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A B C D E F G I L M N P R S T V misc
| ddgraph-package | ddgraph package overview |
| activePaths | Find all active paths in a (partially) directed graph... |
| adjC.allVarInx | Get all the variable indicies in adjC, both target and condSet... |
| adjC.allVarNames | Get all the variable names in adjC, both target and condSet... |
| adjC.condSetSize | Returns the total size of conditioning set for adjC (i... |
| adjC.targetInx | Get all the targetInx values in adjC... |
| adjC.toIDs | Make a list of conditional independence tests and converts them to IDs... |
| biased.bn.fit | Random network with a biased degree distribution |
| biased.graph | Generate random network with degree distribution |
| blockingNodes | Find all such nodes in neighbourhood of source node that are blocking at least one active path leading to another node... |
| blockingVariables | Version of blockingNodes() for DDGraphs... |
| calcDependence | Dependence with target variable |
| calculateNCPCRobustnessStats | Calculate NCPCRobustness statistics... |
| chisq.val | Get the value of chi-square statistics... |
| ciTest | Do conditional independence test on DDDataSet... |
| ciTest-method | Do conditional independence test on DDDataSet... |
| CITestResult | Data class to store the results of a conditional independence test... |
| CITestResult-class | Data class to store the results of a conditional independence test... |
| CITestResultID | Provide a unique ID composing of target, source and conditioning set (all names)... |
| CITestResultVar | Return a string representation of a variable represented with this CITest... |
| classLabels | Class labels |
| classLabels-method | Class labels |
| color.legend.DDGraph | Plot color coding legend |
| combinationsTest | Significant combinations of variables |
| convertPvalueToColorIndex | Convert P-values to color index... |
| convertToFactor | Convert data to factor representation |
| customPlotPCAlgo | Custom plotting for pcalgo |
| datasetName | Dataset name... |
| datasetName-method | Dataset name... |
| dataType | Return data type |
| dataType-method | Return data type |
| DDDataSet | Dataset class for Direct Dependence Graphs... |
| DDDataSet-class | Dataset class for Direct Dependence Graphs... |
| DDGraph | Direct Dependence Graph class... |
| ddgraph | ddgraph package overview |
| DDGraph-class | Direct Dependence Graph class... |
| DDGraphEdge | An edge in an DDGraph... |
| DDGraphEdge-class | An edge in an DDGraph... |
| entropyFromFreq | Calculate entropy from frequencies of observations for discrete data... |
| estimateNetworkDistribution | Estimate network distribution parameters |
| extract.targetInx | Extract all values of targetInx from a list of CITestResult... |
| extractCITestResultProperty | Extract CITestResult properties |
| foldChangeFromFreq | Calculate the fold change when x is of size two (always show it >1)... |
| formulaFalseNeg | Generate class labels by a noisy formula with high false negative rate |
| FurlongDataSet | Data class for the Furlong dataset... |
| FurlongDataSet-class | Data class for the Furlong dataset... |
| graph.to.bn | Convert graphNEL and friends representation to bn... |
| independent.contributions.formula | Generate class labels by independent contributions of two variables |
| independent.contributions.formula.mul | Generate class labels by independent contributions of two variables |
| initialize-method | Construct new DDDataSet object... |
| initialize-method | Construct new DDGraph object... |
| is.binary | Check if data structure has binary data in it |
| logseq | Generate sequence in log scale |
| loocv | Leave-one-out cross validation |
| makeDDDataSet | Construct an DDDataSet object... |
| makeNCPCRobustness | Make a new NCPCRobustness object... |
| mapEnrichmentToColors | Map enrichment values to colors... |
| mapEnrichmentToColorsDual | Map enrichment values into two different palettes for enriched/depleted variables... |
| mcMITest | Wrapper around the bnlearn mc-x2 test |
| mcX2CLoop | the inner loop for myX2c is implemented in C... |
| mcX2Test | Wrapper around the bnlearn mc-x2 test |
| mcX2TestB50k | Wrapper around the bnlearn mc-x2 test (B=50k) |
| mesoBin | A list of binary 'DDDataSet' objects. |
| mesoCont | A list of continuous 'DDDataSet' objects. |
| myX2c | The Monte-Carlo chi-square test... |
| names-method | Names of slots that can be accessed with $ notation... |
| names-method | Names of variables (+class) |
| names-method | Names of properties |
| names-method | Names of variables |
| ncpc | Make a Direct Dependence Graph using the NCPC algorithm... |
| ncpcResampling | NCPC Robustness from resampling |
| NCPCRobustness | NCPC resampling robustness... |
| NCPCRobustness-class | NCPC resampling robustness... |
| pcalgMB | Find the markov blanket for the PC algorithm output... |
| pcalgNBR | Find the neighbourhood for the PC algorithm output... |
| plot | Plot DDGraphs using RGraphviz... |
| plot-method | Plot DDGraphs using RGraphviz... |
| plotBNLearn | A custom plotting function for the BNlearn graphs... |
| plotPCalg | Plot the network inferred by the PC algorithm |
| plotSVMPerformance | Plot SVM performance into a pdf file |
| predSVM | Calculate the decision value of an SVM model |
| prob.distr.norm | Normal distribution function for 'random.bn.fit' |
| prob.distr.unif | Uniform distribution for 'random.bn.fit' |
| pValueAfterMultipleTesting | Multiple testing correction procedure for ncpc() |
| random.bn.fit | Generate a random 'bn.fit' network |
| rawData | Raw data.frame with data |
| rawData-method | Raw data.frame with data |
| readFurlongData | Read the Furlong Dataset |
| recalculateSVMparams | Calculate SVM hyperparameters based on grid search |
| show-method | show method for CITestResult... |
| show-method | show method for DDDataSet... |
| show-method | show method for DDGraph... |
| show-method | show method for DDGraphEdge... |
| signalMatrix | Raw values |
| signalMatrix-method | Raw values |
| svmFeatureSelectionLOOCV | Nested variable selection using LOOCV |
| toDDDataSet | DDDataSet object from FurlongDataSet |
| toDDDataSet-method | DDDataSet object from FurlongDataSet |
| toyExample | A binary fictional toy example 'DDDataSet' object. |
| variableNames | Names of variables (-class) |
| variableNames-method | Names of variables (-class) |
| $-method | Access slots using the dollar notation... |
| $-method | access a specific variable in the dataset by name... |
| $-method | access a property by name... |
| [ | access a specific variable in the dataset by name... |
| [-method | access a specific variable in the dataset by name... |
| [[-method | Access slots using the dollar notation... |
| [[-method | access a specific variable in the dataset by name... |