NEWS

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PhysioAnnotationHub 0.2.1

Documentation

• ?PhysioAnnotationHub now answers: a package help page gives one paragraph on what the package is for, the main entry points grouped by task, and where to go next.
• A vignette carries one task end to end on synthetic or bundled data, offline, and is built and run by R CMD check.
• Runnable @examples added or corrected across 11 help pages. Each runs offline in seconds, writes nothing outside tempdir(), and is executed by R CMD check; anything needing a device, a download or an optional backend is fenced with the reason stated.
• The README's quick start runs as written: it attaches the package, builds its own inputs, and uses only hard dependencies.

PhysioAnnotationHub 0.2.0

• Add free-living physical-behaviour metric -> ICF Activities & Participation mappings (steps_per_day -> d450, mvpa_min / sedentary_min / physical_activity_volume -> d570, walking_bouts -> d455) so tagICF() resolves accelerometry-derived measures.

PhysioAnnotationHub 0.1.0

Initial release as a standalone package in the physio-ecosystem. Provides a centralized anatomical and clinical knowledge hub — muscle, bone, and nerve metadata, clinical code mappings, and a queryable knowledge graph — bundled as curated reference data for downstream musculoskeletal and rehabilitation analyses.

New Features

• Bundled annotation reference data, loaded on demand into a cached hub via loadAnnotationHub() with a print() method summarizing the loaded tables:
  • Muscle annotations (body region, primary/secondary action, innervating nerve, spinal level, muscle type, joint crossed).
  • Bone annotations (body region, bone type, parent structure).
  • Nerve annotations (spinal levels, type, body region, plexus).
  • Clinical code tables mapping ICD-10 and ICF codes to affected/related muscles, body regions, and functional domains.
• Annotation lookup functions with fuzzy (exact-then-substring) matching:
  • getMuscleAnnotation(), getBoneAnnotation(), and getNerveAnnotation() retrieve records by name, or return the full table when called with no query.
  • getClinicalCodes() resolves ICD-10 or ICF codes referencing a given set of muscles.
• Knowledge graph query and traversal over subject–predicate–object triples:
  • queryKG() filters triples by any combination of subject, predicate, and object using grep or exact matching.
  • kgNeighbors() returns all triples within a given number of hops of an entity, following both outgoing and incoming edges.
  • kgShortestPath() finds the shortest path between two entities via breadth-first search, reporting the entity path, the relations traversed (with inverse edges flagged), and the path depth.
• kgEnrichment() performs over-representation analysis of a muscle set against the full background, testing enrichment of actions, innervation, body regions, or spinal levels with fold-enrichment and hypergeometric p-values.

Documentation

• Roxygen2 documentation and examples for all exported functions, plus a package README and pkgdown reference site.
• Bundled CITATION metadata for citing the package.