pcalg: Methods for Graphical Models and Causal Inference

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.

AuthorMarkus Kalisch [aut, cre], Alain Hauser [aut], Martin Maechler [aut], Diego Colombo [ctb], Doris Entner [ctb], Patrik Hoyer [ctb], Antti Hyttinen [ctb], Jonas Peters [ctb], Nicoletta Andri [ctb], Emilija Perkovic [ctb], Preetam Nandy [ctb], Philipp Ruetimann [ctb], Daniel Stekhoven [ctb], Manuel Schuerch [ctb]
Date of publication2016-09-28 17:10:41
MaintainerMarkus Kalisch <kalisch@stat.math.ethz.ch>
LicenseGPL (>= 2)
Version2.4-3
http://pcalg.r-forge.r-project.org/

View on CRAN

Man pages

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

beta.special.pcObj: Compute set of intervention effects in a fast way

binCItest: G square Test for (Conditional) Independence of Binary...

checkTriple: Check Consistency of Conditional Independence for a Triple of...

compareGraphs: Compare two graphs in terms of TPR, FPR and TDR

condIndFisherZ: Test Conditional Independence of Gaussians via Fisher's Z

corGraph: Computing the correlation graph

dag2cpdag: Convert a DAG to a CPDAG

dag2essgraph: Convert a DAG to an Essential Graph

dag2pag: Convert a DAG with latent variables into a PAG

disCItest: G square Test for (Conditional) Independence of Discrete...

dreach: Compute D-SEP(x,y,G)

dsep: Test for d-separation in a DAG

dsepTest: Test for d-separation in a DAG

EssGraph-class: Class '"EssGraph"'

fci: Estimate a PAG by the FCI Algorithm

fciAlgo-class: Class "fciAlgo" of FCI Algorithm Results

fciPlus: Estimate a PAG by the FCI+ Algorithm

find.unsh.triple: Find all Unshielded Triples in an Undirected Graph

gac: Test If Set Satisfies Generalized Adjustment Criterion (GAC)

gAlgo-class: Class '"gAlgo"'

GaussL0penIntScore-class: Class '"GaussL0penIntScore"'

GaussL0penObsScore-class: Class '"GaussL0penObsScore"'

GaussParDAG-class: Class '"GaussParDAG"' of Gaussian Causal Models

gds: Greedy DAG Search to Estimate Markov Equivalence Class of DAG

ges: Estimate the Markov equivalence class of a DAG using GES

getGraph: Get the "graph" Part or Aspect of R Object

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

gies: Estimate Interventional Markov Equivalence Class of a DAG by...

gmB: Graphical Model 5-Dim Binary Example Data

gmD: Graphical Model Discrete 5-Dim Example Data

gmG: Graphical Model 8-Dimensional Gaussian Example Data

gmI: Graphical Model 7-dim IDA Data Examples

gmInt: Graphical Model 8-Dimensional Interventional Gaussian Example...

gmL: Latent Variable 4-Dim Graphical Model Data Example

ida: Estimate Multiset of Possible Total Causal Effects

idaFast: Multiset of Possible Total Causal Effects for Several Target...

iplotPC: Plotting a pcAlgo object using the package igraph

jointIda: Estimate Multiset of Possible Total Joint Effects

legal.path: Check if a 3-node-path is Legal

LINGAM: Linear non-Gaussian Acyclic Models (LiNGAM)

mat2targets: Conversion between an intervention matrix and a list of...

mcor: Compute (Large) Correlation Matrix

pag2mag: Transform a PAG into a MAG in the Corresponding Markov...

ParDAG-class: Class '"ParDAG"' of Parametric Causal Models

pc: Estimate the Equivalence Class of a DAG using the PC...

pcalg-internal: Internal Pcalg Functions

pcAlgo: PC-Algorithm [OLD]: Estimate Skeleton or Equivalence Class of...

pcAlgo-class: Class "pcAlgo" of PC Algorithm Results, incl. Skeleton

pc.cons.intern: Utility for conservative and majority rule in PC and FCI

pcorOrder: Compute Partial Correlations

pcSelect: PC-Select: Estimate subgraph around a response variable

pcSelect.presel: Estimate Subgraph around a Response Variable using...

pdag2allDags: Enumerate All DAGs in a Markov Equivalence Class

pdag2dag: Extend a Partially Directed Acyclic Graph (PDAG) to a DAG

pdsep: Estimate Final Skeleton in the FCI algorithm

plotAG: Plot partial ancestral graphs (PAG)

plotSG: Plot the subgraph around a Specific Node in a Graph Object

possibleDe: Find possible descendants on definite status paths.

