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pcalg (version 2.6-8)

Methods for Graphical Models and Causal Inference

Description

Functions for causal structure learning and causal inference using graphical models. The main algorithms for causal structure learning are PC (for observational data without hidden variables), FCI and RFCI (for observational data with hidden variables), and GIES (for a mix of data from observational studies (i.e. observational data) and data from experiments involving interventions (i.e. interventional data) without hidden variables). For causal inference the IDA algorithm, the Generalized Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC) and some related functions are implemented. Functions for incorporating background knowledge are provided.

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Version

Install

install.packages('pcalg')

Monthly Downloads

1,806

Version

2.6-8

License

GPL (>= 2)

Maintainer

Last Published

November 21st, 2019

Functions in pcalg (2.6-8)

amatType

Types and Display of Adjacency Matrices in Package 'pcalg'
condIndFisherZ

Test Conditional Independence of Gaussians via Fisher's Z
checkTriple

Check Consistency of Conditional Independence for a Triple of Nodes
binCItest

G square Test for (Conditional) Independence of Binary Variables
GaussL0penIntScore-class

Class "GaussL0penIntScore"
dag2pag

Convert a DAG with latent variables into a PAG
beta.special.pcObj

Compute set of intervention effects in a fast way
beta.special

Compute set of intervention effects
dag2essgraph

Convert a DAG to an Essential Graph
addBgKnowledge

Add background knowledge to a CPDAG or PDAG
gAlgo-class

Class "gAlgo"
fci

Estimate a PAG by the FCI Algorithm
backdoor

Find Set Satisfying the Generalized Backdoor Criterion (GBC)
dsep

Test for d-separation in a DAG
fciAlgo-class

Class "fciAlgo" of FCI Algorithm Results
gac

Test If Set Satisfies Generalized Adjustment Criterion (GAC)
dsepTest

Test for d-separation in a DAG
corGraph

Computing the correlation graph
fciPlus

Estimate a PAG by the FCI+ Algorithm
dag2cpdag

Convert a DAG to a CPDAG
find.unsh.triple

Find all Unshielded Triples in an Undirected Graph
gmI

Graphical Model 7-dim IDA Data Examples
getNextSet

Iteration through a list of all combinations of choose(n,k)
gmInt

Graphical Model 8-Dimensional Interventional Gaussian Example Data
getGraph

Get the "graph" Part or Aspect of R Object
legal.path

Check if a 3-node-path is Legal
dreach

Compute D-SEP(x,y,G)
disCItest

G square Test for (Conditional) Independence of Discrete Variables
gmD

Graphical Model Discrete 5-Dim Example Data
iplotPC

Plotting a pcAlgo object using the package igraph
idaFast

Multiset of Possible Total Causal Effects for Several Target Var.s
gmG

Graphical Model 8-Dimensional Gaussian Example Data
mcor

Compute (Large) Correlation Matrix
pc

Estimate the Equivalence Class of a DAG using the PC Algorithm
opt.target

Get an optimal intervention target
mat2targets

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

Compute the optimal adjustment set
pdag2dag

Extend a Partially Directed Acyclic Graph (PDAG) to a DAG
pdsep

Estimate Final Skeleton in the FCI algorithm
randDAG

Random DAG Generation
r.gauss.pardag

Generate a Gaussian Causal Model Randomly
gds

Greedy DAG Search to Estimate Markov Equivalence Class of DAG
pcalg-internal

Internal Pcalg Functions
gmB

Graphical Model 5-Dim Binary Example Data
pc.cons.intern

Utility for conservative and majority rule in PC and FCI
gies

Estimate Interventional Markov Equivalence Class of a DAG by GIES
pcalg2dagitty

Transform the adjacency matrix from pcalg into a dagitty object
ida

Estimate Multiset of Possible Joint Total Causal Effects
gmL

Latent Variable 4-Dim Graphical Model Data Example
pag2mag

Transform a PAG into a MAG in the Corresponding Markov Equivalence Class
shd

Compute Structural Hamming Distance (SHD)
ges

Estimate the Markov equivalence class of a DAG using GES
isValidGraph

Check for a DAG, CPDAG or a maximally oriented PDAG
jointIda

Estimate Multiset of Possible Total Joint Effects
pcSelect

PC-Select: Estimate subgraph around a response variable
udag2pag

Last steps of FCI algorithm: Transform Final Skeleton into FCI-PAG
pcAlgo-class

Class "pcAlgo" of PC Algorithm Results, incl. Skeleton
pcorOrder

Compute Partial Correlations
wgtMatrix

Weight Matrix of a Graph, e.g., a simulated DAG
udag2apag

Last step of RFCI algorithm: Transform partially oriented graph into RFCI-PAG
showAmat

Show Adjacency Matrix of pcAlgo object
pcSelect.presel

Estimate Subgraph around a Response Variable using Preselection
possAn

Find possible ancestors of given node(s).
pcAlgo

PC-Algorithm [OLD]: Estimate Skeleton or Equivalence Class of a DAG
plotAG

Plot partial ancestral graphs (PAG)
pdag2allDags

Enumerate All DAGs in a Markov Equivalence Class
possDe

Find possible descendants of given node(s).
plotSG

Plot the subgraph around a Specific Node in a Graph Object
rmvDAG

Generate Multivariate Data according to a DAG
randomDAG

Generate a Directed Acyclic Graph (DAG) randomly
udag2pdag

Last PC Algorithm Step: Extend Object with Skeleton to Completed PDAG
rfci

Estimate an RFCI-PAG using the RFCI Algorithm
showEdgeList

Show Edge List of pcAlgo object
rmvnorm.ivent

Simulate from a Gaussian Causal Model
simy

Estimate Interventional Markov Equivalence Class of a DAG
visibleEdge

Check visible edge.
possibleDe

[DEPRECATED] Find possible descendants on definite status paths.
qreach

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

Estimate (Initial) Skeleton of a DAG using the PC / PC-Stable Algorithm
trueCov

Covariance matrix of a DAG.
LINGAM

Linear non-Gaussian Acyclic Models (LiNGAM)
EssGraph-class

Class "EssGraph"
adjustment

Compute adjustment sets for covariate adjustment.
GaussL0penObsScore-class

Class "GaussL0penObsScore"
Score-class

Virtual Class "Score"
ages

Estimate an APDAG within the Markov equivalence class of a DAG using AGES
ParDAG-class

Class "ParDAG" of Parametric Causal Models
compareGraphs

Compare two graphs in terms of TPR, FPR and TDR
GaussParDAG-class

Class "GaussParDAG" of Gaussian Causal Models