Structural inference for Bayesian Networks and Variable Selection.

adjustPredictions | Adjust the predictions |

allBannedExceptPPNotBannedIfNotRequired | Make a banned list. |

allDescendants | Get descendants of all nodes. |

allNonDescendants | Get non-descendants of all nodes. |

as.data.frame.epmx | Convert epmx to a data.frame |

as.grain | Convert to grain. |

as.roc | Prepare data for plotting in a ROC plot. |

as.roc.ep | Prepare an edge probability matrix for a ROC plot. |

as.roc.ep.list | Prepare an list of edge probability matrix for a ROC plot. |

as.roc.parental | Prepare a parental for a ROC plot. |

as.roc.parental.list | Prepare a parental list for a ROC plot. |

auroc | Compute the area under an ROC curve. |

auroc.ep | Compute the area under an ROC curve. |

auroc.ep.list | Compute the area under an ROC curve. |

bayes | Bayesian posterior parameter estimates. |

bayes.bn | Bayesian posterior parameter estimates. |

bf | Bayes Factor. |

bf.bnpostmcmc | Bayes Factors. |

BNGibbsSampler | Gibbs sampler for Bayesian Networks. |

BNOrderSampler | Order MCMC sampler for Bayesian Networks. |

bnpost | BN Exact Posterior. |

bnpostmcmc | BN Posterior from MCMC. |

bnpostmcmc.list | List of BN Posteriors from MCMC. |

BNSampler | Create a MCMC sampler (MC^3) for Bayesian Networks. |

BNSamplerBigFlips | Big flips MCMC sampler for Bayesian networks. |

BNSamplerGrzeg | Undocumented. |

BNSamplerMJ | Mode-jumping MCMC sampler for Bayesian Networks. |

BNSamplerPT | Undocumented. |

burnin | Extract burnin |

burnin.sampler | Extract burnin |

checkForNonDuplicated | Remove options that don't duplicate required duplicates. |