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

randDAG: Random DAG Generation

randomDAG: Generate a Directed Acyclic Graph (DAG) randomly

rfci: Estimate an RFCI-PAG using the RFCI Algorithm

r.gauss.pardag: Generate a Gaussian Causal Model Randomly

rmvDAG: Generate Multivariate Data according to a DAG

rmvnorm.ivent: Simulate from a Gaussian Causal Model

Score-class: Virtual Class "Score"

shd: Compute Structural Hamming Distance (SHD)

showAmat: Show Adjacency Matrix of pcAlgo object

showEdgeList: Show Edge List of pcAlgo object

simy: Estimate Interventional Markov Equivalence Class of a DAG

skeleton: Estimate (Initial) Skeleton of a DAG using the PC / PC-Stable...

trueCov: Covariance matrix of a DAG.

udag2apag: Last step of RFCI algorithm: Transform partially oriented...

udag2pag: Last steps of FCI algorithm: Transform Final Skeleton into...

udag2pdag: Last PC Algorithm Step: Extend Object with Skeleton to...

unifDAG: Uniform Sampling of Directed Acyclic Graphs (DAG)

visibleEdge: Check visible edge.

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

Files in this package

pcalg
pcalg/TODO
pcalg/inst
pcalg/inst/CITATION
pcalg/inst/NEWS.Rd
pcalg/inst/xtraR
pcalg/inst/xtraR/graph2ftmatrix.R
pcalg/inst/doc
pcalg/inst/doc/pcalgDoc.R
pcalg/inst/doc/pcalgDoc.Rnw
pcalg/inst/doc/pcalgDoc.pdf
pcalg/inst/doc/mkVignettes.R
pcalg/inst/external
pcalg/inst/external/gac-pags.rds
pcalg/inst/external/N_6_1000.rds
pcalg/inst/external/test_conservative_pc_data2.rda
pcalg/inst/external/test_conservative_pc_data1.rda
pcalg/inst/include
pcalg/inst/include/pcalg
pcalg/inst/include/pcalg/constraint.hpp
pcalg/inst/include/pcalg/armaLapack.hpp
pcalg/inst/include/pcalg/score.hpp
pcalg/inst/include/pcalg/greedy.hpp
pcalg/inst/include/pcalg/gies_debug.hpp
pcalg/tests
pcalg/tests/test_gSquareBin.R
pcalg/tests/test_backdoor.Rout.save
pcalg/tests/test_displayAmat.R
pcalg/tests/test_pdag2dag.R
pcalg/tests/test_idaFast.R
pcalg/tests/test_arges.R
pcalg/tests/test_randomDAG.R
pcalg/tests/test_fci.R
pcalg/tests/test_amat2dag.R
pcalg/tests/test_LINGAM.R
pcalg/tests/test_rmvDAG.R
pcalg/tests/test_getNextSet.R
pcalg/tests/test_pc.R
pcalg/tests/test_ida.R
pcalg/tests/test_mat2targets.R
pcalg/tests/test_dsep.R
pcalg/tests/test_randDAG.R
pcalg/tests/test_jointIda.R
pcalg/tests/test_udag2pdag.R
pcalg/tests/test_pdag2allDags.R
pcalg/tests/test_shd.R
pcalg/tests/test_fciPlus.R
pcalg/tests/test_backdoor.R
pcalg/tests/test_pcorOrder.R
pcalg/tests/discr100k.rda
pcalg/tests/test_dag2cpdag.R
pcalg/tests/test_gac.R
pcalg/tests/test_compareGraphs.R
pcalg/tests/test_skeleton.R
pcalg/tests/test_unifDAG.R
pcalg/tests/test_pcSelect.R
pcalg/tests/test_causalEffect.R
pcalg/tests/test_bicscore.rda
pcalg/tests/test_randDAG.Rout.save
pcalg/tests/test_rfci.R
pcalg/tests/test_bicscore.R
