Methods for Graphical Models and Causal Inference

Documentation for package ‘pcalg’ version 2.7-9

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

-- A --

addBgKnowledge	Add background knowledge to a CPDAG or PDAG
adjustment	Compute adjustment sets for covariate adjustment.
ages	Estimate an APDAG within the Markov equivalence class of a DAG using AGES
amat.cpdag	Types and Display of Adjacency Matrices in Package 'pcalg'
amat.pag	Types and Display of Adjacency Matrices in Package 'pcalg'
amatType	Types and Display of Adjacency Matrices in Package 'pcalg'

-- B --

backdoor	Find Set Satisfying the Generalized Backdoor Criterion (GBC)
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 Joint Total Causal Effects
checkTriple	Check Consistency of Conditional Independence for a Triple of Nodes
coerce-method	Types and Display of Adjacency Matrices in Package 'pcalg'
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 of Discrete Variables
dreach	Compute D-SEP(x,y,G)
dsep	Test for d-separation in a DAG
dsepAM	Test for d-separation in a MAG
dsepAMTest	Test for d-separation in a MAG
dsepTest	Test for d-separation in a DAG

-- E --

EssGraph-class

Class '"EssGraph"'

-- F --

fci	Estimate a PAG with the FCI Algorithm
fciAlgo-class	Class "fciAlgo" of FCI Algorithm Results
fciPlus	Estimate a PAG with the FCI+ Algorithm
find.unsh.triple	Find all Unshielded Triples in an Undirected Graph

-- G --

gac	Test If Set Satisfies Generalized Adjustment Criterion (GAC)
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"' of Gaussian Causal Models
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 of Discrete Variables

-- I --

ida	Estimate Multiset of Possible Joint Total Causal Effects
idaFast	Multiset of Possible Total Causal Effects for Several Target Var.s
iplotPC	Plotting a pcAlgo object using the package igraph
isValidGraph	Check for a DAG, CPDAG or a maximally oriented PDAG

-- J --

jointIda

Estimate Multiset of Possible Total Joint Effects

-- L --

legal.path	Check if a 3-node-path is Legal
LINGAM	Linear non-Gaussian Acyclic Models (LiNGAM)
lingam	Linear non-Gaussian Acyclic Models (LiNGAM)
local.mle-method	Class '"GaussL0penIntScore"'
local.mle-method	Class '"GaussL0penObsScore"'
local.score-method	Class '"GaussL0penIntScore"'
local.score-method	Class '"GaussL0penObsScore"'

-- M --

mat2targets	Conversion between an intervention matrix and a list of intervention targets
mcor	Compute (Large) Correlation Matrix

-- O --

opt.target	Get an optimal intervention target
optAdjSet	Compute the optimal adjustment set

-- P --

pag2anc	Reads off identifiable ancestors and non-ancestors from a directed PAG
pag2conf	Reads off identifiable unconfounded node pairs from a directed PAG
pag2edge	Reads off identifiable parents and non-parents from a directed PAG
pag2magAM	Transform a PAG into a MAG in the Corresponding Markov Equivalence Class
ParDAG-class	Class '"ParDAG"' of Parametric Causal Models
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
pcalg2dagitty	Transform the adjacency matrix from 'pcalg' into a 'dagitty' object
pcAlgo	PC-Algorithm [OLD]: Estimate Skeleton or Equivalence Class of a DAG
pcAlgo-class	Class "pcAlgo" of PC Algorithm Results, incl. Skeleton
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
pdag2allDags	Enumerate All DAGs in a Markov Equivalence Class
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"' of Parametric Causal Models
plot-method	Class "fciAlgo" of FCI Algorithm Results
plot-method	Class "pcAlgo" of PC Algorithm Results, incl. Skeleton
plotAG	Plot partial ancestral graphs (PAG)
plotSG	Plot the subgraph around a Specific Node in a Graph Object
possAn	Find possible ancestors of given node(s).
possDe	Find possible descendants of given node(s).
possibleDe	[DEPRECATED] Find possible descendants on definite status paths.
print.fciAlgo	Class "fciAlgo" of FCI Algorithm Results
print.pcAlgo	Class "pcAlgo" of PC Algorithm Results, incl. Skeleton

-- 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
randDAG	Random DAG Generation
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"
searchAM	Search for certain nodes in a DAG/CPDAG/MAG/PAG
shd	Compute Structural Hamming Distance (SHD)
show-method	Class "fciAlgo" of FCI Algorithm Results
show-method	Class "pcAlgo" of PC Algorithm Results, incl. Skeleton
show.fci.amat	Types and Display of Adjacency Matrices in Package 'pcalg'
show.pc.amat	Types and Display of Adjacency Matrices in Package 'pcalg'
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" of FCI Algorithm Results
summary-method	Class "pcAlgo" of PC Algorithm Results, incl. Skeleton

-- T --

targets2mat	Conversion between an intervention matrix and a list of intervention targets
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

Weight Matrix of a Graph, e.g., a simulated DAG

-- Z --

zStat

Test Conditional Independence of Gaussians via Fisher's Z