| Add background knowledge to a CPDAG or PDAG | addBgKnowledge |
| Compute adjustment sets for covariate adjustment. | adjustment |
| Estimate an APDAG within the Markov equivalence class of a DAG using AGES | ages |
| Types and Display of Adjacency Matrices in Package 'pcalg' | amat.cpdag amat.pag amatType coerce,fciAlgo,amat-method coerce,fciAlgo,matrix-method coerce,LINGAM,amat-method coerce,pcAlgo,amat-method coerce,pcAlgo,matrix-method show.fci.amat show.pc.amat |
| Find Set Satisfying the Generalized Backdoor Criterion (GBC) | backdoor |
| Compute set of intervention effects | beta.special |
| Compute set of intervention effects in a fast way | beta.special.pcObj |
| G square Test for (Conditional) Independence of Binary Variables | binCItest gSquareBin |
| Check Consistency of Conditional Independence for a Triple of Nodes | checkTriple |
| Compare two graphs in terms of TPR, FPR and TDR | compareGraphs |
| Test Conditional Independence of Gaussians via Fisher's Z | condIndFisherZ gaussCItest zStat |
| Computing the correlation graph | corGraph |
| Convert a DAG to a CPDAG | dag2cpdag |
| Convert a DAG to an Essential Graph | dag2essgraph |
| Convert a DAG with latent variables into a PAG | dag2pag |
| G square Test for (Conditional) Independence of Discrete Variables | disCItest gSquareDis |
| Compute D-SEP(x,y,G) | dreach |
| Test for d-separation in a DAG | dsep |
| Test for d-separation in a MAG | dsepAM |
| Test for d-separation in a MAG | dsepAMTest |
| Test for d-separation in a DAG | dsepTest |
| Class '"EssGraph"' | EssGraph-class plot,EssGraph,ANY-method |
| Estimate a PAG with the FCI Algorithm | fci |
| Class "fciAlgo" of FCI Algorithm Results | fciAlgo-class plot,fciAlgo,ANY-method print.fciAlgo show,fciAlgo-method summary,fciAlgo-method |
| Estimate a PAG with the FCI+ Algorithm | fciPlus |
| Find all Unshielded Triples in an Undirected Graph | find.unsh.triple |
| Test If Set Satisfies Generalized Adjustment Criterion (GAC) | gac |
| Class '"gAlgo"' | gAlgo-class |
| Class '"GaussL0penIntScore"' | GaussL0penIntScore-class global.mle,GaussL0penIntScore-method global.score,GaussL0penIntScore-method local.mle,GaussL0penIntScore-method local.score,GaussL0penIntScore-method |
| Class '"GaussL0penObsScore"' | GaussL0penObsScore-class global.mle,GaussL0penObsScore-method global.score,GaussL0penObsScore-method local.mle,GaussL0penObsScore-method local.score,GaussL0penObsScore-method |
| Class '"GaussParDAG"' of Gaussian Causal Models | GaussParDAG-class |
| Greedy DAG Search to Estimate Markov Equivalence Class of DAG | gds |
| Estimate the Markov equivalence class of a DAG using GES | ges |
| Get the "graph" Part or Aspect of R Object | getGraph getGraph,ANY-method getGraph,fciAlgo-method getGraph,matrix-method getGraph,pcAlgo-method getGraph-methods |
| Iteration through a list of all combinations of choose(n,k) | getNextSet |
| Estimate Interventional Markov Equivalence Class of a DAG by GIES | gies |
| Graphical Model 5-Dim Binary Example Data | gmB |
| Graphical Model Discrete 5-Dim Example Data | gmD |
| Graphical Model 8-Dimensional Gaussian Example Data | gmG gmG8 |
| Graphical Model 7-dim IDA Data Examples | gmI gmI7 |
| Graphical Model 8-Dimensional Interventional Gaussian Example Data | gmInt |
| Latent Variable 4-Dim Graphical Model Data Example | gmL |
| Estimate Multiset of Possible Joint Total Causal Effects | causalEffect ida |
| Multiset of Possible Total Causal Effects for Several Target Var.s | idaFast |
