# Network Analysis and Causal Inference Through Structural Equation Modeling

## Documentation for package ‘SEMgraph’ version 1.2.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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
loadPathways | Import pathways and generate a reference network
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
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