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Changelog

Source: NEWS.md

gp3sequences 0.2.0.9000

  • Synchronized README, package description, citation metadata, and pkgdown-facing development status for 0.2.0.9000; README counts are now derived from the public NAMESPACE and vignette sources.

  • Added a common analysis-contract and provenance foundation for systematic 0.3.0 hardening.

  • Added sequence_capabilities(), audit_sequence_analysis(), and compare_sequence_analysis_results() for machine-readable capability, contract, and reproducibility audits.

  • Added deterministic contract, metamorphic, and adversarial test foundations plus a machine-readable public-API validation ledger.

  • Added auditable longitudinal and panel-sequence preparation, summaries, change metrics, and plots.

  • Added bounded non-contiguous subsequence enumeration, prevalence summaries, group comparisons, and plots.

  • Added optional mgcv-based time-varying state and transition models with participant random-effect support.

  • Added dependency-light multichannel and covariate-dependent categorical hidden Markov models.

  • Added design-aware permutation and bootstrap comparisons with explicit associational and causal guardrails.

  • Added six focused visualisation helpers, deterministic tests, an installed-package smoke test, and six synthetic articles.

gp3sequences 0.2.0

  • Released the advanced standalone sequence-analysis API with 46 exported functions and 47 manual pages.

  • Added four integrated workflow articles, bringing the package website to nine synthetic, reproducible articles.

  • Prepared the complete reference and article collection for publication at the main package website.

  • Configured pkgdown so future validated master updates publish directly to the main website.

  • Added four integrated, user-oriented articles covering getting started, validation and preparation, method selection, and a reproducible synthetic case study.

  • Added the complete advanced sequence-analysis roadmap.

  • Added deterministic aligned-position consensus sequences and agreement summaries.

  • Added descriptive between-group state, transition, and length comparisons.

  • Added Levenshtein, LCS, optimal-matching, and transition-profile distances.

  • Added hierarchical, PAM, and CLARA clustering interfaces, validation metrics, representatives, ensembles, and stability resampling.

  • Added transition networks, centrality, communities, higher-order transition models, prediction, and sequence-level bootstrap intervals.

  • Added dependency-light categorical HMM and mixture-HMM estimation, decoding, summaries, and model-comparison tables.

  • Added optional adapters for TraMineR, arulesSequences, GrpString, seqHMM, igraph, and common gp3tools-style data frames.

  • Added four synthetic workflow articles, deterministic tests, and an end-to-end smoke test.

  • Initial public release.

  • Created the independent gp3sequences package scaffold.

  • Added MIT licensing and package-level documentation.

  • Added the initial testthat edition 3 infrastructure.

  • Defined the initial neutral scope and interpretation boundary.

  • Added the initial README and pkgdown website configuration.

  • Added a multi-platform GitHub Actions R CMD check workflow for macOS, Windows, Ubuntu release, and Ubuntu devel.

  • Added a GitHub Actions pkgdown workflow for automated website building and deployment.

  • Added audit_sequence_data() and validate_sequence_data() for structured input diagnostics.

  • Added prepare_sequence_data() with explicit missing-state, duplicate-position, repeated-state, duration, and unknown-state policies.

  • Added encode_sequence_data() for deterministic state dictionaries and transparent state codes.

  • Added summarise_sequence_states(), summarise_sequence_transitions(), and format_sequence_paths() for structural sequence summaries.

  • Added extract_sequence_ngrams() for deterministic contiguous motif enumeration with explicit overlap handling.

  • Added summarise_sequence_motifs(), filter_sequence_motifs(), and format_sequence_motifs() for transparent motif prevalence, filtering, and reporting.

  • Added summarise_sequence_motif_positions() and format_sequence_motif_positions() for deterministic structural location summaries.

  • Added dependency-free plot_sequence_motifs() and plot_sequence_motif_positions() visualisations plus a synthetic contiguous-motif workflow article.