caugi 1.1.0

New Features

• Add normalize_latent_structure(), which normalizes the latent structure of a DAG while preserving the marginal model over observed variables.
• Add minimal_d_separator(), which computes a minimal d-separator between sets of nodes in a DAG, with support for mandatory inclusions and restrictions.
• Add posteriors() query function, which is the dual of anteriors(). It returns all nodes reachable by following paths where every edge is either undirected or directed away from the source node. For DAGs, posteriors() equals descendants(). For PDAGs and AGs, it includes both descendants and nodes reachable via undirected edges.
• You can now specify whether to use an open or closed graph definition for the queries ancestors(), anteriors(), descendants(), and posteriors(). This can be set globally with caugi_options() or locally with the open = TRUE/FALSE argument. The default remains open = TRUE.
• Add is_mpdag() query to check whether a PDAG is closed under Meek’s orientation rules (R1-R4), and meek_closure() to orient all implied edges until Meek closure.

Improvements

• caugi_options() now supports nested key drilling: multiple unnamed arguments traverse nested options (e.g., caugi_options("plot", "tier_style", "fill")).
• Rust remains the single source of truth for graph state. Graph properties (simple, graph_class, nodes, edges) are sourced from the session.
  • A session is always created, including empty graphs (n = 0), which simplifies property access.
  • Deprecated compatibility properties @.state, @name_index_map, @built, and @ptr now warn on access and return NULL.
  • Deprecated compatibility constructor arguments build and state in caugi() now warn and are ignored.
• The inplace parameter in verb functions (add_edges(), remove_edges(), set_edges(), add_nodes(), remove_nodes()). All graph modifications now use copy-on-write semantics for consistency with R conventions. The parameter is deprecated and ignored with a warning.
• Added all.equal and compare_proxy methods for caugi objects to support graph-content comparison in tests.
• Add asp parameter to plot() for controlling the aspect ratio. When asp = 1, the plot respects equal units on both axes, preserving the layout coordinates. Works like base R’s asp parameter (y/x aspect ratio) (#195).
• Add pdag_to_dag() function that generates a random DAG consistent with a given CPDAG/PDAG structure if possible (#201).

Bug Fixes

• Fixed a bug causing plot() to use incorrect layout if node names were not in the same order as in the graph object (#198).
• Fixed set_edges() so that it correctly replaces symmetric edges in simple graphs.

Deprecations

• The parameter all in districts() has been deprecated. Use districts() without arguments to get all districts.

caugi 1.0.0

New Features

• Add support for Ancestral Graphs (AGs), which combine directed (-->), bidirected (<->), and undirected (---) edges while satisfying ancestral graph constraints. New functions: is_ag(), is_mag().
• Add mode argument to neighbors()/neighbours() to filter neighbors by edge direction or type ("all", "in", "out", "undirected", "bidirected", "partial"). This is a structural query, and not a semantic query!
• neighbors() now supports class = "UNKNOWN" graphs, including mode-based filtering.
• Add simulate_data() that enables simulation from DAGs using SEMs. Standard linear Gaussian SEMs are defaults, but more importantly custom SEMs are available.
• Add "AUTO" parameter for class in caugi objects. This automatically picks the graph class in order DAG, UG, PDAG, ADMG, AG.
• Add Ancestral Graphs (AG) with support for directed, bidirected, and undirected edges, plus new queries is_ag() and is_mag() and m-separation for AGs.
• Add exogenize() function that exogenizes variables for any graph type. Current implementation is written in R, but it is so simple that it might be preferable over a Rust implementation. This might be changed later.
• Add latent_project() function that does latent projection from DAGs to ADMGs.
• Add native caugi serialization format for saving and loading graphs. New functions: write_caugi(), read_caugi(), caugi_serialize(), and caugi_deserialize(). The format is a versioned JSON schema that captures graph structure, class, and optional metadata (comments and tags).
• Add plot() method for visualizing graphs using various layout algorithms. The plot is rendered using grid graphics and returns a caugi_plot object that can be customized with node_style, edge_style, and label_style arguments. The plot() method accepts layouts as strings, functions, or pre-computed data.frames.
• Add caugi_layout() function to compute node coordinates for graph visualization.
• Add dedicated layout functions: caugi_layout_sugiyama(), caugi_layout_fruchterman_reingold(), caugi_layout_kamada_kawai(), caugi_layout_bipartite(), and caugi_layout_tiered(). Each function provides an API for its specific algorithm.
• Add to_dot() and write_dot() functions for exporting caugi graphs to DOT (graphviz) format. The resulting object is a new S7 class, caugi_export, which has a knit_print() method for rendering DOT graphs in R Markdown and Quarto documents.
• Add GraphML and Mermaid import/export support: to_graphml, write_graphml, read_graphml, to_mermaid, write_mermaid, and read_mermaid
• Add plot composition operators for creating multi-plot layouts: + and | for horizontal arrangement, / for vertical stacking. Compositions can be nested arbitrarily (e.g., (p1 + p2) / p3).
• Add caugi_options() function for setting global defaults for plot appearance, including composition spacing and default styles for nodes, edges, labels, and titles.
• Add caugi_default_options() function to query or reset to package default options.
• Add a new vignette, “Graph Visualization with caugi”, demonstrating the new plotting capabilities and customization options.

