Package: rCausalMGM 1.0.1

Panayiotis V Benos

rCausalMGM: Scalable Causal Discovery and Model Selection on Mixed Datasets with 'rCausalMGM'

Scalable methods for learning causal graphical models from mixed data, including continuous, discrete, and censored variables. The package implements CausalMGM, which combines a convex, score-based approach for learning an initial moralized graph with a producer-consumer scheme that enables efficient parallel conditional independence testing in constraint-based causal discovery algorithms. The implementation supports high-dimensional datasets and provides individual access to core components of the workflow, including MGM and the PC-Stable and FCI-Stable causal discovery algorithms. To support practical applications, the package includes multiple model selection strategies, including information criteria based on likelihood and model complexity, cross-validation for out-of-sample likelihood estimation, and stability-based approaches that assess graph robustness across subsamples.

Authors:Tyler C Lovelace [aut], Max Dudek [aut], Jack Fiore [aut], Panayiotis V Benos [aut, cre]

rCausalMGM_1.0.1.tar.gz
rCausalMGM_1.0.1.tar.gz(r-4.7-arm64)rCausalMGM_1.0.1.tar.gz(r-4.7-x86_64)rCausalMGM_1.0.1.tar.gz(r-4.6-arm64)rCausalMGM_1.0.1.tar.gz(r-4.6-x86_64)
rCausalMGM_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
rCausalMGM/json (API)
NEWS

# Install 'rCausalMGM' in R:
install.packages('rCausalMGM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblascppopenmp

2.40 score 25 scripts 511 downloads 47 exports 7 dependencies

Last updated from:9e0101244c. Checks:6 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK485
linux-devel-x86_64OK478
source / vignettesOK499
linux-release-arm64OK523
linux-release-x86_64OK445
wasm-releaseOK390

Exports:adjMat2GraphallMetricsbootstrapbosscoxmgmcoxmgmCVcoxmgmPathcpdagcreateKnowledgefciCVfciStablefciStarsgraphTablegraspgrowShrinkMBloadGraphmgmmgmCVmgmfciCVmgmPathmgmpcCVmoralpagpcCVpcStablepcStarsplot.graphplot.graphCVplot.graphPathplot.graphSTARSplot.graphSTEPSprint.graphprint.graphCVprint.graphPathprint.graphSTARSprint.graphSTEPSprint.knowledgeprintGraphprMetricsprMetricsAdjacencyprMetricsCausalprMetricsOrientationsaveGraphSHDsimRandomDAGskeletonsteps

Dependencies:BHlatticeMatrixRcppRcppArmadilloRcppThreadsurvival

Readme and manuals

Help Manual

Help pageTopics
Convert an adjacency matrix into a graphadjMat2Graph
Combined graph recovery metricsallMetrics
Runs bootstrapping for a causal graph on the dataset.bootstrap
Runs the BOSS causal discovery algorithm on the datasetboss
Calculate the CoxMGM graph on a dataset.coxmgm
Implements k-fold cross-validation for CoxMGMcoxmgmCV
Estimates a solution path for CoxMGMcoxmgmPath
Calculate the CPDAG for a given DAGcpdag
A function to create a prior knowledge object for use with causal discovery algorithmscreateKnowledge
Implements k-fold cross-validation for FCI-StablefciCV
Runs the causal discovery algorithm FCI-Stable on a dataset.fciStable
Implements StARS for FCI-StablefciStars
A function to generate a data.frame for objects from graph class. It incorporates adjacency and orientation frequency if estimates of edge stability are available.graphTable
Runs the GRaSP causal discovery algorithm on the datasetgrasp
Implements Grow-Shrink algorithm for Markov blanket identificationgrowShrinkMB
Load a graph from a ".txt" fileloadGraph
Calculate the Mixed Graphical Model (MGM) graph on a dataset.mgm
Implements k-fold cross-validation for MGMmgmCV
Implements k-fold cross-validation for MGM-FCI-StablemgmfciCV
Estimates a solution path for MGMmgmPath
Implements k-fold cross-validation for MGM-PC-StablemgmpcCV
Calculate the moral graph for a given DAGmoral
Calculate the PAG for a given DAG and set of latent variablespag
Implements k-fold cross-validation for PC-StablepcCV
Runs the causal discovery algorithm PC-Stable on a dataset.pcStable
Implements StARS for PC-StablepcStars
A plot override function for the graph classplot.graph
A plot override function for the graphCV classplot.graphCV
A plot override function for the graphPath classplot.graphPath
A plot override function for the graphSTARS classplot.graphSTARS
A plot override function for the graphSTEPS classplot.graphSTEPS
A print override function for the graph classprint.graph
A print override function for the graphCV classprint.graphCV
A print override function for the graphPath classprint.graphPath
A print override function for the graphSTARS classprint.graphSTARS
A print override function for the graphSTEPS classprint.graphSTEPS
A print override function for the knowledge classprint.knowledge
Display a graph object as text.printGraph
Combined adjaceny and orientation precision-recall metricsprMetrics
Adjacency Precision-Recall MetricsprMetricsAdjacency
Causal Orientaion Precision-Recall Metrics for CPDAGsprMetricsCausal
Orientation Precision-Recall MetricsprMetricsOrientation
Save a graph to a file. Supported file types are ".txt" and ".sif".saveGraph
Structural Hamming Distance (SHD)SHD
A function to simulate a random forward DAG from a SEM model.simRandomDAG
Calculate the undirected skeleton for a given DAGskeleton
Implements StEPS and StARS for MGMsteps