| 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. |
