Package index • caugi

The caugi object

caugi(): Create a caugi from edge expressions.

Queries

ancestors(): Get ancestors of nodes in a caugi
anteriors(): Get anteriors of nodes in a caugi
children(): Get children of nodes in a caugi
descendants(): Get descendants of nodes in a caugi
districts(): Get districts (c-components) of an ADMG
edge_types(): Get the edge types of a caugi.
edges() E(): Get edges of a caugi.
exogenous(): Get all exogenous nodes in a caugi
is_acyclic(): Is the caugi acyclic?
is_admg(): Is the caugi graph an ADMG?
is_ag(): Is the caugi graph an AG?
is_caugi(): Is it a caugi graph?
is_cpdag(): Is the caugi graph a CPDAG?
is_dag(): Is the caugi graph a DAG?
is_empty_caugi(): Is the caugi graph empty?
is_mag(): Is the caugi graph a MAG?
is_pdag(): Is the caugi graph a PDAG?
is_ug(): Is the caugi graph an UG?
m_separated(): M-separation test for AGs and ADMGs
markov_blanket(): Get Markov blanket of nodes in a caugi
neighbors() neighbours(): Get neighbors of nodes in a caugi
nodes() vertices() V(): Get nodes or edges of a caugi
parents(): Get parents of nodes in a caugi
same_nodes(): Same nodes?
spouses(): Get spouses (bidirected neighbors) of nodes in an ADMG
subgraph(): Get the induced subgraph
topological_sort(): Get a topological ordering of a DAG

Verbs

build(): Build the graph now
add_edges() remove_edges() set_edges() add_nodes() remove_nodes(): Manipulate nodes and edges of a caugi

Adjustment and d-separation

adjustment_set(): Compute an adjustment set
all_adjustment_sets_admg(): Get all valid adjustment sets in an ADMG
all_backdoor_sets(): Get all backdoor sets up to a certain size.
d_separated(): Are X and Y d-separated given Z?
is_valid_adjustment_admg(): Is a set a valid adjustment set in an ADMG?
is_valid_backdoor(): Is a backdoor set valid?

Simulation

generate_graph(): Generate a caugi using Erdős-Rényi.
simulate_data(): Simulate data from a caugi DAG.

Metrics

aid(): Adjustment Identification Distance
hd(): Hamming Distance
shd(): Structural Hamming Distance

Edge Registry

register_caugi_edge(): Register a new edge type in the global registry.
caugi_registry() reset_caugi_registry() seal_caugi_registry(): caugi edge registry

Methods

length: Length of a caugi
print: Print a caugi

Conversions

as_adjacency(): Convert a caugi to an adjacency matrix
as_bnlearn(): Convert a caugi to a bnlearn network
as_caugi(): Convert to a caugi
as_dagitty(): Convert a caugi to a dagitty graph
as_igraph(): Convert a caugi to an igraph object

Operations

condition_marginalize(): Marginalize and/or condition on variables in an ancestral graph (AG)
exogenize(): Exogenize a graph
latent_project(): Project latent variables from a DAG to an ADMG
moralize(): Moralize a DAG
mutate_caugi(): Mutate caugi class
skeleton(): Get the skeleton of a graph

Importing and Exporting to and from Other Formats

caugi_deserialize(): Deserialize caugi Graph from JSON String
caugi_dot(): S7 Class for DOT Export
caugi_export(): S7 Base Class for Caugi Exports
caugi_graphml(): S7 Class for GraphML Export
caugi_mermaid(): S7 Class for Mermaid Export
caugi_serialize(): Serialize caugi Graph to JSON String
export-classes: Export Format Classes
format-caugi: Caugi Native Format Serialization
format-dot: DOT Format Export and Import
format-graphml: GraphML Format Export and Import
format-mermaid: Mermaid Format Export
knit_print.caugi_export: Knit Print Method for caugi_export
read_caugi(): Read caugi Graph from File
read_graphml(): Read GraphML File to caugi Graph
to_dot(): Export caugi Graph to DOT Format
to_graphml(): Export caugi Graph to GraphML Format
to_mermaid(): Export caugi Graph to Mermaid Format
write_caugi(): Write caugi Graph to File
write_dot(): Write caugi Graph to DOT File
write_graphml(): Write caugi Graph to GraphML File
write_mermaid(): Write caugi Graph to Mermaid File

Plotting

add-caugi_plot-caugi_plot pipe-caugi_plot-caugi_plot: Compose Plots Horizontally
caugi_layout(): Compute Graph Layout
caugi_layout_bipartite(): Bipartite Graph Layout
caugi_layout_fruchterman_reingold(): Fruchterman-Reingold Force-Directed Layout
caugi_layout_kamada_kawai(): Kamada-Kawai Stress Minimization Layout
caugi_layout_sugiyama(): Sugiyama Hierarchical Layout
caugi_layout_tiered(): Tiered Graph Layout
caugi_plot(): S7 Class for caugi Plot
divide-caugi_plot-caugi_plot: Compose Plots Vertically
plot: Create a caugi Graph Plot Object

Options

caugi_default_options(): Default options for caugi
caugi_options(): Get or set global options for caugi