$,CITestResult-method   Access slots using the dollar notation...
$,DDDataSet-method      access a specific variable in the dataset by
                        name...
$,DDGraph-method        access a property by name...
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...
DDDataSet-class         Dataset class for Direct Dependence Graphs...
DDGraph-class           Direct Dependence Graph class...
DDGraphEdge-class       An edge in an DDGraph...
FurlongDataSet-class    Data class for the Furlong dataset...
NCPCRobustness-class    NCPC resampling robustness...
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,DDDataSet-method
                        Do conditional independence test on
                        DDDataSet...
classLabels,FurlongDataSet-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
dataType,DDDataSet-method
                        Return data type
datasetName,DDDataSet-method
                        Dataset name...
ddgraph-package         ddgraph package overview
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
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,DDDataSet-method
                        Construct new DDDataSet object...
initialize,DDGraph-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,CITestResult-method
                        Names of slots that can be accessed with $
                        notation...
names,DDDataSet-method
                        Names of variables (+class)
names,DDGraph-method    Names of properties
names,FurlongDataSet-method
                        Names of variables
ncpc                    Make a Direct Dependence Graph using the NCPC
                        algorithm...
ncpcResampling          NCPC Robustness from resampling
pValueAfterMultipleTesting
                        Multiple testing correction procedure for
                        ncpc()
pcalgMB                 Find the markov blanket for the PC algorithm
                        output...
pcalgNBR                Find the neighbourhood for the PC algorithm
                        output...
plot,DDGraph,missing-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'
random.bn.fit           Generate a random 'bn.fit' network
rawData,DDDataSet-method
                        Raw data.frame with data
readFurlongData         Read the Furlong Dataset
recalculateSVMparams    Calculate SVM hyperparameters based on grid
                        search
show,CITestResult-method
                        show method for CITestResult...
show,DDDataSet-method   show method for DDDataSet...
show,DDGraph-method     show method for DDGraph...
show,DDGraphEdge-method
                        show method for DDGraphEdge...
signalMatrix,FurlongDataSet-method
                        Raw values
svmFeatureSelectionLOOCV
                        Nested variable selection using LOOCV
toDDDataSet,FurlongDataSet-method
                        DDDataSet object from FurlongDataSet
toyExample              A binary fictional toy example 'DDDataSet'
                        object.
variableNames,DDDataSet-method
                        Names of variables (-class)
