Distinguish direct and indirect interactions with Graphical Modelling


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Documentation for package ‘ddgraph’ version 1.12.0

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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

-- A --

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...

-- B --

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...

-- C --

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

-- D --

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...

-- E --

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

-- F --

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...

-- G --

graph.to.bn Convert graphNEL and friends representation to bn...

-- I --

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

-- L --

logseq Generate sequence in log scale
loocv Leave-one-out cross validation

-- M --

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...

-- N --

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...

-- P --

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()

-- R --

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

-- S --

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

-- T --

toDDDataSet DDDataSet object from FurlongDataSet
toDDDataSet-method DDDataSet object from FurlongDataSet
toyExample A binary fictional toy example 'DDDataSet' object.

-- V --

variableNames Names of variables (-class)
variableNames-method Names of variables (-class)

-- misc --

$-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...