Distinguish direct and indirect interactions with Graphical Modelling

activePaths | Find all active paths in a (partially) directed graph... |

adjC-dot-allVarInx | Get all the variable indicies in adjC, both target and... |

adjC-dot-allVarNames | Get all the variable names in adjC, both target and... |

adjC-dot-condSetSize | Returns the total size of conditioning set for adjC (i... |

adjC-dot-targetInx | Get all the targetInx values in adjC... |

adjC-dot-toIDs | Make a list of conditional independence tests and converts... |

biased-dot-bn-dot-fit | Random network with a biased degree distribution |

biased-dot-graph | Generate random network with degree distribution |

blockingNodes | Find all such nodes in neighbourhood of source node that are... |

blockingVariables | Version of blockingNodes() for DDGraphs... |

calcDependence | Dependence with target variable |

calculateNCPCRobustnessStats | Calculate NCPCRobustness statistics... |

chisq-dot-val | Get the value of chi-square statistics... |

ciTest-comma-DDDataSet-dash-method | Do conditional independence test on DDDataSet... |

CITestResult-dash-class | Data class to store the results of a conditional independence... |

CITestResultID | Provide a unique ID composing of target, source and... |

CITestResultVar | Return a string representation of a variable represented with... |

classLabels-comma-FurlongDataSet-dash-method | Class labels |

color-dot-legend-dot-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-comma-DDDataSet-dash-method | Dataset name... |

dataType-comma-DDDataSet-dash-method | Return data type |

DDDataSet-dash-class | Dataset class for Direct Dependence Graphs... |

DDGraph-dash-class | Direct Dependence Graph class... |

DDGraphEdge-dash-class | An edge in an DDGraph... |

ddgraph-package | ddgraph package overview |

entropyFromFreq | Calculate entropy from frequencies of observations for... |

estimateNetworkDistribution | Estimate network distribution parameters |

extractCITestResultProperty | Extract CITestResult properties |

extract-dot-targetInx | Extract all values of targetInx from a list of... |

foldChangeFromFreq | Calculate the fold change when x is of size two (always show... |

formulaFalseNeg | Generate class labels by a noisy formula with high false... |

FurlongDataSet-dash-class | Data class for the Furlong dataset... |

graph-dot-to-dot-bn | Convert graphNEL and friends representation to bn... |

independent-dot-contributions-dot-formula | Generate class labels by independent contributions of two... |

independent-dot-contributions-dot-formula-dot-mul | Generate class labels by independent contributions of two... |

initialize-comma-DDDataSet-dash-method | Construct new DDDataSet object... |

initialize-comma-DDGraph-dash-method | Construct new DDGraph object... |

is-dot-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... |

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-comma-CITestResult-dash-method | Names of slots that can be accessed with $ notation... |

names-comma-DDDataSet-dash-method | Names of variables (+class) |

names-comma-DDGraph-dash-method | Names of properties |

names-comma-FurlongDataSet-dash-method | Names of variables |

ncpc | Make a Direct Dependence Graph using the NCPC algorithm... |

ncpcResampling | NCPC Robustness from resampling |

NCPCRobustness-dash-class | NCPC resampling robustness... |

operators-dash-CITestResult | Access slots using the dollar notation... |

operators-dash-DDDataSet | access a specific variable in the dataset by name... |

operators-dash-DDGraph | access a property by name... |

pcalgMB | Find the markov blanket for the PC algorithm output... |

pcalgNBR | Find the neighbourhood for the PC algorithm output... |

plotBNLearn | A custom plotting function for the BNlearn graphs... |

plot-comma-DDGraph-comma-missing-dash-method | Plot DDGraphs using RGraphviz... |

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-dot-distr-dot-norm | Normal distribution function for 'random.bn.fit' |

prob-dot-distr-dot-unif | Uniform distribution for 'random.bn.fit' |

pValueAfterMultipleTesting | Multiple testing correction procedure for ncpc() |

random-dot-bn-dot-fit | Generate a random 'bn.fit' network |

rawData-comma-DDDataSet-dash-method | Raw data.frame with data |

readFurlongData | Read the Furlong Dataset |

recalculateSVMparams | Calculate SVM hyperparameters based on grid search |

show-comma-CITestResult-dash-method | show method for CITestResult... |

show-comma-DDDataSet-dash-method | show method for DDDataSet... |

show-comma-DDGraph-dash-method | show method for DDGraph... |

show-comma-DDGraphEdge-dash-method | show method for DDGraphEdge... |

signalMatrix-comma-FurlongDataSet-dash-method | Raw values |

svmFeatureSelectionLOOCV | Nested variable selection using LOOCV |

toDDDataSet-comma-FurlongDataSet-dash-method | DDDataSet object from FurlongDataSet |

toyExample | A binary fictional toy example 'DDDataSet' object. |

variableNames-comma-DDDataSet-dash-method | Names of variables (-class) |

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