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pcalg (version 2.2-4)

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

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Version

Install

install.packages('pcalg')

Monthly Downloads

1,575

Version

2.2-4

License

GPL (>= 2)

Maintainer

Markus Kalisch

Last Published

July 23rd, 2015

Functions in pcalg (2.2-4)

dreach

Compute D-SEP(x,y,G)
GaussParDAG-class

Class "GaussParDAG" of Gaussian Causal Models
mat2targets

Construct a list of intervention targets and a target index vector
pcSelect.presel

Estimate Subgraph around a Response Variable using Preselection
backdoor

Find Set Satisfying the Generalized Backdoor Criterion
beta.special.pcObj

Compute set of intervention effects in a fast way
dag2cpdag

Convert a DAG to a CPDAG
dsep

Test for d-separation in a DAG
wgtMatrix

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

Estimate Multiset of Possible Total Joint Effects
gies

Estimate Interventional Markov Equivalence Class of a DAG by GIES
gac

Test If Set Satisfies Generalized Adjustment Criterion (GAC)
binCItest

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

Compute set of intervention effects
rfci

Estimate an RFCI-PAG using the RFCI Algorithm
getNextSet

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

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

Random DAG Generation
disCItest

G square Test for (Conditional) Independence of Discrete Variables
pc.cons.intern

Utility for conservative and majority rule in PC and FCI
plotAG

Plot partial ancestral graphs (PAG)
pdag2dag

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

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

PC-Select: Estimate subgraph around a response variable
EssGraph-class

Class "EssGraph"
find.unsh.triple

Find all Unshielded Triples in an Undirected Graph
gmG

Graphical Model 8-Dimensional Gaussian Example Data
gAlgo-class

Class "gAlgo"
gmB

Graphical Model 5-Dim Binary Example Data
gds

Greedy DAG Search to Estimate Markov Equivalence Class of DAG
pc

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

Estimate Multiset of Possible Total Causal Effects
Score-class

Virtual Class "Score"
rmvnorm.ivent

Simulate from a Gaussian Causal Model
checkTriple

Check Consistency of Conditional Independence for a Triple of Nodes
possibleDe

Find possible descendants on definite status paths.
mcor

Compute (Large) Correlation Matrix
rmvDAG

Generate Multivariate Data according to a DAG
udag2pag

Last steps of FCI algorithm: Transform Final Skeleton into FCI-PAG
dag2pag

Convert a DAG with latent variables into a PAG
pcalg-internal

Internal Pcalg Functions
fci

Estimate a PAG by the FCI Algorithm
fciPlus

Estimate a PAG by the FCI+ Algorithm
showAmat

Show Adjacency Matrix of pcAlgo object
GaussL0penIntScore-class

Class "GaussL0penIntScore"
pdsep

Estimate Final Skeleton in the FCI algorithm
ParDAG-class

Class "ParDAG" of Parametric Causal Models
GaussL0penObsScore-class

Class "GaussL0penObsScore"
getGraph

Get the "graph" Part or Aspect of R Object
fciAlgo-class

Class "fciAlgo" of FCI Algorithm Results
iplotPC

Plotting a pcAlgo object using the package igraph
plotSG

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

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

Covariance matrix of a DAG.
visibleEdge

Check visible edge.
simy

Estimate Interventional Markov Equivalence Class of a DAG
udag2pdag

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

Show Edge List of pcAlgo object
udag2apag

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

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

Computing the correlation graph
r.gauss.pardag

Generate a Gaussian Causal Model Randomly
gmI

Graphical Model 7-dim IDA Data Examples
condIndFisherZ

Test Conditional Independence of Gaussians via Fisher's Z
gmD

Graphical Model Discrete 5-Dim Example Data
legal.path

Check if a 3-node-path is Legal
pcAlgo-class

Class "pcAlgo" of PC Algorithm Results
dsepTest

Test for d-separation in a DAG
gmL

Latent Variable 4-Dim Graphical Model Data Example
LINGAM

Linear non-Gaussian Additive Models (LiNGAM)
dag2essgraph

Convert a DAG to an Essential Graph
ges

Estimate the Markov equivalence class of a DAG using GES
pag2mag

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

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

Graphical Model 8-Dimensional Interventional Gaussian Example Data
randomDAG

Generate a Directed Acyclic Graph (DAG) randomly
shd

Compute Structural Hamming Distance (SHD)
unifDAG

Uniform Sampling of Directed Acyclic Graphs (DAG)
pcorOrder

Compute Partial Correlations