# Distinguish direct and indirect interactions with Graphical Modelling

## Documentation for package ‘ddgraph’ version 1.2.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

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...