BNSamplerMJ: Mode-jumping MCMC sampler for Bayesian Networks.

In rjbgoudie/structmcmc: Structural inference for Bayesian Networks and Variable Selection.

Description

The sampler samples Bayesian Networks (ie models).

Usage

  BNSamplerMJ(data, initial, prior, return = "network",
    logScoreFUN = logScoreMultDirFUN(),
    logScoreParameters = list(hyperparameters = "bdeu"),
    constraint = NULL, modejumping = F, verbose = F,
    keepTape = F)

Arguments

data	The data.
initial	An object of class 'bn'. The starting value of the MCMC.
prior	A function that returns the prior score of the supplied bn.
return	Either "network" or "contingency".
logScoreFUN	A list of four elements: offline A function that computes the logScore of a Bayesian Network online A function that incrementally computes the logScore of a Bayesian Network local A function that computes the local logScore of a Bayesian Network prepare A function that prepares the data, and any further pre-computation required by the logScore functions. For Multinomial-Dirichlet models, logScoreMultDirFUN returns the appropriate list; for Normal models with Zellner g-priors, logScoreNormalFUN returns the appropriate list.
logScoreParameters	A list of parameters that are passed to logScoreFUN.
constraint	A matrix of dimension ncol(data) x ncol(data) giving constraints to the sample space. The (i, j) element is: 1 if the edge i -> j is required -1 if the edge i -> is excluded. 0 if the edge i -> j is not constrained. The diagonal of constraint must be all 0.
modejumping	Either a logical of length 1, or a list. When no mode-jumping is desired, use modejumping = F. For mode-jumping, use a list with the following components: modes A bn.list of modes. modesLogScores Optionally, a numeric vector, containing the logScores of the modes. checkModesAcyclic A logical of length 1 modesPreFiltered A logical of length 1 modeJumpingProbability A numeric of length 1. Default 0.25 dontCheckModesValid A logical of length 1
verbose	A logical of length 1, indicating whether verbose output should be printed.
keepTape	A logical of length 1, indicating whether a full log (tape) of the MCMC sampler should be kept. Enabling this option can be very memory-intensive.

Value

A function, which when called draws the next sample of the MCMC.

See Also

BNSampler, BNGibbsSampler, BNSamplerPT, BNSamplerGrzeg, BNSamplerBigFlips. Internally uses whichGraphsNotNeighbours

rjbgoudie/structmcmc documentation built on Nov. 3, 2020, 3:41 a.m.