Learn R Programming

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

pcalg (version 2.5-0)

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, the Generalized Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC) and some related functions are implemented. Functions for incorporating background knowledge are provided.

Copy Link

Version

Install

install.packages('pcalg')

Monthly Downloads

1,927

Version

2.5-0

License

GPL (>= 2)

Maintainer

Markus Kalisch

Last Published

July 12th, 2017

Functions in pcalg (2.5-0)

LINGAM

Linear non-Gaussian Acyclic Models (LiNGAM)
ParDAG-class

Class "ParDAG" of Parametric Causal Models
EssGraph-class

Class "EssGraph"
GaussL0penIntScore-class

Class "GaussL0penIntScore"
GaussL0penObsScore-class

Class "GaussL0penObsScore"
GaussParDAG-class

Class "GaussParDAG" of Gaussian Causal Models
Score-class

Virtual Class "Score"
addBgKnowledge

Add background knowledge to a CPDAG or PDAG
adjustment

Compute adjustment sets for covariate adjustment.
amatType

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

Find Set Satisfying the Generalized Backdoor Criterion (GBC)
beta.special

Compute set of intervention effects
dag2cpdag

Convert a DAG to a CPDAG
dsepTest

Test for d-separation in a DAG
fci

Estimate a PAG by the FCI Algorithm
checkTriple

Check Consistency of Conditional Independence for a Triple of Nodes
compareGraphs

Compare two graphs in terms of TPR, FPR and TDR
fciAlgo-class

Class "fciAlgo" of FCI Algorithm Results
beta.special.pcObj

Compute set of intervention effects in a fast way
binCItest

G square Test for (Conditional) Independence of Binary Variables
dag2pag

Convert a DAG with latent variables into a PAG
dag2essgraph

Convert a DAG to an Essential Graph
find.unsh.triple

Find all Unshielded Triples in an Undirected Graph
gAlgo-class

Class "gAlgo"
disCItest

G square Test for (Conditional) Independence of Discrete Variables
gac

Test If Set Satisfies Generalized Adjustment Criterion (GAC)
gds

Greedy DAG Search to Estimate Markov Equivalence Class of DAG
iplotPC

Plotting a pcAlgo object using the package igraph
isValidGraph

Check for a DAG, CPDAG or a maximally oriented PDAG
pag2mag

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

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

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

Test Conditional Independence of Gaussians via Fisher's Z
corGraph

Computing the correlation graph
dreach

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

Test for d-separation in a DAG
possAn

Find possible ancestors of given node(s).
randDAG

Random DAG Generation
randomDAG

Generate a Directed Acyclic Graph (DAG) randomly
gmB

Graphical Model 5-Dim Binary Example Data
gmD

Graphical Model Discrete 5-Dim Example Data
ida

Estimate Multiset of Possible Total Causal Effects
gmG

Graphical Model 8-Dimensional Gaussian Example Data
gmI

Graphical Model 7-dim IDA Data Examples
mat2targets

Conversion between an intervention matrix and a list of intervention targets
fciPlus

Estimate a PAG by the FCI+ Algorithm
getNextSet

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

Estimate Interventional Markov Equivalence Class of a DAG by GIES
jointIda

Estimate Multiset of Possible Total Joint Effects
idaFast

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

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

PC-Select: Estimate subgraph around a response variable
pdag2allDags

Enumerate All DAGs in a Markov Equivalence Class
pdag2dag

Extend a Partially Directed Acyclic Graph (PDAG) to a DAG
rmvnorm.ivent

Simulate from a Gaussian Causal Model
shd

Compute Structural Hamming Distance (SHD)
trueCov

Covariance matrix of a DAG.
udag2apag

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

Check if a 3-node-path is Legal
pc.cons.intern

Utility for conservative and majority rule in PC and FCI
pcAlgo-class

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

Estimate Final Skeleton in the FCI algorithm
plotAG

Plot partial ancestral graphs (PAG)
rfci

Estimate an RFCI-PAG using the RFCI Algorithm
rmvDAG

Generate Multivariate Data according to a DAG
ges

Estimate the Markov equivalence class of a DAG using GES
getGraph

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

Graphical Model 8-Dimensional Interventional Gaussian Example Data
gmL

Latent Variable 4-Dim Graphical Model Data Example
pcSelect.presel

Estimate Subgraph around a Response Variable using Preselection
pcalg-internal

Internal Pcalg Functions
qreach

Compute Possible-D-SEP(x,G) of a node x in a PDAG G
r.gauss.pardag

Generate a Gaussian Causal Model Randomly
unifDAG

Uniform Sampling of Directed Acyclic Graphs (DAG)
visibleEdge

Check visible edge.
mcor

Compute (Large) Correlation Matrix
pcalg2dagitty

Transform the adjacency matrix from pcalg into a dagitty object
pcorOrder

Compute Partial Correlations
possDe

Find possible descendants of given node(s).
showAmat

Show Adjacency Matrix of pcAlgo object
showEdgeList

Show Edge List of pcAlgo object
udag2pag

Last steps of FCI algorithm: Transform Final Skeleton into FCI-PAG
udag2pdag

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

[DEPRECATED] Find possible descendants on definite status paths.
simy

Estimate Interventional Markov Equivalence Class of a DAG
skeleton

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

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