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pcalg (version 2.4-5)

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) and the Generalized Adjustment Criterion (GAC) are implemented.

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Version

Install

install.packages('pcalg')

Monthly Downloads

1,927

Version

2.4-5

License

GPL (>= 2)

Maintainer

Markus Kalisch

Last Published

February 22nd, 2017

Functions in pcalg (2.4-5)

corGraph

Computing the correlation graph
checkTriple

Check Consistency of Conditional Independence for a Triple of Nodes
dag2cpdag

Convert a DAG to a CPDAG
binCItest

G square Test for (Conditional) Independence of Binary Variables
beta.special

Compute set of intervention effects
amatType

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

Test Conditional Independence of Gaussians via Fisher's Z
beta.special.pcObj

Compute set of intervention effects in a fast way
compareGraphs

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

Find Set Satisfying the Generalized Backdoor Criterion (GBC)
dsep

Test for d-separation in a DAG
dsepTest

Test for d-separation in a DAG
dreach

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

G square Test for (Conditional) Independence of Discrete Variables
dag2pag

Convert a DAG with latent variables into a PAG
fciPlus

Estimate a PAG by the FCI+ Algorithm
dag2essgraph

Convert a DAG to an Essential Graph
fci

Estimate a PAG by the FCI Algorithm
EssGraph-class

Class "EssGraph"
fciAlgo-class

Class "fciAlgo" of FCI Algorithm Results
GaussL0penObsScore-class

Class "GaussL0penObsScore"
gds

Greedy DAG Search to Estimate Markov Equivalence Class of DAG
GaussL0penIntScore-class

Class "GaussL0penIntScore"
getNextSet

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

Test If Set Satisfies Generalized Adjustment Criterion (GAC)
getGraph

Get the "graph" Part or Aspect of R Object
find.unsh.triple

Find all Unshielded Triples in an Undirected Graph
gAlgo-class

Class "gAlgo"
GaussParDAG-class

Class "GaussParDAG" of Gaussian Causal Models
ges

Estimate the Markov equivalence class of a DAG using GES
iplotPC

Plotting a pcAlgo object using the package igraph
gmD

Graphical Model Discrete 5-Dim Example Data
gmB

Graphical Model 5-Dim Binary Example Data
gmL

Latent Variable 4-Dim Graphical Model Data Example
gies

Estimate Interventional Markov Equivalence Class of a DAG by GIES
gmG

Graphical Model 8-Dimensional Gaussian Example Data
idaFast

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

Graphical Model 7-dim IDA Data Examples
gmInt

Graphical Model 8-Dimensional Interventional Gaussian Example Data
ida

Estimate Multiset of Possible Total Causal Effects
mcor

Compute (Large) Correlation Matrix
pcalg-internal

Internal Pcalg Functions
LINGAM

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

Class "ParDAG" of Parametric Causal Models
pc

Estimate the Equivalence Class of a DAG using the PC Algorithm
mat2targets

Conversion between an intervention matrix and a list of intervention targets
pc.cons.intern

Utility for conservative and majority rule in PC and FCI
legal.path

Check if a 3-node-path is Legal
pag2mag

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

Estimate Multiset of Possible Total Joint Effects
pcSelect

PC-Select: Estimate subgraph around a response variable
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
pcAlgo

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

Compute Partial Correlations
plotSG

Plot the subgraph around a Specific Node in a Graph Object
pcSelect.presel

Estimate Subgraph around a Response Variable using Preselection
pcAlgo-class

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

Plot partial ancestral graphs (PAG)
randomDAG

Generate a Directed Acyclic Graph (DAG) randomly
r.gauss.pardag

Generate a Gaussian Causal Model Randomly
possibleDe

Find possible descendants on definite status paths.
rmvnorm.ivent

Simulate from a Gaussian Causal Model
rfci

Estimate an RFCI-PAG using the RFCI Algorithm
qreach

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

Virtual Class "Score"
rmvDAG

Generate Multivariate Data according to a DAG
shd

Compute Structural Hamming Distance (SHD)
randDAG

Random DAG Generation
showEdgeList

Show Edge List of pcAlgo object
simy

Estimate Interventional Markov Equivalence Class of a DAG
visibleEdge

Check visible edge.
skeleton

Estimate (Initial) Skeleton of a DAG using the PC / PC-Stable Algorithm
udag2pdag

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

Covariance matrix of a DAG.
unifDAG

Uniform Sampling of Directed Acyclic Graphs (DAG)
udag2pag

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

Show Adjacency Matrix of pcAlgo object
udag2apag

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

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