Man pages for Bioconductor-mirror/ddgraph
Distinguish direct and indirect interactions with Graphical Modelling

activePathsFind all active paths in a (partially) directed graph...
adjC-dot-allVarInxGet all the variable indicies in adjC, both target and...
adjC-dot-allVarNamesGet all the variable names in adjC, both target and...
adjC-dot-condSetSizeReturns the total size of conditioning set for adjC (i...
adjC-dot-targetInxGet all the targetInx values in adjC...
adjC-dot-toIDsMake a list of conditional independence tests and converts...
biased-dot-bn-dot-fitRandom network with a biased degree distribution
biased-dot-graphGenerate random network with degree distribution
blockingNodesFind all such nodes in neighbourhood of source node that are...
blockingVariablesVersion of blockingNodes() for DDGraphs...
calcDependenceDependence with target variable
calculateNCPCRobustnessStatsCalculate NCPCRobustness statistics...
chisq-dot-valGet the value of chi-square statistics...
ciTest-comma-DDDataSet-dash-methodDo conditional independence test on DDDataSet...
CITestResult-dash-classData class to store the results of a conditional independence...
CITestResultIDProvide a unique ID composing of target, source and...
CITestResultVarReturn a string representation of a variable represented with...
classLabels-comma-FurlongDataSet-dash-methodClass labels
color-dot-legend-dot-DDGraphPlot color coding legend
combinationsTestSignificant combinations of variables
convertPvalueToColorIndexConvert P-values to color index...
convertToFactorConvert data to factor representation
customPlotPCAlgoCustom plotting for pcalgo
datasetName-comma-DDDataSet-dash-methodDataset name...
dataType-comma-DDDataSet-dash-methodReturn data type
DDDataSet-dash-classDataset class for Direct Dependence Graphs...
DDGraph-dash-classDirect Dependence Graph class...
DDGraphEdge-dash-classAn edge in an DDGraph...
ddgraph-packageddgraph package overview
entropyFromFreqCalculate entropy from frequencies of observations for...
estimateNetworkDistributionEstimate network distribution parameters
extractCITestResultPropertyExtract CITestResult properties
extract-dot-targetInxExtract all values of targetInx from a list of...
foldChangeFromFreqCalculate the fold change when x is of size two (always show...
formulaFalseNegGenerate class labels by a noisy formula with high false...
FurlongDataSet-dash-classData class for the Furlong dataset...
graph-dot-to-dot-bnConvert graphNEL and friends representation to bn...
independent-dot-contributions-dot-formulaGenerate class labels by independent contributions of two...
independent-dot-contributions-dot-formula-dot-mulGenerate class labels by independent contributions of two...
initialize-comma-DDDataSet-dash-methodConstruct new DDDataSet object...
initialize-comma-DDGraph-dash-methodConstruct new DDGraph object...
is-dot-binaryCheck if data structure has binary data in it
logseqGenerate sequence in log scale
loocvLeave-one-out cross validation
makeDDDataSetConstruct an DDDataSet object...
makeNCPCRobustnessMake a new NCPCRobustness object...
mapEnrichmentToColorsMap enrichment values to colors...
mapEnrichmentToColorsDualMap enrichment values into two different palettes for...
mcMITestWrapper around the bnlearn mc-x2 test
mcX2CLoopthe inner loop for myX2c is implemented in C...
mcX2TestWrapper around the bnlearn mc-x2 test
mcX2TestB50kWrapper around the bnlearn mc-x2 test (B=50k)
mesoBinA list of binary 'DDDataSet' objects.
mesoContA list of continuous 'DDDataSet' objects.
myX2cThe Monte-Carlo chi-square test...
names-comma-CITestResult-dash-methodNames of slots that can be accessed with $ notation...
names-comma-DDDataSet-dash-methodNames of variables (+class)
names-comma-DDGraph-dash-methodNames of properties
names-comma-FurlongDataSet-dash-methodNames of variables
ncpcMake a Direct Dependence Graph using the NCPC algorithm...
ncpcResamplingNCPC Robustness from resampling
NCPCRobustness-dash-classNCPC resampling robustness...
operators-dash-CITestResultAccess slots using the dollar notation...
operators-dash-DDDataSetaccess a specific variable in the dataset by name...
operators-dash-DDGraphaccess a property by name...
pcalgMBFind the markov blanket for the PC algorithm output...
pcalgNBRFind the neighbourhood for the PC algorithm output...
plotBNLearnA custom plotting function for the BNlearn graphs...
plot-comma-DDGraph-comma-missing-dash-methodPlot DDGraphs using RGraphviz...
plotPCalgPlot the network inferred by the PC algorithm
plotSVMPerformancePlot SVM performance into a pdf file
predSVMCalculate the decision value of an SVM model
prob-dot-distr-dot-normNormal distribution function for 'random.bn.fit'
prob-dot-distr-dot-unifUniform distribution for 'random.bn.fit'
pValueAfterMultipleTestingMultiple testing correction procedure for ncpc()
random-dot-bn-dot-fitGenerate a random 'bn.fit' network
rawData-comma-DDDataSet-dash-methodRaw data.frame with data
readFurlongDataRead the Furlong Dataset
recalculateSVMparamsCalculate SVM hyperparameters based on grid search
show-comma-CITestResult-dash-methodshow method for CITestResult...
show-comma-DDDataSet-dash-methodshow method for DDDataSet...
show-comma-DDGraph-dash-methodshow method for DDGraph...
show-comma-DDGraphEdge-dash-methodshow method for DDGraphEdge...
signalMatrix-comma-FurlongDataSet-dash-methodRaw values
svmFeatureSelectionLOOCVNested variable selection using LOOCV
toDDDataSet-comma-FurlongDataSet-dash-methodDDDataSet object from FurlongDataSet
toyExampleA binary fictional toy example 'DDDataSet' object.
variableNames-comma-DDDataSet-dash-methodNames of variables (-class)
Bioconductor-mirror/ddgraph documentation built on June 1, 2017, 7:32 a.m.