BayesianTools0.1.8 package

Adapts pCR values

The Adaptive Metropolis Algorithm

Provides the default settings for the different samplers in runMCMC

BayesianTools

Helper function for calculating beta

Calculates the marginal likelihood of a chain via bridge sampling

Simulation-based calibration tests

Checks if an object is of class 'BayesianSetup'

Function to combine chains

Convert coda::mcmc objects to BayesianTools::mcmcSampler

Checks if thin is consistent with nTotalSamples samples and if not cor...

Flexible function to create correlation density plots

Creates a standardized collection of prior, likelihood and posterior f...

Convenience function to create a beta prior

Creates a standardized likelihood class#'

Convenience function to create an object of class mcmcSamplerList from...

Creates a standardized posterior class

Creates a standardized prior class

Fits a density function to a multivariate sample

Factory that creates a proposal generator

Convenience function to create an object of class SMCSamplerList from ...

Convenience function to create a truncated normal prior

Convenience function to create a simple uniform prior distribution

Differential-Evolution MCMC

Differential-Evolution MCMC zs

Deviance information criterion

The Delayed Rejection Algorithm

The Delayed Rejection Adaptive Metropolis Algorithm

DREAM

DREAMzs

factorMatrice

Gelman Diagnostics

Generates matrix of CR values based on pCR

Factory to generate a parallel executor of an existing function

Multivariate normal likelihood

Determine the parameters in the block update

getblockSettings

Calculate confidence region from an MCMC or similar sample

Creates a DHARMa object

getPanels

Returns possible sampler types

Calculates predictive distribution based on the parameters

Calculates Bayesian credible (confidence) and predictive intervals bas...

Produce multivariate normal proposal

Extracts the sample from a bayesianOutput

Function to get the setup from a bayesianOutput

Calculate posterior volume

Helper function for blow and hop moves

Standard GOF metrics Startvalues for sampling with nrChains > 1 : if y...

AR1 type likelihood function

Normal / Gaussian Likelihood function

Funktion to compute log(sum(exp(x))

The Metropolis Algorithm

Helper function to change an object to a coda mcmc class,

calculates the Maxiumum APosteriori value (MAP)

Calcluated the marginal likelihood from a set of MCMC samples

Plot MCMC marginals

Plot marginals as densities

Plot marginals as violin plot

Run multiple chains

Merge Chains

Creates a Metropolis-type MCMC with options for covariance adaptatin, ...

Function to calculate the metropolis ratio

Allows to mix a given parameter vector with a default parameter vector

Diagnostic Plot

Performs a one-factor-at-a-time sensitivity analysis for the posterior...

Plots a time series, with the option to include confidence and predict...

Plots residuals of a time series

Creates a time series plot typical for an MCMC / SMC fit

Helper function to create proposal

Rescale

Main wrapper function to start MCMCs, particle MCMCs and SMCs

Gets n equally spaced samples (rows) from a matrix or vector

gets samples while adopting the MCMC proposal generator

Function to scale matrices

Help function to find starvalues and proposalGenerator settings

SMC sampler

Function to close cluster in BayesianSetup

Helper function for sum of x*x

Banana-shaped density function

GelmanMeng test function

Test function infinity ragged

3d Mutivariate Normal likelihood

Normal likelihood

Fake model, returns a ax + b linear response to 2-param vector

Function to thin matrices

Trace plot for MCMC class

T-walk MCMC

Wrapper for step function

Main function that is executing and evaluating the moves

Determine the groups of correlated parameters

To update settings of an existing proposal genenerator

Very simple ecosystem model

C version of the VSEM model

Create an example dataset, and from that a likelihood or posterior for...

Create a random radiation (PAR) time series

returns the default values for the VSEM

calculates the WAIC