Articles¶
The documentation includes the complete set of 15 Python-native ports of the
frozen gp3sequences 0.3.0 vignette topics. Use this page as a methodological
reading path rather than a flat list.
Foundations¶
Getting Started
End-to-end structural workflow: audit, preparation, summaries, motifs, distance, clustering, consensus, groups, and transitions.
Choosing a Method
Map structural research questions to motifs, consensus, distances, networks, HMMs, panels, or design-aware inference.
Validation & Preparation
Make sequence order, missingness, duration, repeated states, and preprocessing decisions explicit.
Synthetic Case Study
Combine the package layers in one reproducible analysis without treating every method as mandatory.
Pattern discovery and descriptive comparison¶
- Contiguous Motif Workflow — exact adjacent patterns, motif positions, prevalence, filtering, and reporting.
- Bounded Non-Contiguous Subsequence Mining — ordered patterns with explicit gap / span constraints.
- Consensus Sequences and Descriptive Group Comparisons — aligned modal structure and descriptive contrasts.
Whole-sequence geometry¶
- Sequence Distances, Clustering, and Stability — distance families, clustering, representatives, validation, bootstrap stability, and ensemble logic.
Transition structure and latent models¶
- Transition Networks and Higher-Order Models — first-order directed networks, centrality, communities, higher-order contexts, backoff, and prediction.
- Latent Sequence Models and Optional Adapters — categorical and mixture HMMs plus optional ecosystem handoffs.
- Multichannel and Covariate-Dependent HMMs — joint channels and covariate-dependent transition structure.
Inference, longitudinal structure, and time¶
- Design-Aware Sequence Group Inference — declared designs and randomization-based group testing.
- Longitudinal and Panel Sequence Workflows — repeated sequence panels, change summaries, and panel comparisons.
- Time-Varying Condition Comparisons
— changing transition probabilities and validated
mssm-based smooth models.
Visualisation¶
- Extended Sequence Visualisations — sequence index, state distribution, entropy, distance heatmap, cluster silhouette, and transition network views.
- Plot gallery — visual inventory plus exact plotting calls.
Porting contract¶
Each methodology article retains the frozen vignette topic and methodological scope while using Python scientific objects. R-only backend identities are represented through documented semantic adapters rather than by pretending to recreate S3/S4 object identity.
The article set is part of the frozen documentation contract: all 15 article names are tested by the documentation suite.