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pcalg (version 2.7-4)

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

1,927

Version

2.7-4

License

GPL (>= 2)

Maintainer

Markus Kalisch

Last Published

November 25th, 2021

Functions in pcalg (2.7-4)

LINGAM

Linear non-Gaussian Acyclic Models (LiNGAM)
GaussL0penObsScore-class

Class "GaussL0penObsScore"
GaussL0penIntScore-class

Class "GaussL0penIntScore"
EssGraph-class

Class "EssGraph"
adjustment

Compute adjustment sets for covariate adjustment.
ParDAG-class

Class "ParDAG" of Parametric Causal Models
GaussParDAG-class

Class "GaussParDAG" of Gaussian Causal Models
corGraph

Computing the correlation graph
ages

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

G square Test for (Conditional) Independence of Binary Variables
addBgKnowledge

Add background knowledge to a CPDAG or PDAG
Score-class

Virtual Class "Score"
amatType

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

Find Set Satisfying the Generalized Backdoor Criterion (GBC)
dsep

Test for d-separation in a DAG
dsepAM

Test for d-separation in a MAG
beta.special.pcObj

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

Compute set of intervention effects
compareGraphs

Compare two graphs in terms of TPR, FPR and TDR
fci

Estimate a PAG with the FCI Algorithm
fciAlgo-class

Class "fciAlgo" of FCI Algorithm Results
checkTriple

Check Consistency of Conditional Independence for a Triple of Nodes
condIndFisherZ

Test Conditional Independence of Gaussians via Fisher's Z
dag2essgraph

Convert a DAG to an Essential Graph
dsepAMTest

Test for d-separation in a MAG
gds

Greedy DAG Search to Estimate Markov Equivalence Class of DAG
ges

Estimate the Markov equivalence class of a DAG using GES
fciPlus

Estimate a PAG with the FCI+ Algorithm
disCItest

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

Compute D-SEP(x,y,G)
find.unsh.triple

Find all Unshielded Triples in an Undirected Graph
dag2cpdag

Convert a DAG to a CPDAG
dsepTest

Test for d-separation in a DAG
gmI

Graphical Model 7-dim IDA Data Examples
gAlgo-class

Class "gAlgo"
gmInt

Graphical Model 8-Dimensional Interventional Gaussian Example Data
gac

Test If Set Satisfies Generalized Adjustment Criterion (GAC)
isValidGraph

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

Estimate Multiset of Possible Total Joint Effects
pag2anc

Reads off identifiable ancestors and non-ancestors from a directed PAG
optAdjSet

Compute the optimal adjustment set
gmL

Latent Variable 4-Dim Graphical Model Data Example
legal.path

Check if a 3-node-path is Legal
mat2targets

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

Estimate Multiset of Possible Joint Total Causal Effects
pcSelect

PC-Select: Estimate subgraph around a response variable
pcAlgo

PC-Algorithm [OLD]: Estimate Skeleton or Equivalence Class of a DAG
pdag2allDags

Enumerate All DAGs in a Markov Equivalence Class
pdag2dag

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

Plotting a pcAlgo object using the package igraph
pc

Estimate the Equivalence Class of a DAG using the PC Algorithm
idaFast

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

Get the "graph" Part or Aspect of R Object
getNextSet

Iteration through a list of all combinations of choose(n,k)
pag2mag

Transform a PAG into a MAG in the Corresponding Markov Equivalence Class
dag2pag

Convert a DAG with latent variables into a PAG
gies

Estimate Interventional Markov Equivalence Class of a DAG by GIES
possDe

Find possible descendants of given node(s).
pag2conf

Reads off identifiable unconfounded node pairs from a directed PAG
pag2edge

Reads off identifiable parents and non-parents from a directed PAG
plotSG

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

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

Show Edge List of pcAlgo object
randomDAG

Generate a Directed Acyclic Graph (DAG) randomly
simy

Estimate Interventional Markov Equivalence Class of a DAG
pcalg2dagitty

Transform the adjacency matrix from pcalg into a dagitty object
randDAG

Random DAG Generation
gmB

Graphical Model 5-Dim Binary Example Data
rmvDAG

Generate Multivariate Data according to a DAG
rfci

Estimate an RFCI-PAG using the RFCI Algorithm
udag2pag

Last steps of FCI algorithm: Transform Final Skeleton into FCI-PAG
udag2apag

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

Check visible edge.
udag2pdag

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

Compute Structural Hamming Distance (SHD)
showAmat

Show Adjacency Matrix of pcAlgo object
pcAlgo-class

Class "pcAlgo" of PC Algorithm Results, incl. Skeleton
opt.target

Get an optimal intervention target
pc.cons.intern

Utility for conservative and majority rule in PC and FCI
possAn

Find possible ancestors of given node(s).
gmD

Graphical Model Discrete 5-Dim Example Data
gmG

Graphical Model 8-Dimensional Gaussian Example Data
mcor

Compute (Large) Correlation Matrix
pdsep

Estimate Final Skeleton in the FCI algorithm
pcorOrder

Compute Partial Correlations
skeleton

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

Plot partial ancestral graphs (PAG)
pcSelect.presel

Estimate Subgraph around a Response Variable using Preselection
pcalg-internal

Internal Pcalg Functions
searchAM

Search for certain nodes in a DAG/CPDAG/MAG/PAG
wgtMatrix

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

Compute Possible-D-SEP(x,G) of a node x in a PDAG G
rmvnorm.ivent

Simulate from a Gaussian Causal Model
r.gauss.pardag

Generate a Gaussian Causal Model Randomly
trueCov

Covariance matrix of a DAG.