# gp3sequences 0.3.0
* Added CRAN status, download, DOI, GitHub Actions, pkgdown, and license badges; added canonical CRAN, website, source, issue, and CRAN-check links; and documented CRAN and GitHub installation paths.
* Synchronized README, package description, citation metadata, and pkgdown-facing release status for 0.3.0; 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.
