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

AdaptpCRAdapts pCR values
AMThe Adaptive Metropolis Algorithm
applySettingsDefaultProvides the default settings for the different samplers in...
betaFunHelper function for calculating beta
bridgesampleCalculates the marginal likelihood of a chain via bridge...
calibrationTestSimulation-based calibration tests
checkBayesianSetupChecks if an object is of class 'BayesianSetup'
combineChainsFunction to combine chains
convertCodaConvert coda::mcmc objects to BayesianTools::mcmcSampler
correctThinChecks if thin is consistent with nTotalSamples samples and...
correlationPlotFlexible function to create correlation density plots
createBayesianSetupCreates a standardized collection of prior, likelihood and...
createBetaPriorConvenience function to create a beta prior
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
gelmanDiagnosticsGelman Diagnostics
generateCRvaluesGenerates matrix of CR values based on pCR
generateParallelExecuterFactory to generate a parallel executor of an existing...
generateTestDensityMultiNormalMultivariate normal likelihood
getBlockDetermine the parameters in the block update
getCredibleIntervalsCalculate confidence region from an MCMC or similar sample
getDharmaResidualsCreates a DHARMa object
getPossibleSamplerTypesReturns possible sampler types
getPredictiveDistributionCalculates predictive distribution based on the parameters
getPredictiveIntervalsCalculates Bayesian credible (confidence) and predictive...
getRmvnormProduce multivariate normal proposal
getSampleExtracts the sample from a bayesianOutput
getSetupFunction to get the setup from a bayesianOutput
getVolumeCalculate posterior volume
GfunHelper function for blow and hop moves
GOFStandard GOF metrics Startvalues for sampling with nrChains >...
likelihoodAR1AR1 type likelihood function
likelihoodIidNormalNormal / Gaussian Likelihood function
logSumExpFunktion to compute log(sum(exp(x))
MThe Metropolis Algorithm
makeObjectClassCodaMCMCHelper function to change an object to a coda mcmc class,
MAPcalculates the Maxiumum APosteriori value (MAP)
marginalLikelihoodCalcluated the marginal likelihood from a set of MCMC samples
marginalPlotPlot MCMC marginals
marginalPlotDensityPlot marginals as densities
marginalPlotViolinPlot marginals as violin plot
mcmcMultipleChainsRun multiple chains
mergeChainsMerge 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...
plotDiagnosticDiagnostic Plot
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
propFunHelper function to create proposal
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
scaleMatrixFunction to scale matrices
setupStartProposalHelp function to find starvalues and proposalGenerator...
smcSamplerSMC sampler
stopParallelFunction to close cluster in BayesianSetup
sumSquareHelper function for sum of x*x
testDensityBananaBanana-shaped density function
testDensityGelmanMengGelmanMeng test function
testDensityInfinityTest function infinity ragged
testDensityMultiNormal3d Mutivariate Normal likelihood
testDensityNormalNormal likelihood
testLinearModelFake model, returns a ax + b linear response to 2-param...
thinMatrixFunction to thin matrices
tracePlotTrace plot for MCMC class
TwalkT-walk MCMC
TwalkMoveWrapper for step function
TwalkstepsMain function that is executing and evaluating the moves
updateGroupsDetermine the groups of correlated parameters
updateProposalGeneratorTo update settings of an existing proposal genenerator
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 Feb. 16, 2023, 8:44 p.m.