Package: causalDisco 0.9.4

causalDisco: Tools for Causal Discovery on Observational Data

Various tools for inferring causal models from observational data. The package includes an implementation of the temporal Peter-Clark (TPC) algorithm. Petersen, Osler and Ekstrøm (2021) <doi:10.1093/aje/kwab087>. It also includes general tools for evaluating differences in adjacency matrices, which can be used for evaluating performance of causal discovery procedures.

Authors:Anne Helby Petersen [aut, cre], Tobias Ellegaard [email protected] Larsen [ctb], Claus Thorn [email protected] Ekstrøm [ctb]

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causalDisco.pdf |causalDisco.html✨
causalDisco/json (API)
NEWS

# Install 'causalDisco' in R:
install.packages('causalDisco', repos = c('https://annennenne.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/annennenne/causaldisco/issues

Datasets:

On CRAN:

Conda:

4.76 score 19 stars 10 scripts 233 downloads 41 exports 68 dependencies

Last updated 28 days agofrom:bd11778a76. Checks:5 OK, 2 ERROR, 2 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 03 2025
R-4.5-winNOTEMar 03 2025
R-4.5-macNOTEMar 03 2025
R-4.5-linuxERRORMar 03 2025
R-4.4-winOKMar 03 2025
R-4.4-macOKMar 03 2025
R-4.4-linuxERRORMar 03 2025
R-4.3-winOKMar 03 2025
R-4.3-macOKMar 03 2025

Exports:adj_confusionamatas.graphNELaverage_degreecompareconfusioncorTestdir_confusiondir_confusion_originaledgesessgraph2amatevaluateF1fciFDRFORG1gausCorScoregraph2amatis_cpdagis_pdagmaketikzmaxnedgesnDAGsnedgesNPVpcplotTempoMechprecisionprobmat2amatrecallregTestshdsimDAGsimGausFromDAGspecificitytamattfcitgestpctplot

Dependencies:abindbase64encbdsmatrixBHBiocGenericsBiocManagerbslibcachemclicliprclueclustercolorspacecorpcorcpp11curlDEoptimRdigestevaluatefarverfastICAfastmapfontawesomefsgenericsggmgluegraphgtoolshighrhtmltoolsigraphjquerylibjsonliteknitrlabelinglatticelifecyclelmtestmagickmagrittrMASSMatrixmemoisemimemunsellpcalgpkgconfigR6rappdirsRBGLRColorBrewerRcppRcppArmadilloRgraphvizrlangrmarkdownrobustbasesassscalessfsmisctinytexvcdvctrsviridisLitexfunyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Compute confusion matrix for comparing two adjacency matricesadj_confusion
Extract adjacency matrix from tpdag, cpdag, tpag or pag objectamat
Convert adjacency matrix to graphNEL objectas.graphNEL
Compute average degree for adjacency matrixaverage_degree
Compare two tpdag or tskeleton objectscompare
Compute confusion matrix for comparing two adjacency matricesconfusion
Test for vanishing partial correlationscorTest
Compute confusion matrix for comparing two adjacency matricesdir_confusion
Compute confusion matrix for comparing two adjacency matricesdir_confusion_original
List of edges in adjacency matrixedges
Convert essential graph to adjacency matrixessgraph2amat
Evaluate adjacency matrix estimationevaluate
Evaluate adjacency matrix estimationevaluate.array
Evaluate adjacency matrix estimationevaluate.matrix
Evaluate adjacency matrix estimationevaluate.tamat
F1 scoreF1
Perform causal discovery using the FCI algorithmfci
False Discovery RateFDR
False Omission RateFOR
G1 scoreG1
Gaussian L0 score computed on correlation matrixgausCorScore
Convert graphNEL object to adjacency matrixgraph2amat
Check for CPDAGis_cpdag
Check for PDAGis_pdag
Generate Latex tikz code for plotting a temporal DAG, PDAG or PAG.maketikz
Compute maximal number of edges for graphmaxnedges
Number of different DAGsnDAGs
Number of edges in adjacency matrixnedges
Negative predictive valueNPV
Perform causal discovery using the PC algorithmpc
Plot partial ancestral graph (PAG)plot.pag
Plot adjacency matrix with order informationplot.tamat
Plot temporal partial ancestral graph (TPAG)plot.tpag
Plot temporal partially directed acyclic graph (TPDAG)plot.tpdag
Plot temporal skeletonplot.tskeleton
Plot temporal data generating mechanismplotTempoMech
Precisionprecision
Convert a matrix of probabilities into an adjacency matrixprobmat2amat
Recallrecall
Regression-based information loss testregTest
Structural hamming distance between adjacency matricesshd
Simulate a random DAGsimDAG
Simulate Gaussian data according to DAGsimGausFromDAG
Specificityspecificity
Make a temporal adjacency matrixtamat
Temporal Bayesian Dirichlet equivalent uniform (Score criterion)TemporalBDeu-class
Temporal Bayesian Information Criterion (Score criterion)TemporalBIC-class
Perform causal discovery using the temporal FCI algorithm (TFCI)tfci
Estimate the restricted Markov equivalence class using Temporal Greedy Equivalence Searchtges
Perform causal discovery using the temporal PC algorithm (TPC)tpc
Simulated data exampletpcExample
Plot temporal graph via Latextplot