Man pages for sbfnk/fitR
Tool box for fitting dynamic infectious disease models to time series
| burnAndThin | Burn and thin MCMC chain |
| calibrateSmc | A data set resulting from calibrating the number of particles... |
| computeDic | Compute the DIC |
| computeDistanceAbc | Compute the distance between a model and data for ABC |
| distanceOscillation | Distance weighted by number of oscillations |
| dLogPosterior | Posterior distribution for a fitmodel |
| dLogPosteriorWrapper | A wrapper for 'dLogPosterior' |
| dTrajObs | Log-likelihood of a trajectory for a deterministic model |
| epi1 | Time-series of an outbreak simulated using an SIR model. |
| epi2 | Time-series of an outbreak simulated using an SIR model with... |
| epi3 | Time-series of an outbreak simulated using an SIR model. |
| epi4 | Time-series of an outbreak simulated using an SIR model with... |
| export2Tracer | Export trace in Tracer format |
| fitmodel | Constructor of fitmodel object |
| fluTdc1971 | Time-series of the 1971 influenza epidemic in... |
| margLogLikeSto | Marginal log-likelihood for a stochastic model |
| mcmcEpi1 | Markov-chain Monte Carlo (MCMC) trace of a fit of the SIR... |
| mcmcEpi3 | Markov-chain Monte Carlo (MCMC) trace of a fit of the SIR... |
| mcmcEpi4 | Markov-chain Monte Carlo (MCMC) trace of a fit of the SIR... |
| mcmcMh | Metropolis-Hastings MCMC |
| mcmcSeit4l | Markov-chain Monte Carlo (MCMC) outputs of a fit of the... |
| mcmcSeit4lInfoPriorTheta1 | Markov-chain Monte Carlo (MCMC) outputs of a fit of the... |
| mcmcSeit4lInfoPriorTheta2 | Markov-chain Monte Carlo (MCMC) outputs of a fit of the... |
| mcmcSeit4lTheta1 | Markov-chain Monte Carlo (MCMC) outputs of a fit of the... |
| mcmcSeit4lTheta2 | Markov-chain Monte Carlo (MCMC) outputs of a fit of the... |
| mcmcSeitl | Markov-chain Monte Carlo (MCMC) outputs of a fit of the SEITL... |
| mcmcSeitlInfoPriorTheta1 | Markov-chain Monte Carlo (MCMC) outputs of a fit of the SEITL... |
| mcmcSeitlInfoPriorTheta2 | Markov-chain Monte Carlo (MCMC) outputs of a fit of the SEITL... |
| mcmcSeitlTheta1 | Markov-chain Monte Carlo (MCMC) outputs of a fit of the SEITL... |
| mcmcSeitlTheta2 | Markov-chain Monte Carlo (MCMC) outputs of a fit of the SEITL... |
| 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 |
| pmcmcSeit4lInfoPrior128 | Markov-chain Monte Carlo (MCMC) outputs of a fit of the... |
| pmcmcSeit4lInfoPrior16 | Markov-chain Monte Carlo (MCMC) outputs of a fit of the... |
| printNamedVector | Print named vector |
| rTrajObs | Generate an observation trajectory for a fitmodel |
| seit2lDeter | The deterministic SEIT2L model with constant population size |
| seit2lStoch | The stochastic SEIT2L model with constant population size |
| seit4lDeter | The deterministic SEIT4L model with constant population size |
| seit4lStoch | The stochastic SEIT4L model with constant population size |
| seitlDeter | The deterministic SEITL model with constant population size |
| seitlDistanceOscillation | ABC distance with oscillations |
| seitlStoch | 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 |
| sir2popDeter | The deterministic SIR model with two populations. |
| sirDeter | A simple deterministic SIR model with constant population... |
| sirExpDeter | A simple deterministic SIR model with constant population... |
| sirReportingDeter | A simple deterministic SIR model with constant population... |
| sirStoch | A simple stochastic SIR model with constant population size |
| testFitmodel | Test a fitmodel |
| updateCovmat | Update covariance matrix |