pcalg/tests/test_dag2essgraph.R
pcalg/tests/test_wgtMatrix.R
pcalg/tests/test_gies.R
pcalg/tests/test_gSquareDis.R
pcalg/src
pcalg/src/Makevars
pcalg/src/gies.cpp
pcalg/src/score.cpp
pcalg/src/greedy.cpp
pcalg/src/constraint.cpp
pcalg/src/Makevars.win
pcalg/NAMESPACE
pcalg/data
pcalg/data/gmInt.rda
pcalg/data/gmL.rda
pcalg/data/gmG.rda
pcalg/data/gmI.rda
pcalg/data/gmD.rda
pcalg/data/gmB.rda
pcalg/data/datalist
pcalg/R
pcalg/R/AllClasses.R pcalg/R/jointIda.R pcalg/R/gies.R
pcalg/R/sysdata.rda
pcalg/R/gacFuns.R pcalg/R/lingamFuns.R pcalg/R/deprecated.R pcalg/R/pcalg.R pcalg/R/Aaux.R pcalg/R/zzz.R pcalg/R/genRandDAG.R
pcalg/vignettes
pcalg/vignettes/Mybib.bib
pcalg/vignettes/Figure2FAT.pdf
pcalg/vignettes/Figure1FAT.pdf
pcalg/vignettes/pcalgDoc.Rnw
pcalg/vignettes/jsslogo.jpg
pcalg/MD5
pcalg/build
pcalg/build/vignette.rds
pcalg/DESCRIPTION
pcalg/ChangeLog
pcalg/man
pcalg/man/dreach.Rd pcalg/man/EssGraph-class.Rd pcalg/man/getNextSet.Rd pcalg/man/dag2essgraph.Rd pcalg/man/rmvDAG.Rd pcalg/man/pcSelect.Rd pcalg/man/legal.path.Rd pcalg/man/getGraph.Rd pcalg/man/unifDAG.Rd pcalg/man/pcSelect.presel.Rd pcalg/man/trueCov.Rd pcalg/man/visibleEdge.Rd pcalg/man/checkTriple.Rd pcalg/man/udag2apag.Rd pcalg/man/pcorOrder.Rd pcalg/man/possibleDe.Rd pcalg/man/wgtMatrix.Rd pcalg/man/pcAlgo-class.Rd pcalg/man/find.unsh.triple.Rd pcalg/man/mat2targets.Rd pcalg/man/compareGraphs.Rd pcalg/man/GaussL0penIntScore-class.Rd pcalg/man/gAlgo-class.Rd pcalg/man/GaussL0penObsScore-class.Rd pcalg/man/gmInt.Rd pcalg/man/pc.cons.intern.Rd pcalg/man/backdoor.Rd pcalg/man/idaFast.Rd pcalg/man/udag2pag.Rd pcalg/man/gmG.Rd pcalg/man/plotAG.Rd pcalg/man/r.gauss.pardag.Rd pcalg/man/dag2cpdag.Rd pcalg/man/gmD.Rd pcalg/man/gmL.Rd pcalg/man/ParDAG-class.Rd pcalg/man/showEdgeList.Rd pcalg/man/gac.Rd pcalg/man/condIndFisherZ.Rd pcalg/man/amatType.Rd pcalg/man/corGraph.Rd pcalg/man/GaussParDAG-class.Rd pcalg/man/fciAlgo-class.Rd pcalg/man/shd.Rd pcalg/man/pdsep.Rd pcalg/man/qreach.Rd pcalg/man/ges.Rd pcalg/man/Score-class.Rd pcalg/man/dsep.Rd pcalg/man/gmB.Rd pcalg/man/randDAG.Rd pcalg/man/mcor.Rd pcalg/man/skeleton.Rd pcalg/man/rfci.Rd pcalg/man/LINGAM.Rd pcalg/man/pc.Rd pcalg/man/udag2pdag.Rd pcalg/man/pcAlgo.Rd pcalg/man/randomDAG.Rd pcalg/man/ida.Rd pcalg/man/jointIda.Rd pcalg/man/gds.Rd pcalg/man/beta.special.pcObj.Rd pcalg/man/beta.special.Rd pcalg/man/fciPlus.Rd pcalg/man/fci.Rd pcalg/man/pdag2dag.Rd pcalg/man/dag2pag.Rd pcalg/man/pag2mag.Rd pcalg/man/plotSG.Rd pcalg/man/gmI.Rd pcalg/man/dsepTest.Rd pcalg/man/binCItest.Rd pcalg/man/showAmat.Rd pcalg/man/disCItest.Rd pcalg/man/rmvnorm.ivent.Rd pcalg/man/pdag2allDags.Rd pcalg/man/simy.Rd pcalg/man/gies.Rd pcalg/man/pcalg-internal.Rd pcalg/man/iplotPC.Rd
pcalg/cleanup

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