gp3sequences 0.3.2 — release candidate (not published)

October 2026 documentation and reproducibility

• Adds a non-exported participant-versus-transition-weighted state-fraction audit, executable tests, and a two-figure synthetic article. No public sequence estimand or API is changed.
• Release gate: complete exact-source R CMD check –as-cran, review installed source tarball and cross-platform tests, audit publication metadata, then publish an immutable GitHub tag and submit to CRAN with maintainer confirmation.
• Current CRAN baseline at candidate preparation: 0.3.0. The candidate has not been submitted to CRAN or published as a GitHub Release.

gp3sequences 0.3.1

Release maintenance

• Registers the September 2026 ecosystem-methods article in the pkgdown article index so the complete documentation site builds successfully.
• Adds exact-tag R CMD check triggering for immutable v* release tags and extends the matrix with Ubuntu oldrel-1.
• Preserves the complete 0.3.0 scientific API, defaults, estimands, analysis contracts, modelling semantics, and interpretation boundaries.
• The existing annotated v0.3.0 tag remains immutable and unchanged.

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.