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pcalg (version 2.0-1)

Methods for graphical models and causal inference

Description

This package contains several 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 observational and interventional data without hidden variables). For causal inference the IDA algorithm and the generalized backdoor criterion is implemented.

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Version

Install

install.packages('pcalg')

Monthly Downloads

2,763

Version

2.0-1

License

GPL (>= 2)

Maintainer

Markus Kalisch

Last Published

March 6th, 2014

Functions in pcalg (2.0-1)

possibleDe

Find possible descendants on definite status paths.
fci

Estimate a PAG, using the FCI-algorithm
pag2mag

Transform a PAG into a MAG in the Corresponding Markov Equivalence Class
pcSelect.presel

Estimate Subgraph around a Response Variable using Preselection
plotAG

Plot partial ancestral graphs (PAG)
dsepTest

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

Compute set of intervention effects in a fast way
gmL

Latent Variable 4-Dim Graphical Model Data Example
GaussL0penObsScore-class

Class "GaussL0penObsScore"
gmD

Graphical Model Discrete 5-Dim Example Data
wgtMatrix

Compute weight matrix of simulated DAG.
qreach

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

Class "GaussParDAG"
dag2cpdag

Convert a DAG to a CPDAG
pc

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

Computing the correlation graph
beta.special

Compute set of intervention effects
gmG

Graphical Model 8-Dimensional Gaussian Example Data
skeleton

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

Class "pcAlgo"
jointIda

Estimate Multiset of Possible Total Joint Effects
condIndFisherZ

Test Conditional Independence of Gaussians via Fisher's Z
gies

Estimate Interventional Markov Equivalence Class of a DAG by GIES
gAlgo-class

Class "gAlgo"
dsep

Test for d-separation in a DAG
dag2essgraph

Convert a DAG to an Essential Graph
pcSelect

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

Class "ParDAG"
getNextSet

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

G square Test for (conditional) Independence for Discrete Data
r.gauss.pardag

Generate a Gaussian Causal Model Randomly
legal.path

Check if a 3-node-path is Legal
ida

Estimate Multiset of Possible Total Causal Effects
gds

Greedy DAG Search to Estimate Markov Equivalence Class of DAG
showAmat

Show Adjacency Matrix of pcAlgo object
backdoor

Find Set Satisfying the Generalized Backdoor Criterion
randomDAG

Generate a Directed Acyclic Graph (DAG) randomly
rmvnorm.ivent

Simulate from a Gaussian Causal Model
pdag2dag

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

Estimate the Markov equivalence class of a DAG using GES
gmI

Graphical Model 7-dim IDA Data Examples
gmB

Graphical Model 5-Dim Binary Example Data
udag2pag

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

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

Compare two graphs in terms of TPR, FPR and TDR
mat2targets

Construct a list of intervention targets and a target index vector
binCItest

G square Test for (Conditional) Independence of Binary Variables
udag2pdag

Last PC Algorithm Step: Extend Object with Skeleton to Completed PDAG
GaussL0penIntScore-class

Class "GaussL0penIntScore"
pcAlgo

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

Compute Structural Hamming Distance (SHD)
fciAlgo-class

Class "fciAlgo"
find.unsh.triple

Find all Unshielded Triples in an Undirected Graph
showEdgeList

Show Edge List of pcAlgo object
dreach

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

Graphical Model 8-Dimensional Interventional Gaussian Example Data
pdsep

Estimate Final Skeleton in the FCI algorithm
idaFast

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

Plot the subgraph around a Specific Node in a Graph Object
pcalg-internal

Internal Pcalg Functions
pc.cons.intern

Utility for conservative and majority rule in PC and FCI
simy

Estimate Interventional Markov Equivalence Class of a DAG
fciPlus

Estimate a PAG, using the FCI+ algorithm
checkTriple

Check Consistency of Conditional Independence for a Triple of Nodes
iplotPC

Plotting a pcAlgo object using the package igraph
rfci

Estimate an RFCI-PAG using the RFCI Algorithm
udag2apag

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

Generate Multivariate Data according to a DAG
trueCov

Covariance matrix of a DAG.
Score-class

Virtual Class "Score"
EssGraph-class

Class "EssGraph"
mcor

Compute (Large) Correlation Matrix
pcorOrder

Compute Partial Correlations
dag2pag

Convert a DAG with latent variables into a PAG
visibleEdge

Check visible edge.