Man pages for sbfnk/fitR
Tool box for fitting dynamic infectious disease models to time series.

ABCLogPosteriorABC logged posterior distribution
burnAndThinBurn and thin MCMC chain
computeDICCompute the DIC
computeDistanceABCCompute the distance between a model and data for ABC
distanceOscillationDistance weighted by number of oscillations
dTrajObsLog-likelihood of a trajectory for a deterministic model
export2TracerExport trace in Tracer format
fitmodelConstructor of fitmodel object
FluTdC1971Time-series of the 1971 influenza epidemic in...
logPosteriorPosterior distribution for a fitmodel
logPosteriorWrapperA wrapper for 'logPosterior'
margLogLikeStoMarginal log-likelihood for a stochastic model
mcmcMHMetropolis-Hasting MCMC
measlesTime-series of a measles outbreak
particleFilterRun a particle filter for fitmodel object
plotESSBurnPlot Effective Sample Size (ESS) against burn-in
plotFitPlot fit of model to data
plotHPDregion2D2D highest posterior density region
plotPosteriorDensityPlot MCMC posterior densities
plotPosteriorFitPlot MCMC posterior fit
plotSMCPlot result of SMC
plotTracePlot MCMC trace
plotTrajPlot model trajectories
printNamedVectorPrint named vector
rTrajObsGenerate an observation trajectory for a fitmodel
SEIT2L_deterThe deterministic SEIT2L model with constant population size
SEIT2L_pompThe SEIT2L model for pomp
SEIT2L_pomp_rThe SEIT2L model for pomp, using only R code
SEIT2L_stochThe stochastic SEIT2L model with constant population size
SEIT4L_deterThe deterministic SEIT4L model with constant population size
SEIT4L_pompThe SEIT4L model for pomp
SEIT4L_pomp_rThe SEIT4L model for pomp, using only R code
SEIT4L_stochThe stochastic SEIT4L model with constant population size
SEITL_deterThe deterministic SEITL model with constant population size
SEITL_distanceOscillationABC distance with oscillations
SEITL_pompThe SEITL model for pomp
SEITL_pomp_rThe SEITL model for pomp, using only R code
SEITL_stochThe stochastic SEITL model with constant population size
simulateFinalStateAtExtinctionSimulate model until extinction
simulateModelReplicatesSimulate several replicate of the model
simulateModelStochasticSimulate forward a stochastic model
SIRA simple deterministic SIR model with constant population...
SIR_expA simple deterministic SIR model with constant population...
SIR_reportingA simple deterministic SIR model with constant population...
SIR_stochA simple stochastic SIR model with constant population size
testFitmodelTest a fitmodel
updateCovmatUpdate covariance matrix
sbfnk/fitR documentation built on Aug. 12, 2017, 7:47 a.m.