Package: causalDisco 1.1.0.9000

Bjarke Hautop Kristensen

causalDisco: Tools for Causal Discovery on Observational Data

Tools for causal structure learning from observational data, with emphasis on temporally ordered variables. The package implements the Temporal Peter–Clark (TPC) algorithm (Petersen, Osler & EkstrÃļm, 2021; <doi:10.1093/aje/kwab087>), the Temporal Greedy Equivalence Search (TGES) algorithm (Larsen, EkstrÃļm & Petersen, 2025; <doi:10.48550/arXiv.2502.06232>) and Temporal Fast Causal Inference (TFCI). It provides a unified framework for specifying background knowledge, which can be incorporated into the implemented algorithms from the R packages 'bnlearn' (Scutari, 2010; <doi:10.18637/jss.v035.i03>) and 'pcalg' (Kalish et al., 2012; <doi:10.18637/jss.v047.i11>), as well as the Java library 'Tetrad' (Scheines et al., 1998; <doi:10.1207/s15327906mbr3301_3>). The package further includes utilities for visualization, comparison, and evaluation of graph structures, facilitating performance evaluation and methodological studies.

Authors:Bjarke Hautop Kristensen [aut, cre], Frederik Fabricius-Bjerre [aut], Anne Helby Petersen [aut], Claus Thorn EkstrÃļm [aut], Tobias Ellegaard Larsen [ctb]

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

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

Bug tracker:https://github.com/disco-coders/causaldisco/issues

Pkgdown/docs site:https://disco-coders.github.io

Datasets:

On CRAN:

Conda:

causal-discoverycausal-inference

6.32 score 22 stars 42 scripts 428 downloads 75 exports 95 dependencies

Last updated from:67c5849875. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK221
source / vignettesOK294
linux-release-x86_64OK253
macos-release-arm64OK173
macos-oldrel-arm64OK228
windows-develOK206
windows-releaseOK220
windows-oldrelOK202
wasm-releaseOK225

Exports:add_exoadd_exogenousadd_tieradd_to_tieradd_varsaidas_bnlearn_knowledgeas_pcalg_constraintsas_tetrad_knowledgeBnlearnSearchbossboss_fciCausalDiscoSearchconfusionconvert_tiers_to_forbiddencor_testdeparse_knowledgediscodistribute_engine_argsevaluatef1_scorefalse_omission_ratefast_iambfcifdrforbid_edgeg1_scoregenerate_dag_datagesget_tiersgfcigraspgrasp_fcigshdiambiamb_fdrinstall_tetradinter_iambknowledgeknowledge_to_caugilist_registered_tetrad_algorithmsmake_methodmake_runnermake_tikznew_disco_methodnpvpcPcalgSearchprecisionrecallreg_testregister_tetrad_algorithmremove_edgeremove_tiersremove_varsreorder_tiersreposition_tierrequire_edgereset_tetrad_alg_registryseq_tiersset_knowledgeshdsim_dagsp_fcispecificityTetradSearchtfcitfci_runtgestges_runtpctpc_rununfreezeverify_tetrad

Dependencies:abindbackportsbdsmatrixBHBiocGenericsBiocManagerbitbit64bnlearnbootbroomcaugicheckmateclicliprclueclustercodetoolscolorspacecorpcorcpp11crayondata.tableDEoptimRdigestdplyrfastICAforcatsforeachgenericsggmglmnetgluegraphgtoolshavenhmsigraphiteratorsjomolatticelifecyclelme4lmtestmagrittrMASSMatrixmicdmiceminqamitmlnlmenloptrnnetnumDerivordinalpanpcalgpillarpkgconfigprettyunitsprogresspurrrR6RBGLrbibutilsRcppRcppArmadilloRcppEigenRcppParallelRdpackreadrreformulasRfastrlangrobustbaserpartS7sfsmiscshapestringistringrsurvivaltibbletidyrtidyselecttzdbucminfutf8vcdvctrsvroomwithrziggzoo

