Man pages for BayesianTools
General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics

AMThe Adaptive Metropolis Algorithm
applySettingsDefaultProvides the default settings for the different samplers in...
bridgesampleCalculates the marginal likelihood of a chain via bridge...
checkBayesianSetupChecks if an object is of class 'BayesianSetup'
convertCodaConvert coda::mcmc objects to BayesianTools::mcmcSampler
correctThinChecks if thin is conistent with nTotalSamples samples and if...
correlationPlotFlexible function to create correlation density plots
createBayesianSetupCreates a standardized collection of prior, likelihood and...
createBetaPriorConvenience function to create a beta prior
createBreakMatcreate break matrix
createLikelihoodCreates a standardized likelihood class#'
createMcmcSamplerListConvenience function to create an object of class...
createPosteriorCreates a standardized posterior class
createPriorCreates a standardized prior class
createPriorDensityFits a density function to a multivariate sample
createProposalGeneratorFactory that creates a proposal generator
createSmcSamplerListConvenience function to create an object of class...
createTruncatedNormalPriorConvenience function to create a truncated normal prior
createUniformPriorConvenience function to create a simple uniform prior...
DEDifferential-Evolution MCMC
DEzsDifferential-Evolution MCMC zs
DICDeviance information criterion
DRThe Delayed Rejection Algorithm
DRAMThe Delayed Rejection Adaptive Metropolis Algorithm
gelmanDiagnosticsRuns Gelman Diagnotics over an BayesianOutput
generateParallelExecuterFactory to generate a parallel executer of an existing...
generateTestDensityMultiNormalMultivariate normal likelihood
getCredibleIntervalsCalculate confidence region from an MCMC or similar sample
getDharmaResidualsCreates a DHARMa object
getMetropolisDefaultSettingsReturns Metropolis default settings
getPanelsCalculates the panel combination for par(mfrow = )
getPossibleSamplerTypesReturns possible sampler types
getPredictiveDistributionCalculates predictive distribution based on the parameters
getPredictiveIntervalsCalculates Bayesian credible (confidence) and predictive...
getSampleExtracts the sample from a bayesianOutput
getVolumeCalculate posterior volume
GOFStandard GOF metrics Startvalues for sampling with nrChains >...
histMarginalhistogram for marginalPlot
likelihoodAR1AR1 type likelihood function
likelihoodIidNormalNormal / Gaussian Likelihood function
logSumExpFunktion to compute log(sum(exp(x))
MThe Metropolis Algorithm
MAPcalculates the Maxiumum APosteriori value (MAP)
marginalLikelihoodCalcluated the marginal likelihood from a set of MCMC samples
marginalPlotPlot MCMC marginals
mcmcMultipleChainsRun multiple chains
MetropolisCreates a Metropolis-type MCMC with options for covariance...
metropolisRatioFunction to calculate the metropolis ratio
package-deprecatedAllows to mix a given parameter vector with a default...
plotHistplot histogram
plotSensitivityPerforms a one-factor-at-a-time sensitivity analysis for the...
plotTimeSeriesPlots a time series, with the option to include confidence...
plotTimeSeriesResidualsPlots residuals of a time series
plotTimeSeriesResultsCreates a time series plot typical for an MCMC / SMC fit
runMCMCMain wrapper function to start MCMCs, particle MCMCs and SMCs
sampleEquallySpacedGets n equally spaced samples (rows) from a matrix or vector
sampleMetropolisgets samples while adopting the MCMC proposal generator
setupStartProposalHelp function to find starvalues and proposalGenerator...
smcSamplerSMC sampler
stopParallelFunction to close cluster in BayesianSetup
testDensityBananaBanana-shaped density function
testDensityInfinityTest function infinity ragged
testDensityMultiNormal3d Mutivariate Normal likelihood
testDensityNormalNormal likelihood
testLinearModelFake model, returns a ax + b linear response to 2-param...
tracePlotTrace plot for MCMC class
TwalkT-walk MCMC
updateProposalGeneratorTo update settings of an existing proposal genenerator
violinPlotViolin Plot
VSEMVery simple ecosystem model
vsemCC version of the VSEM model
VSEMcreateLikelihoodCreate an example dataset, and from that a likelihood or...
VSEMcreatePARCreate a random radiation (PAR) time series
VSEMgetDefaultsreturns the default values for the VSEM
WAICcalculates the WAIC
BayesianTools documentation built on Dec. 23, 2017, 5:26 p.m.