| Plotting a pcAlgo object using the package igraph | iplotPC |
| Check for a DAG, CPDAG or a maximally oriented PDAG | isValidGraph |
| Estimate Multiset of Possible Total Joint Effects | jointIda |
| Check if a 3-node-path is Legal | legal.path |
| Linear non-Gaussian Acyclic Models (LiNGAM) | LINGAM lingam |
| Conversion between an intervention matrix and a list of intervention targets | mat2targets targets2mat |
| Compute (Large) Correlation Matrix | mcor |
| Get an optimal intervention target | opt.target |
| Compute the optimal adjustment set | optAdjSet |
| Reads off identifiable ancestors and non-ancestors from a directed PAG | pag2anc |
| Reads off identifiable unconfounded node pairs from a directed PAG | pag2conf |
| Reads off identifiable parents and non-parents from a directed PAG | pag2edge |
| Transform a PAG into a MAG in the Corresponding Markov Equivalence Class | pag2magAM |
| Class '"ParDAG"' of Parametric Causal Models | ParDAG-class plot,ParDAG,ANY-method |
| Estimate the Equivalence Class of a DAG using the PC Algorithm | pc |
| Utility for conservative and majority rule in PC and FCI | pc.cons.intern triple2numb |
| Transform the adjacency matrix from 'pcalg' into a 'dagitty' object | pcalg2dagitty |
| PC-Algorithm [OLD]: Estimate Skeleton or Equivalence Class of a DAG | pcAlgo pcAlgo.Perfect |
| Class "pcAlgo" of PC Algorithm Results, incl. Skeleton | pcAlgo-class plot,pcAlgo,ANY-method print.pcAlgo show,pcAlgo-method summary,pcAlgo-method |
| Compute Partial Correlations | pcorOrder |
| PC-Select: Estimate subgraph around a response variable | pcSelect |
| Estimate Subgraph around a Response Variable using Preselection | pcSelect.presel |
| Enumerate All DAGs in a Markov Equivalence Class | pdag2allDags |
| Extend a Partially Directed Acyclic Graph (PDAG) to a DAG | pdag2dag |
| Estimate Final Skeleton in the FCI algorithm | pdsep |
| Plot partial ancestral graphs (PAG) | plotAG |
| Plot the subgraph around a Specific Node in a Graph Object | plotSG |
| Find possible ancestors of given node(s). | possAn |
| Find possible descendants of given node(s). | possDe |
| [DEPRECATED] Find possible descendants on definite status paths. | possibleDe |
| Compute Possible-D-SEP(x,G) of a node x in a PDAG G | qreach |
| Generate a Gaussian Causal Model Randomly | r.gauss.pardag |
| Random DAG Generation | randDAG |
| Generate a Directed Acyclic Graph (DAG) randomly | randomDAG |
| Estimate an RFCI-PAG using the RFCI Algorithm | rfci |
| Generate Multivariate Data according to a DAG | rmvDAG |
| Simulate from a Gaussian Causal Model | rmvnorm.ivent |
| Virtual Class "Score" | Score-class |
| Search for certain nodes in a DAG/CPDAG/MAG/PAG | searchAM |
| Compute Structural Hamming Distance (SHD) | shd |
| Show Adjacency Matrix of pcAlgo object | showAmat |
| Show Edge List of pcAlgo object | showEdgeList |
| Estimate Interventional Markov Equivalence Class of a DAG | simy |
| Estimate (Initial) Skeleton of a DAG using the PC / PC-Stable Algorithm | skeleton |
| Covariance matrix of a DAG. | trueCov |
| Last step of RFCI algorithm: Transform partially oriented graph into RFCI-PAG | udag2apag |
| Last steps of FCI algorithm: Transform Final Skeleton into FCI-PAG | udag2pag |
| Last PC Algorithm Step: Extend Object with Skeleton to Completed PDAG | udag2pdag udag2pdagRelaxed udag2pdagSpecial |
| Check visible edge. | visibleEdge |
| Weight Matrix of a Graph, e.g., a simulated DAG | wgtMatrix |
