Methods for graphical models and causal inference


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Documentation for package ‘pcalg’ version 2.0-2

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B C D E F G I L M P Q R S T U V W Z

-- B --

backdoor Find Set Satisfying the Generalized Backdoor Criterion
beta.special Compute set of intervention effects
beta.special.pcObj Compute set of intervention effects in a fast way
binCItest G square Test for (Conditional) Independence of Binary Variables

-- C --

causalEffect Estimate Multiset of Possible Total Causal Effects
checkTriple Check Consistency of Conditional Independence for a Triple of Nodes
compareGraphs Compare two graphs in terms of TPR, FPR and TDR
condIndFisherZ Test Conditional Independence of Gaussians via Fisher's Z
corGraph Computing the correlation graph

-- D --

dag2cpdag Convert a DAG to a CPDAG
dag2essgraph Convert a DAG to an Essential Graph
dag2pag Convert a DAG with latent variables into a PAG
disCItest G square Test for (conditional) Independence for Discrete Data
dreach Compute D-SEP(x,y,G)
dsep Test for d-separation in a DAG
dsepTest Test for d-separation in a DAG

-- E --

EssGraph-class Class '"EssGraph"'

-- F --

fci Estimate a PAG, using the FCI-algorithm
fciAlgo-class Class "fciAlgo"
find.unsh.triple Find all Unshielded Triples in an Undirected Graph

-- G --

gAlgo-class Class '"gAlgo"'
gaussCItest Test Conditional Independence of Gaussians via Fisher's Z
GaussL0penIntScore-class Class '"GaussL0penIntScore"'
GaussL0penObsScore-class Class '"GaussL0penObsScore"'
GaussParDAG-class Class '"GaussParDAG"'
gds Greedy DAG Search to Estimate Markov Equivalence Class of DAG
ges Estimate the Markov equivalence class of a DAG using GES
getGraph Get the "graph" Part or Aspect of R Object
getGraph-method Get the "graph" Part or Aspect of R Object
getGraph-methods Get the "graph" Part or Aspect of R Object
getNextSet Iteration through a list of all combinations of choose(n,k)
gies Estimate Interventional Markov Equivalence Class of a DAG by GIES
global.mle-method Class '"GaussL0penIntScore"'
global.mle-method Class '"GaussL0penObsScore"'
global.score-method Class '"GaussL0penIntScore"'
global.score-method Class '"GaussL0penObsScore"'
gmB Graphical Model 5-Dim Binary Example Data
gmD Graphical Model Discrete 5-Dim Example Data
gmG Graphical Model 8-Dimensional Gaussian Example Data
gmG8 Graphical Model 8-Dimensional Gaussian Example Data
gmI Graphical Model 7-dim IDA Data Examples
gmI7 Graphical Model 7-dim IDA Data Examples
gmInt Graphical Model 8-Dimensional Interventional Gaussian Example Data
gmL Latent Variable 4-Dim Graphical Model Data Example
gSquareBin G square Test for (Conditional) Independence of Binary Variables
gSquareDis G square Test for (conditional) Independence for Discrete Data

-- I --

ida Estimate Multiset of Possible Total Causal Effects
idaFast Multiset of Possible Total Causal Effects for Several Target Var.s
iplotPC Plotting a pcAlgo object using the package igraph

-- L --

legal.path Check if a 3-node-path is Legal
local.mle-method Class '"GaussL0penIntScore"'
local.mle-method Class '"GaussL0penObsScore"'
local.score-method Class '"GaussL0penIntScore"'
local.score-method Class '"GaussL0penObsScore"'

-- M --

mat2targets Construct a list of intervention targets and a target index vector
mcor Compute (Large) Correlation Matrix

-- P --

pag2magAM Transform a PAG into a MAG in the Corresponding Markov Equivalence Class
ParDAG-class Class '"ParDAG"'
pc Estimate the Equivalence Class of a DAG using the PC Algorithm
pc.cons.intern Utility for conservative and majority rule in PC and FCI
pcAlgo PC-Algorithm [OLD]: Estimate Skeleton or Equivalence Class of a DAG
pcAlgo-class Class "pcAlgo"
pcAlgo.Perfect PC-Algorithm [OLD]: Estimate Skeleton or Equivalence Class of a DAG
pcorOrder Compute Partial Correlations
pcSelect PC-Select: Estimate subgraph around a response variable
pcSelect.presel Estimate Subgraph around a Response Variable using Preselection
pdag2dag Extend a Partially Directed Acyclic Graph (PDAG) to a DAG
pdsep Estimate Final Skeleton in the FCI algorithm
plot-method Class '"EssGraph"'
plot-method Class '"ParDAG"'
plot-method Class "fciAlgo"
plot-method Class "pcAlgo"
plotAG Plot partial ancestral graphs (PAG)
plotSG Plot the subgraph around a Specific Node in a Graph Object
possibleDe Find possible descendants on definite status paths.

-- Q --

qreach Compute Possible-D-SEP(x,G) of a node x in a PDAG G

-- R --

r.gauss.pardag Generate a Gaussian Causal Model Randomly
randomDAG Generate a Directed Acyclic Graph (DAG) randomly
rfci Estimate an RFCI-PAG using the RFCI Algorithm
rmvDAG Generate Multivariate Data according to a DAG
rmvnorm.ivent Simulate from a Gaussian Causal Model

-- S --

Score-class Virtual Class "Score"
shd Compute Structural Hamming Distance (SHD)
show-method Class "fciAlgo"
show-method Class "pcAlgo"
showAmat Show Adjacency Matrix of pcAlgo object
showEdgeList Show Edge List of pcAlgo object
simy Estimate Interventional Markov Equivalence Class of a DAG
skeleton Estimate (Initial) Skeleton of a DAG using the PC / PC-Stable Algorithm
summary-method Class "fciAlgo"
summary-method Class "pcAlgo"

-- T --

triple2numb Utility for conservative and majority rule in PC and FCI
trueCov Covariance matrix of a DAG.

-- U --

udag2apag Last step of RFCI algorithm: Transform partially oriented graph into RFCI-PAG
udag2pag Last steps of FCI algorithm: Transform Final Skeleton into FCI-PAG
udag2pdag Last PC Algorithm Step: Extend Object with Skeleton to Completed PDAG
udag2pdagRelaxed Last PC Algorithm Step: Extend Object with Skeleton to Completed PDAG
udag2pdagSpecial Last PC Algorithm Step: Extend Object with Skeleton to Completed PDAG

-- V --

visibleEdge Check visible edge.

-- W --

wgtMatrix Compute weight matrix of simulated DAG.

-- Z --

zStat Test Conditional Independence of Gaussians via Fisher's Z