Readme and manuals

Help Manual

Help pageTopics
causalDisco: Causal Discovery in RcausalDisco-package causalDisco
Merge Knowledge Objects+.Knowledge
Add Exogenous Variables to Knowledgeadd_exo add_exogenous
Add a Tier to Knowledgeadd_tier
Add Variables to a Tier in Knowledgeadd_to_tier
Add Variables to Knowledgeadd_vars
Convert Knowledge to bnlearn Knowledgeas_bnlearn_knowledge
Convert Knowledge to pcalg Knowledgeas_pcalg_constraints
Convert Knowledge to Tetrad Knowledgeas_tetrad_knowledge
R6 Interface to bnlearn Search AlgorithmsBnlearnSearch
BOSS Algorithm for Causal Discoveryboss
BOSS-FCI Algorithm for Causal Discoveryboss_fci
Simulated Categorical Datacat_data
Simulated Categorical Data with MCARcat_data_mcar
Simulated Ordered Categorical Datacat_ord_data
R6 Interface to causalDisco Search AlgorithmsCausalDiscoSearch
Confusion Matrixconfusion
Convert Tiered Knowledge to Forbidden Knowledgeconvert_tiers_to_forbidden
Test for Vanishing Partial Correlationscor_test
Deparse a Knowledge Object into Knowledge DSL Codedeparse_knowledge
Perform Causal Discoverydisco
Distribute and Validate Engine Argumentsdistribute_engine_args
Evaluate Causal Graph Estimatesevaluate
F1 scoref1_score
False Omission Ratefalse_omission_rate
FCI Algorithm for Causal Discoveryfci
False Discovery Ratefdr
Add Forbidden Edges to Knowledgeforbid_edge
G1 scoreg1_score
Generate Synthetic Data from a Linear Gaussian DAGgenerate_dag_data
GES Algorithm for Causal Discoveryges
Get Tiers from Knowledgeget_tiers
GFCI Algorithm for Causal Discoverygfci
GRaSP Algorithm for Causal Discoverygrasp
GRaSP-FCI Algorithm for Causal Discoverygrasp_fci
GS Algorithm for Causal Discoverygs
IAMB Family of Causal Discovery Algorithmsfast_iamb iamb iamb-family iamb_fdr inter_iamb
Install Tetrad GUIinstall_tetrad
Define Background Knowledgeknowledge
Convert Knowledge to Caugiknowledge_to_caugi
List Registered Tetrad Algorithmslist_registered_tetrad_algorithms
Create a Custom Causal Discovery Methodmake_method
Create a Custom Runner for a Causal Discovery Algorithmmake_runner
Generate TikZ Code from a Causal Graphmake_tikz
Simulated Mixed Datamix_data
Add a New causalDisco Methodnew_disco_method
Negative Predictive Valuenpv
Simulated Numerical Datanum_data
Simulated Numerical Data with Latent Variablenum_data_latent
PC Algorithm for Causal Discoverypc
R6 Interface to pcalg Search AlgorithmsPcalgSearch
Plot Method for causalDisco Objectsplot
Plot a Disco Objectplot.Disco
Plot a Knowledge Objectplot.Knowledge
Precisionprecision
Print a Disco Objectprint.Disco
Print a Knowledge Objectprint.Knowledge
Recallrecall
Regression-based Information Loss Testreg_test
Register a New Tetrad Algorithmregister_tetrad_algorithm
Remove an Edge from Knowledgeremove_edge
Remove Tiers from Knowledgeremove_tiers
Remove Variables from Knowledgeremove_vars
Reorder Tiers in Knowledgereorder_tiers
Move a Tier Relative to Another in Knowledgereposition_tier
Add Required Edges to Knowledgerequire_edge
Reset the Tetrad Algorithm Registryreset_tetrad_alg_registry
Generate a Bundle of Tier–Variable Formulasseq_tiers
Set Background Knowledge to Disco Methodset_knowledge set_knowledge.disco_method
Simulate a Random DAGsim_dag
SP-FCI Algorithm for Causal Discoverysp_fci
Specificityspecificity
Summarize a Disco Objectsummary.Disco
Summarize a Knowledge Objectsummary.Knowledge
R6 Interface to Tetrad Search AlgorithmsTetradSearch
TFCI Algorithm for Causal Discoverytfci
Run the TFCI Algorithm for Causal Discoverytfci_run
TGES Algorithm for Causal Discoverytges
Run the TGES Algorithm for Causal Discoverytges_run
TPC Algorithm for Causal Discoverytpc
Simulated Life-Course Datatpc_example
Run the TPC Algorithm for Causal Discoverytpc_run
Unfreeze a Knowledge Object.unfreeze
Check Tetrad Installationverify_tetrad