pcalg: Methods for Graphical Models and Causal Inference

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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.

Author
Markus 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 publication
2016-09-27 09:15:29
Maintainer
Markus Kalisch <kalisch@stat.math.ethz.ch>
License
GPL (>= 2)
Version
2.4-3
URLs

View on R-Forge

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