | Update covariance matrix |

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