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pcalg (version 2.0-10)

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

2,763

Version

2.0-10

License

GPL (>= 2)

Maintainer

Markus Kalisch

Last Published

March 19th, 2015

Functions in pcalg (2.0-10)

GaussL0penObsScore-class

Class "GaussL0penObsScore"
dag2cpdag

Convert a DAG to a CPDAG
find.unsh.triple

Find all Unshielded Triples in an Undirected Graph
GaussParDAG-class

Class "GaussParDAG"
condIndFisherZ

Test Conditional Independence of Gaussians via Fisher's Z
GaussL0penIntScore-class

Class "GaussL0penIntScore"
compareGraphs

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

Check Consistency of Conditional Independence for a Triple of Nodes
getGraph

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

Virtual Class "Score"
beta.special

Compute set of intervention effects
pcSelect.presel

Estimate Subgraph around a Response Variable using Preselection
corGraph

Computing the correlation graph
pc.cons.intern

Utility for conservative and majority rule in PC and FCI
getNextSet

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

Graphical Model 8-Dimensional Gaussian Example Data
dreach

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

Graphical Model 8-Dimensional Interventional Gaussian Example Data
jointIda

Estimate Multiset of Possible Total Joint Effects
iplotPC

Plotting a pcAlgo object using the package igraph
backdoor

Find Set Satisfying the Generalized Backdoor Criterion
ges

Estimate the Markov equivalence class of a DAG using GES
plotSG

Plot the subgraph around a Specific Node in a Graph Object
EssGraph-class

Class "EssGraph"
ParDAG-class

Class "ParDAG"
pag2mag

Transform a PAG into a MAG in the Corresponding Markov Equivalence Class
dag2essgraph

Convert a DAG to an Essential Graph
pcalg-internal

Internal Pcalg Functions
mat2targets

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

Show Adjacency Matrix of pcAlgo object
dsep

Test for d-separation in a DAG
wgtMatrix

Compute weight matrix of simulated DAG.
pcSelect

PC-Select: Estimate subgraph around a response variable
r.gauss.pardag

Generate a Gaussian Causal Model Randomly
pc

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

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

Estimate Final Skeleton in the FCI algorithm
fciAlgo-class

Class "fciAlgo"
gies

Estimate Interventional Markov Equivalence Class of a DAG by GIES
idaFast

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

Latent Variable 4-Dim Graphical Model Data Example
gmB

Graphical Model 5-Dim Binary Example Data
disCItest

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

Greedy DAG Search to Estimate Markov Equivalence Class of DAG
gmD

Graphical Model Discrete 5-Dim Example Data
gmI

Graphical Model 7-dim IDA Data Examples
simy

Estimate Interventional Markov Equivalence Class of a DAG
rmvDAG

Generate Multivariate Data according to a DAG
qreach

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

Simulate from a Gaussian Causal Model
pdag2dag

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

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

Show Edge List of pcAlgo object
possibleDe

Find possible descendants on definite status paths.
udag2pdag

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

Estimate a PAG, using the FCI+ algorithm
randomDAG

Generate a Directed Acyclic Graph (DAG) randomly
visibleEdge

Check visible edge.
fci

Estimate a PAG, using the FCI-algorithm
gAlgo-class

Class "gAlgo"
dsepTest

Test for d-separation in a DAG
legal.path

Check if a 3-node-path is Legal
pcAlgo

PC-Algorithm [OLD]: Estimate Skeleton or Equivalence Class of a DAG
udag2pag

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

Estimate an RFCI-PAG using the RFCI Algorithm
ida

Estimate Multiset of Possible Total Causal Effects
pcAlgo-class

Class "pcAlgo"
dag2pag

Convert a DAG with latent variables into a PAG
plotAG

Plot partial ancestral graphs (PAG)
trueCov

Covariance matrix of a DAG.
mcor

Compute (Large) Correlation Matrix
pcorOrder

Compute Partial Correlations
shd

Compute Structural Hamming Distance (SHD)
beta.special.pcObj

Compute set of intervention effects in a fast way
udag2apag

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