# Causal Graph Interface

## Documentation for package ‘caugi’ version 1.1.0

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

## Help Pages

A B C D E F G H I K L M N P R S T V W

## -- A --

add-caugi_plot-caugi_plot | Compose Plots Horizontally
add_edges | Manipulate nodes and edges of a 'caugi'
add_nodes | Manipulate nodes and edges of a 'caugi'
adjustment_set | Compute an adjustment set
aid | Adjustment Identification Distance
all_adjustment_sets_admg | Get all valid adjustment sets in an ADMG
all_backdoor_sets | Get all backdoor sets up to a certain size.
ancestors | Get ancestors of nodes in a 'caugi'
anteriors | Get anteriors of nodes in a 'caugi'
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

## -- B --

build | Build the 'caugi' graph

## -- C --

caugi | Create a 'caugi' from edge expressions.
caugi_default_options | Default options for caugi
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_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_mermaid | S7 Class for Mermaid Export
caugi_options | Get or set global options for caugi
caugi_plot | S7 Class for caugi Plot
caugi_registry | 'caugi' edge registry
caugi_serialize | Serialize caugi Graph to JSON String
caugi_verbs | Manipulate nodes and edges of a 'caugi'
children | Get children of nodes in a 'caugi'
condition_marginalize | Marginalize and/or condition on variables in an ancestral graph (AG)

## -- D --

dag_from_pdag | Extend a PDAG to a DAG using the Dor-Tarsi Algorithm
descendants | Get descendants of nodes in a 'caugi'
districts | Get districts (c-components) of an ADMG or AG
divide-caugi_plot-caugi_plot | Compose Plots Vertically
d_separated | Are X and Y d-separated given Z?

## -- E --

E | Get edges of a 'caugi'.
edges | Get edges of a 'caugi'.
edge_types | Get the edge types of a 'caugi'.
exogenize | Exogenize a graph
exogenous | Get all exogenous nodes in a 'caugi'
export-classes | Export Format Classes

## -- F --

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

## -- G --

generate_graph | Generate a 'caugi' using Erdős-Rényi.

## -- H --

hd | Hamming Distance

## -- I --

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_mpdag | Is the 'caugi' graph an MPDAG?
is_pdag | Is the 'caugi' graph a PDAG?
is_simple | Is the 'caugi' graph simple?
is_ug | Is the 'caugi' graph an UG?
is_valid_adjustment_admg | Is a set a valid adjustment set in an ADMG?
is_valid_backdoor | Is a backdoor set valid?

## -- K --

knit_print.caugi_export | Knit Print Method for caugi_export

## -- L --

latent_project | Project latent variables from a DAG to an ADMG
length | Length of a 'caugi'

## -- M --

markov_blanket | Get Markov blanket of nodes in a 'caugi'
meek_closure | Apply Meek closure to a PDAG
minimal_d_separator | Compute a minimal d-separator
moralize | Moralize a DAG
mutate_caugi | Mutate 'caugi' class
m_separated | M-separation test for AGs and ADMGs

## -- N --

neighbors | Get neighbors of nodes in a 'caugi'
neighbours | Get neighbors of nodes in a 'caugi'
nodes | Get nodes or edges of a 'caugi'
normalize_latent_structure | Normalize latent structure in a DAG

## -- P --

parents | Get parents of nodes in a 'caugi'
pipe-caugi_plot-caugi_plot | Compose Plots Horizontally
plot | Create a caugi Graph Plot Object
posteriors | Get posteriors of nodes in a 'caugi'
print | Print a 'caugi'

## -- R --

read_caugi | Read caugi Graph from File
read_graphml | Read GraphML File to caugi Graph
register_caugi_edge | Register a new edge type in the global registry.
registry | 'caugi' edge registry
remove_edges | Manipulate nodes and edges of a 'caugi'
remove_nodes | Manipulate nodes and edges of a 'caugi'
reset_caugi_registry | 'caugi' edge registry

## -- S --

same_nodes | Same nodes?
seal_caugi_registry | 'caugi' edge registry
set_edges | Manipulate nodes and edges of a 'caugi'
shd | Structural Hamming Distance
simulate_data | Simulate data from a 'caugi' DAG.
skeleton | Get the skeleton of a graph
spouses | Get spouses (bidirected neighbors) of nodes in an ADMG
subgraph | Get the induced subgraph

## -- T --

topological_sort | Get a topological ordering of a DAG
to_dot | Export caugi Graph to DOT Format
to_graphml | Export caugi Graph to GraphML Format
to_mermaid | Export caugi Graph to Mermaid Format

## -- V --

V | Get nodes or edges of a 'caugi'
vertices | Get nodes or edges of a 'caugi'

## -- W --

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