conductance | Conductance. |

convertEPMatrixToColumns | Convert edge prob matrix to a column matrix |

cumep | Cumulative edge probabilities. |

cumep.bnpostmcmc.list | Cumulative edge probabilities. |

cumep.samplers | Cumulative edge probabilities. |

cummean | Cumulative mean. |

cummean.matrix | Cumulative mean. |

cumtvd | Cumulative total variation distance. |

cumtvd.list | List of cumulative total variation distance. |

dagGivenOrder | Sample a DAG given an order (weighted) |

decim | Find the non-integer part of a number |

defaultBanned | Maximal banned list. |

dotplot.ep | Dotplot of posterior edge probabilities. |

dotplot.ep.list | Dotplot of list of posterior edge probabilities. |

dotplot.gp | Dotplot of posterior graph probabilities. |

dotplot.gp.list | Dotplot of posterior graph probabilities. |

draw | Draw samples from a MCMC sampler. |

drawPT | Undocumented. |

drawSamplesByStepCount | Draw samples from a MCMC sampler, by step count. |

drawSamplesByTime | Draw samples from a MCMC sampler, by time. |

eachChangesChoicesForRequired | Each changes choices for required. |

edgeIsFlippable | Find flippable edges. |

eht | Expected hitting time. |

eht.bnpost | Expected hitting time. |

enforceForbiddenConstraint | Undocumented. |

entropy | Entropy. |

entropy.bnpost | Entropy. |

enumerateParentsTable | Table of all possible parents of a node. |

enumerateParentsTableNode | Table of all possible parents of a node. |

ep | Posterior edge probabilities. |

ep.bnpost | Posterior edge probabilities. |

ep.bnpostmcmc | Posterior edge probabiities. |

ep.bnpostmcmc.list | Posterior edge probabilities. |

ep.list | List of posterior edge probabilities. |

epmx | Edge probabilties matrix. |

epmx.bnpostmcmc | Edge probabilities matrix. |

epmx.bnpostmcmc.list | Edge probabilities matrix. |

epmxPlotInternal | (Internal) Plot of cumulative edge probabilities. |

epmx.sampler | Edge probabilities matrix from a sampler. |

epmx.samplers | Edge probabilities matrix. |

ep.parental.contingency | Posterior edge probabilities. |

ep.parental.list | Posterior edge probabilities. |

ep.sampler | Extract posterior edge probabiities from a sampler. |

ep.table | Computes the edge probabilities implied by a table. |

eval.prior | Compute prior score of a Bayesian network. |

exactposterior | Posterior distribution on Bayesian networks. |

fastid | Fast ID of a graph. |

fdfAsInt | Convert a data frame of factors to integers. |

gelman | Gelman and Rubin's convergence diagnostic |

gelman.samplers | Gelman and Rubin's convergence diagnostic |

getAllConsistentWithDAG | Get all consistent with DAG |

getBannedFromConstraint | Resample a pair of nodes together. |

getNewGraph | List graphs in change node neighbourhood. |

getNijkCounts | Undocumented. |

getPossibleParents | Get possible parents. |

getRequiredFromConstraint | Resample a pair of nodes together. |

getRowsThatContain | Create lookup table for parentsTable. |

gp | Posterior graph probabilities. |

gp.bnpost | Posterior graph probaiblities. |

gp.bnpostmcmc | Posterior graph probabilities. |

gp.bnpostmcmc.list | Posterior graph probabilities. |

gp.list | List of posterior graph probabilities. |

gp.sampler | Retreive graph probabilities from sampler |

graphProbGivenOrder | Probability of a graph given an order. |

hp | Hitting probability. |

intAsFDF | Convert a data frame of integers to factors. |

internal-onload | Internal function. |

intersect2 | Fast, dangerous set intersect. |

intersection | Multiple intersection function |

isConsistentWithOrder | Is a BN consistent with an order? |

is.valid.hyp | Checks validity. |

is.valid.localPriors | Check validity. |

is.valid.prior | Check validity. |

kronecker_delta | Metric: Kronecker delta |

length.bnpostmcmc | Number of samples drawn. |

length.sampler | Number of samples drawn. |

levelplot.bnpostmcmc | Levelplot of BN Posterior from MCMC. |

levelplot.ep | Levelplot of posterior edge probabilities. |

levelplot.ep.list | Levelplot of posterior edge probabilities. |

localLogScoreMultDir | Local Multinomial-Dirichlet Log marginal likelihood. |

localLogScoreNormal | Local Normal-inverse-gamma (with g-prior) Log marginal... |

localPartitionFunction | Undocumented. |

logNumMHNeighbours | (Log) Number of neighbouring networks. |

logOrderLikelihood | Log likelihood of an order |

logScoreMultDir | Multinomial-Dirichlet Log marginal likelihood. |

logScoreMultDir.bn | Compute the log marginal likelihood of the supplied Bayesian... |

logScoreMultDir.bn.list | Multinomial-Dirichlet Log marginal likelihood. |

logScoreMultDir.bnpostmcmc | Log scores of best graphs. |

logScoreMultDirFUN | Multinomial-Dirichlet Log marginal likelihood. |

logScoreMultDirIncremental | Multinomial-Dirichlet Log marginal likelihood (online). |

logScoreMultDirOffline | Multinomial-Dirichlet Log marginal likelihood (offline). |

logScoreMultDirPrepare | Internal functions. |

logScoreNormal | Normal-inverse-gamma (with g-prior) Log marginal likelihood. |

logScoreNormal.bn | Normal-inverse-gamma (with g-prior) Log marginal likelihood. |

logScoreNormal.bn.list | Normal-inverse-gamma (with g-prior) Log marginal likelihood. |

logScoreNormalFUN | Normal Log marginal likelihood. |

logScoreNormalIncremental | Normal-inverse-gamma (with g-prior) Log marginal likelihood... |

logScoreNormalOffline | Normal-inverse-gamma (with g-prior) Log marginal likelihood... |