Improvements

• Add favicons for the package website.
• Standardize is_caugi() validation calls internally.
• Adopt air as the R code formatter for the package.
• caugi_layout_tiered() now returns a tier column and orientation attribute in the layout data.frame, allowing plot() to automatically use tier information without requiring the tiers argument to be passed again.

Bug Fixes

• Fix typo in error messages and documentation examples.
• Remove unused index_name_map parameter from internal .cg_state() function.
• Fix interpretation of directed edge endpoint positions in the Rust backend, improving correctness of direction-dependent algorithms/metrics (e.g. topological sorting and structural Hamming distance computations).
• Fix bug in is_cpdag function that returns TRUE on non-complete PDAGs.
• Fix bug in shd returning positive values for equivalent graphs given in shuffled order.

caugi 0.4.0

• Add support for Acyclic Directed Mixed Graphs (ADMGs), which combine directed edges representing causal relationships with bidirected edges representing latent confounding.
• Add new functions for querying ADMGs: is_admg(), spouses(), districts(), and m_separated() (generalization of d-separation for graphs with bidirected edges).
• Add functions for adjustment set validation in ADMGs: is_valid_adjustment_admg() and all_adjustment_sets_admg() implementing the Generalized Adjustment Criterion.
• Add mutate_caugi() function that allows conversion from one graph type to another.
• Add custom printing method for caugi objects.
• Add optional edges_df argument to caugi() for easier construction from existing data frames containing the columns from, edge, and to.
• Improve error handling across all graph types (DAG, PDAG, UG, ADMG) with more descriptive error messages.
• Update as_adjacency() and as_igraph() to support bidirected edges.
• Update as_caugi() documentation to include “ADMG” as a valid class type for conversion.

caugi 0.3.2

• Change website to caugi.org/.
• Minor modifications to CONTRIBUTING.md.
• Minor README rewrite.

caugi 0.3.1

• Remove the use of lockBinding and unlockBinding in the package to silence R CMD check notes.

caugi 0.3.0

• Add mutate_caugi function that allows conversion from one graph type to another.
• Add custom printing method.
• Add optional edges_df argument to caugi for easier construction from existing data frames containing the columns from, edge, and to.
• Update How to use caugi in a package vignette to use new conversion functionality.
• Add CONTRIBUTING.md to github.

caugi 0.2.1

• Update function documentation to make package CRAN ready.
• Update performance vignette and change it to article.
• Add Michael Sachs and Johan Larsson to Authors in DESCRIPTION.
• Patch S4 class reading for as_caugi.

caugi 0.2.0

• Drop dependencies on dplyr and tibble.
• Improve performance by letting all data wrangling be done by data.table.
• Edges and nodes are now data.tables.

caugi 0.1.0

• Add Undirected Graphs (UG) to caugi.
• Refactor Rust backend for DAGs.
• Add NEWS.md!