Change Log

This change log describes updates to the Tetrad documentation (this ReadTheDocs manual). These changes will first appear in the next public release of Tetrad; the manual is not yet linked from any released version of the software.

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2025 — Manual Overhaul for Next Release

  1. New Tetrad Interface Manual • Added a new Tetrad Interface section that replaces the old “classic” HTML manual for GUI usage. • Introduced task-oriented pages for: • Main Window and workspace • Working with Data • Graph box and graph editor • Parametric Model and Instantiated Model boxes • Estimator, Updater, Regression • Data, Simulation, Search, Latent Clusters, Latent Structure, Knowledge, Compare, and Note boxes • Added box-by-box documentation with screenshots for all core boxes. • Created separate detail callouts for: • Parametric model families (Bayes, SEM, Hybrid, Generalized) • Instantiated model families (Bayes, SEM, Hybrid, Generalized) • Updaters (Junction Tree, Approximate, Row Summing, SEM) • Grid Search and Markov Checker • Documented Pipelines, Logging, and File → Settings options in the main window description.

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  1. Tests and Scores Documentation • Added individual pages for all major tests and scores, including: • FisherZ, GSquare, ChiSquare, CCI, KCI, Basis-Function LRT, Conditional Gaussian and Degenerate Gaussian LRTs, Mvplrt, MSeparationTest, ProbabilisticTest, SemBicTest, PoissonBicTest. • SemBicScore, DiscreteBicScore, BDeuScore, ConditionalGaussianBicScore, DegenerateGaussianBicScore, BasisFunctionBicScore, EbicScore, GicScores, MSepScore, MVPBicScore, PoissonPriorScore, ZhangShenBoundScore. • Each page now includes: • A clear description of when to use the test or score. • Parameters derived from the code’s getParameters() definitions. • Cross-references to relevant algorithms (e.g., FGES, BOSS, GRaSP). • Added a “Tests and Scores — Alphabetical” index and updated “Choosing Tests and Scores” to point to the new catalog.

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  1. Algorithm and Terminology Updates • Renamed LV-Dumb to LV-Heuristic throughout the manual and catalog to reflect a clearer, more professional name. • Updated references to LV-Lite to use the current name FCIT in the interface and documentation. • Added a full GIN (Generalized Independent Noise) algorithm page, including a paper-compliant description of the clustering step, root-peeling causal ordering, latent-DAG construction, parameters (alpha, verbose), and examples; updated Search-box cross-references to reflect the new implementation. • Standardized summary sections and “When to use / When not to use” wording across several algorithms (e.g., CStaR, Factor Analysis, MIM-Build variants, TSC, BOSS-related methods). • Clarified the roles of Py-Tetrad, RPy-Tetrad, and causal-learn in the “Interfacing Tools” page.

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  1. References and Clean-Up • Updated and completed citations for tests and scores, including: • BDeu, Conditional and Degenerate Gaussian methods, EBIC, GIC, Zhang–Shen bounds, Basis-Function methods, and others. • Fixed numerous small issues: • Terminology and parameter names, • Minor wording errors and outdated descriptions, • Consistency of notation and style across pages. • Verified that the HTML build, PDF output, and search all work cleanly, including proper rendering of equations and tables.

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  1. Estimation Workflow and Simulation Pipelines • Added an “Estimate model parameters” overview page describing: • Conversion from graph → Parametric Model, • Using an Estimator with a Data or Simulation node, • Producing Instantiated Models with fitted parameters and fit indices. • Refined the Simulation and Utilities overview to: • Emphasize the box-based workflow (Graph → Parametric Model → Instantiated Model → Simulation → Data → Search → Grid Search → Compare), • Remove legacy references to Tools menus, • Show how simulation, resampling, and grid search integrate into workbench pipelines.

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  1. Data subset / resample editor • Added a Data subset / resample detail page under the Tetrad Interface “box-by-box” documentation. • Documented: • Two-list variable selector (Available vs. Selected) and column-order semantics. • Sorting options, paste-based variable selection, and error handling for malformed input. • Row-selection syntax (1–100, 150, 200–250) and behavior for invalid ranges. • Sampling modes (Use rows as-is, Shuffle rows, Subsample, Bootstrap), the Sample size field, and the Seed option. • Clarified that this component is a safe, reproducible alternative to manual row/column deletion in the Data box.

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  1. Regression box: adjustment and IDA tools • Updated the Regression box documentation to reflect that: • The Adjustments and total effects component (based on Recursive Adjustment / GAC sets), and • The IDA Check component now both reside in the Regression box with consistent UI and shared notation. • Added a new IDA Check detail page, including: • The distinction between standard IDA (Maathuis et al. 2009) and Optimal IDA (Witte et al. 2020), • Description of the Show Optimal IDA checkbox and regex-based Pair filter, • Column-by-column explanations of: Pair, Min TE, Max TE, IDA Min Effect, True TE, Sq Dist, and clarified which apply only in simulated-data settings. • Revised the IDA Check layout and updated screenshots to reflect the modern interface.

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Further tweaks and minor additions (e.g., small screenshot updates, style harmonization) are not listed individually.