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pcalg (version 2.2-0)

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 and the generalized backdoor criterion is implemented.

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Version

Install

install.packages('pcalg')

Monthly Downloads

1,818

Version

2.2-0

License

GPL (>= 2)

Maintainer

Markus Kalisch

Last Published

May 13th, 2015

Functions in pcalg (2.2-0)

fciPlus

Estimate a PAG, using the FCI+ algorithm
dsep

Test for d-separation in a DAG
qreach

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

Random DAG Generation
legal.path

Check if a 3-node-path is Legal
beta.special.pcObj

Compute set of intervention effects in a fast way
randomDAG

Generate a Directed Acyclic Graph (DAG) randomly
gmI

Graphical Model 7-dim IDA Data Examples
compareGraphs

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

G square Test for (conditional) Independence for Discrete Data
skeleton

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

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

Find Set Satisfying the Generalized Backdoor Criterion
possibleDe

Find possible descendants on definite status paths.
mcor

Compute (Large) Correlation Matrix
getNextSet

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

Show Adjacency Matrix of pcAlgo object
ida

Estimate Multiset of Possible Total Causal Effects
fci

Estimate a PAG, using the FCI-algorithm
plotAG

Plot partial ancestral graphs (PAG)
pc

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

Check Consistency of Conditional Independence for a Triple of Nodes
ParDAG-class

Class "ParDAG"
gmD

Graphical Model Discrete 5-Dim Example Data
binCItest

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

Graphical Model 8-Dimensional Interventional Gaussian Example Data
GaussL0penIntScore-class

Class "GaussL0penIntScore"
GaussParDAG-class

Class "GaussParDAG"
rfci

Estimate an RFCI-PAG using the RFCI Algorithm
pcSelect

PC-Select: Estimate subgraph around a response variable
rmvDAG

Generate Multivariate Data according to a DAG
wgtMatrix

Compute weight matrix of simulated DAG.
udag2pag

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

Computing the correlation graph
gmB

Graphical Model 5-Dim Binary Example Data
dag2cpdag

Convert a DAG to a CPDAG
iplotPC

Plotting a pcAlgo object using the package igraph
pdag2dag

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

Latent Variable 4-Dim Graphical Model Data Example
jointIda

Estimate Multiset of Possible Total Joint Effects
pag2mag

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

Class "pcAlgo"
dreach

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

Greedy DAG Search to Estimate Markov Equivalence Class of DAG
pcAlgo

PC-Algorithm [OLD]: Estimate Skeleton or Equivalence Class of a DAG
mat2targets

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

Plot the subgraph around a Specific Node in a Graph Object
Uniform DAG Sampling

Sample DAG uniformly
visibleEdge

Check visible edge.
getGraph

Get the "graph" Part or Aspect of R Object
udag2pdag

Last PC Algorithm Step: Extend Object with Skeleton to Completed PDAG
pcSelect.presel

Estimate Subgraph around a Response Variable using Preselection
pcalg-internal

Internal Pcalg Functions
find.unsh.triple

Find all Unshielded Triples in an Undirected Graph
rmvnorm.ivent

Simulate from a Gaussian Causal Model
LINGAM

Linear non-Gaussian Additive Models
gies

Estimate Interventional Markov Equivalence Class of a DAG by GIES
ges

Estimate the Markov equivalence class of a DAG using GES
dsepTest

Test for d-separation in a DAG
EssGraph-class

Class "EssGraph"
pc.cons.intern

Utility for conservative and majority rule in PC and FCI
pcorOrder

Compute Partial Correlations
Score-class

Virtual Class "Score"
beta.special

Compute set of intervention effects
condIndFisherZ

Test Conditional Independence of Gaussians via Fisher's Z
fciAlgo-class

Class "fciAlgo"
gAlgo-class

Class "gAlgo"
udag2apag

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

Covariance matrix of a DAG.
GaussL0penObsScore-class

Class "GaussL0penObsScore"
dag2essgraph

Convert a DAG to an Essential Graph
dag2pag

Convert a DAG with latent variables into a PAG
gmG

Graphical Model 8-Dimensional Gaussian Example Data
pdsep

Estimate Final Skeleton in the FCI algorithm
r.gauss.pardag

Generate a Gaussian Causal Model Randomly
simy

Estimate Interventional Markov Equivalence Class of a DAG
showEdgeList

Show Edge List of pcAlgo object
shd

Compute Structural Hamming Distance (SHD)