Learn R Programming

⚠️There's a newer version (2.7-12) of this package.Take me there.

pcalg (version 2.4-2)

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.

Copy Link

Version

Install

install.packages('pcalg')

Monthly Downloads

3,666

Version

2.4-2

License

GPL (>= 2)

Maintainer

Markus Kalisch

Last Published

September 26th, 2016

Functions in pcalg (2.4-2)

binCItest

G square Test for (Conditional) Independence of Binary Variables
dag2cpdag

Convert a DAG to a CPDAG
beta.special.pcObj

Compute set of intervention effects in a fast way
compareGraphs

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

Computing the correlation graph
backdoor

Find Set Satisfying the Generalized Backdoor Criterion (GBC)
amatType

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

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

Compute set of intervention effects
checkTriple

Check Consistency of Conditional Independence for a Triple of Nodes
dsep

Test for d-separation in a DAG
dag2essgraph

Convert a DAG to an Essential Graph
EssGraph-class

Class "EssGraph"
dag2pag

Convert a DAG with latent variables into a PAG
dreach

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

Class "fciAlgo" of FCI Algorithm Results
dsepTest

Test for d-separation in a DAG
fciPlus

Estimate a PAG by the FCI+ Algorithm
fci

Estimate a PAG by the FCI Algorithm
disCItest

G square Test for (Conditional) Independence of Discrete Variables
GaussL0penIntScore-class

Class "GaussL0penIntScore"
gAlgo-class

Class "gAlgo"
GaussParDAG-class

Class "GaussParDAG" of Gaussian Causal Models
getGraph

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

Greedy DAG Search to Estimate Markov Equivalence Class of DAG
GaussL0penObsScore-class

Class "GaussL0penObsScore"
find.unsh.triple

Find all Unshielded Triples in an Undirected Graph
ges

Estimate the Markov equivalence class of a DAG using GES
gac

Test If Set Satisfies Generalized Adjustment Criterion (GAC)
getNextSet

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

Estimate Interventional Markov Equivalence Class of a DAG by GIES
gmG

Graphical Model 8-Dimensional Gaussian Example Data
gmInt

Graphical Model 8-Dimensional Interventional Gaussian Example Data
gmB

Graphical Model 5-Dim Binary Example Data
gmL

Latent Variable 4-Dim Graphical Model Data Example
gmI

Graphical Model 7-dim IDA Data Examples
iplotPC

Plotting a pcAlgo object using the package igraph
idaFast

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

Estimate Multiset of Possible Total Causal Effects
gmD

Graphical Model Discrete 5-Dim Example Data
jointIda

Estimate Multiset of Possible Total Joint Effects
mcor

Compute (Large) Correlation Matrix
pc

Estimate the Equivalence Class of a DAG using the PC Algorithm
ParDAG-class

Class "ParDAG" of Parametric Causal Models
legal.path

Check if a 3-node-path is Legal
pag2mag

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

Linear non-Gaussian Acyclic Models (LiNGAM)
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
pcalg-internal

Internal Pcalg Functions
plotAG

Plot partial ancestral graphs (PAG)
plotSG

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

PC-Algorithm [OLD]: Estimate Skeleton or Equivalence Class of a DAG
pdag2dag

Extend a Partially Directed Acyclic Graph (PDAG) to a DAG
pcSelect.presel

Estimate Subgraph around a Response Variable using Preselection
pdag2allDags

Enumerate All DAGs in a Markov Equivalence Class
pcorOrder

Compute Partial Correlations
pcSelect

PC-Select: Estimate subgraph around a response variable
pdsep

Estimate Final Skeleton in the FCI algorithm
pcAlgo-class

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

Find possible descendants on definite status paths.
qreach

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

Simulate from a Gaussian Causal Model
shd

Compute Structural Hamming Distance (SHD)
Score-class

Virtual Class "Score"
showAmat

Show Adjacency Matrix of pcAlgo object
r.gauss.pardag

Generate a Gaussian Causal Model Randomly
randDAG

Random DAG Generation
randomDAG

Generate a Directed Acyclic Graph (DAG) randomly
rfci

Estimate an RFCI-PAG using the RFCI Algorithm
udag2apag

Last step of RFCI algorithm: Transform partially oriented graph into RFCI-PAG
udag2pag

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

Show Edge List of pcAlgo object
skeleton

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

Estimate Interventional Markov Equivalence Class of a DAG
trueCov

Covariance matrix of a DAG.
visibleEdge

Check visible edge.
wgtMatrix

Weight Matrix of a Graph, e.g., a simulated DAG
udag2pdag

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

Uniform Sampling of Directed Acyclic Graphs (DAG)