logScoreNormalPrepare | Internal functions. |

logsumexp | Undocumented. |

makeRowPredictions | Make row predictions |

map | Maximum aposteriori graph. |

map.bnpost | Maximum aposteriori graph. |

map.bnpostmcmc | Maximum aposteriori graph. |

map.sampler | Retreive MAP from sampler |

marginalGivenIntervention | Get marginal probabilities, given an intervention. |

marginalGivenOthers | Get all marginal probabilities. |

matrix2 | Fast, dangerous matrix generation. |

mcmcposterior | Posterior distribution on Bayesian networks. |

ml | Maximum likelihood estimates. |

ml.bn | Maximum likelihood estimates for parameters of a BN. |

mukherjeeBioinformaticsPrior | Mukherjee Bioinformatics prior. |

mwep | Moving window edge probiilities. |

mwep.bnpostmcmc.list | Moving window edge probabilities. |

mwep.samplers | Moving window edge probabilities. |

mwmean | Moving window mean. |

mwmean.matrix | Moving window mean. |

new_queue | Priority queue |

new_stack | Most-recently used stack. |

nonDescendants | Find nonDescendants. |

numberDAGsGivenOrder | Number of BNs consistent with an order. |

nunique | Number of unique. |

options.grid | input a list x. |

orderFlipOperator | Draw order proposal using flip-operator |

parentalFromEPThreshold | Threshold posterior edge probabilities. |

parentalToCPDAG | Convert 'parental list' to CPDAGs. |

plot.bnpostmcmc | Plot top graphs. |

plotTape | Plot tape. |

posterior | Posterior distribution on Bayesian networks. |

predict.bn | Predict a Multinomial-Dirichlet model |

predictGivenNoParents | Predict a node, given no parents |

predictGivenParents | Predict a node, given parents |

predictModelAverageNode | Predict a Multinomial-Dirichlet model |

predictNode | Predict a Multinomial-Dirichlet model |

prepareGPPlot | Internal function. |

prepareLevelPlot | Internal function. |

print.sampler | Print a sampler |

priorGraph | A standard 'graph prior'. |

priorUniform | A uniform prior for graphs. |

queryFinding | Query an independence network, given a finding. |

removeDuplicates | Remove duplicates |

requireSomethingFromEachParent | Require something from each parent. |

residsNormal | Residuals from a Normal model |

residsNormalNode | Residuals for a single node for a Normal model |

residualsMultDir | Residuals from a Multinomial-Dirichlet model |

residualsMultDirNode | Residuals for a single node for a Multinomial-Dirichlet model |

rocplot | Plot an ROC curve. |

routesAddEdges | Update a routes matrix (edge addition). |

routesRemoveEdges | Update a routes matrix (edge removal). |

rowProbabiltiesToResponse | Get prediction for a row |

rowSums2 | Fast, dangerous row sums. |

sampleNode | Sample the parents of a single node (Gibbs sampler). |

samplePair | Sample the parents of a pair of nodes (Gibbs sampler). |

samplePair2 | Sample the parents of a pair of nodes (Gibbs sampler) v2. |

sampleQuadruple | Sample the parents of a quadruple of nodes (Gibbs sampler). |

sampleQuintuple | Sample the parents of a quintuple of nodes (Gibbs sampler). |

samplers | List of MCMC Samplers |

sampleTriple | Sample the parents of a triple of nodes (Gibbs sampler). |

satisfiesConstraint | Undocumented. |

scoreBIC | Undocumented. |

scoreParents | Undocumented. |

scoreParentsTable | Score a node-level parentsTable. |

scoreParentsTableNode | Score a node-level parentsTable. |

setdiff3 | Fast, dangerous set difference. |

setupConstraint | Setup constraint. |

shrinkep | Internal function. |

splom.bnpostmcmc.list | Scatterplot matrix of edge probabilities between runs. |

splom.epmx | Plot of cumulative edge probabilities. |

square_error | Metric: Square error |

statistics | Extract statistics from a sampler. |

statistics.sampler | Extract statistics from a sampler. |

steps | Number of samples drawn. |

steps.sampler | Number of samples drawn. |

structmcmc | The structmcmc package. |

summary.gp | Summary of posterior graph probabilities. |

summary.sampler | Summarising MCMC samplers |

top | Top posterior graph. |

top.bnpost | Top graph from BN Posterior. |

top.bnpostmcmc | Top graph from BN Posterior. |

top.sampler | Retreive top graph from sampler |

topScoringGraph | Get modal graph given an order. |

tp | Transition probabilities. |

tp.bnpost | Transition probabilities. |

transposeEdgeIsAddable | Find togglable edges. |

transposeEdgeIsRemovable | Find togglable edges. |

transposeEdgeIsTogglable | Find togglable edges. |

validStartEnd | Check validity of start and end. |

whichGraphsNotNeighbours | Identify neighbouring graphs. |

whichNum | Find rows satisfying equality. |

whichParentSetRows | Find relevants rows of a parentsTable. |

xyplot.cumtvd | Plot cumulative total variation distance. |

xyplot.cumtvd.list | Plot of cumulative total variation distance. |

xyplot.epmx | Plot of cumulative edge probabilities. |

xyplot.gp | Scatterplot of posterior graph probabilities. |

xyplot.gp.list | Scatterplot of posterior graph probablities. |

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