Network Analysis and Causal Inference Through Structural
Equation Modeling
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Documentation for package ‘SEMgraph’ version 1.2.1
Help Pages
| alsData | Amyotrophic Lateral Sclerosis (ALS) dataset |
| ancestors | Node ancestry utilities |
| ancestry | Node ancestry utilities |
| clusterGraph | Topological graph clustering |
| clusterScore | Module scoring |
| colorGraph | Vertex and edge graph coloring on the base of fitting |
| cplot | Subgraph mapping |
| dagitty2graph | Graph conversion from dagitty to igraph |
| descendants | Node ancestry utilities |
| extractClusters | Cluster extraction utility |
| factor.analysis | Factor analysis for high dimensional data |
| gplot | Graph plotting with renderGraph |
| graph2dag | Convert directed graphs to directed acyclic graphs (DAGs) |
| graph2dagitty | Graph conversion from igraph to dagitty |
| graph2lavaan | Graph to lavaan model |
| kegg | KEGG interactome |
| kegg.pathways | KEGG pathways |
| lavaan2graph | lavaan model to graph |
| localCI.test | Conditional Independence (CI) local tests of an acyclic graph |
| mergeNodes | Graph nodes merging by a membership attribute |
| modelSearch | Optimal model search strategies |
| orientEdges | Assign edge orientation of an undirected graph |
| pairwiseMatrix | Pairwise plotting of multivariate data |
| parameterEstimates | Parameter Estimates of a fitted SEM |
| parents | Node ancestry utilities |
| pathFinder | Perturbed path search utility |
| predictSink | SEM-based out-of-sample predictions |
| properties | Graph properties summary and graph decomposition |
| resizeGraph | Interactome-assisted graph re-seizing |
| sachs | Sachs multiparameter flow cytometry data and consensus model |
| SEMace | Compute the Average Causal Effect (ACE) for a given source-sink pair |
| SEMbap | Bow-free covariance search and data de-correlation |
| SEMdag | Estimate a DAG from an input (or empty) graph |
| SEMdci | SEM-based differential network analysis |
| SEMgsa | SEM-based gene set analysis |
| SEMpath | Search for directed or shortest paths between pairs of source-sink nodes |
| SEMrun | Fit a graph as a Structural Equation Model (SEM) |
| SEMtree | Tree-based structure learning methods |
| Shipley.test | Missing edge testing implied by a DAG with Shipley's basis-set |
| siblings | Node ancestry utilities |
| summary.GGM | GGM model summary |
| summary.RICF | RICF model summary |
| transformData | Transform data methods |
| weightGraph | Graph weighting methods |