Package 'PhysioAnnotationHub'

Get bone annotations

Description

Get bone annotations

Usage

getBoneAnnotation(bones = NULL, hub = NULL, fuzzy = TRUE)

Arguments

bones	Character vector of bone names (NULL for all)
hub	AnnotationHub object
fuzzy	Logical; use fuzzy matching (default TRUE)

Value

data.frame of bone annotations

Examples

getBoneAnnotation("Occipital")

---

Get clinical codes for muscles

Description

Get clinical codes for muscles

Usage

getClinicalCodes(muscles, system = c("icd10", "icf"), hub = NULL)

Arguments

muscles	Character vector of muscle names
system	Character; "icd10" or "icf" (default "icd10")
hub	AnnotationHub object

Value

data.frame of matching clinical codes

Examples

getClinicalCodes("Rectus abdominis", system = "icd10")

---

Retrieve a published ICF Core Set

Description

Returns the categories of a published WHO ICF Core Set for a health condition. Currently the Brief ICF Core Set for Stroke (Geyh 2004) is bundled; the data are the officially published category lists, not derived.

Usage

getCoreSet(condition, level = c("brief", "comprehensive"), hub = NULL)

Arguments

condition	Condition name (e.g. "Stroke"); case-insensitive.
level	"brief" or "comprehensive" (default "brief").
hub	Optional PhysioAnnotationHub.

Value

A data frame of ICF categories (icf_code, category_title, component, ...) for the requested Core Set.

References

Geyh et al. 2004, ICF Core Sets for Stroke; ICF Research Branch.

See Also

[icfCategories()], [tagICF()]

Examples

getCoreSet("Stroke")

---

Get muscle annotations

Description

Get muscle annotations

Usage

getMuscleAnnotation(muscles = NULL, hub = NULL, fuzzy = TRUE)

Arguments

muscles	Character vector of muscle names (NULL for all)
hub	AnnotationHub object
fuzzy	Logical; use fuzzy matching (default TRUE)

Value

data.frame of muscle annotations

Examples

getMuscleAnnotation("Trapezius")
nrow(getMuscleAnnotation())   # the whole muscle table

---

Get nerve annotations

Description

Get nerve annotations

Usage

getNerveAnnotation(nerves = NULL, hub = NULL)

Arguments

nerves	Character vector of nerve names (NULL for all)
hub	AnnotationHub object

Value

data.frame of nerve annotations

Examples

getNerveAnnotation("Accessory")

---

Look up ICF category titles

Description

Resolves ICF category codes to their titles (across the hub's Core-Set, metric-link, and clinical ICF tables).

Usage

icfCategories(codes, hub = NULL)

Arguments

codes	A character vector of ICF codes (e.g. c("b730", "d450")).
hub	Optional PhysioAnnotationHub.

Value

A data frame with icf_code and title (NA title for an unknown code).

See Also

[getCoreSet()], [tagICF()]

Examples

icfCategories(c("b730", "d450"))

---

Functional enrichment analysis for a set of muscles

Description

Tests whether a set of muscles is enriched for specific annotations (actions, innervation, body regions) compared to the full set.

Usage

kgEnrichment(
  muscles,
  annotation_type = c("action", "nerve", "body_region", "spinal_level"),
  hub = NULL
)

Arguments

muscles	Character vector of muscle names (query set)
annotation_type	Character; "action", "nerve", "body_region", "spinal_level"
hub	AnnotationHub object

Value

data.frame with term, count, expected, fold_enrichment, p_value

Examples

kgEnrichment(
  c("Trapezius", "Latissimus Dorsi", "Serratus Posterior Superior"),
  annotation_type = "body_region"
)

---

Get KG neighbors of an entity

Description

Get KG neighbors of an entity

Usage

kgNeighbors(entity, depth = 1, hub = NULL)

Arguments

entity	Character; entity name
depth	Integer; traversal depth (default 1)
hub	AnnotationHub object

Value

data.frame of all triples within depth hops

Examples

head(kgNeighbors("Trapezius"))

---

Find shortest path between two entities in the KG

Description

Find shortest path between two entities in the KG

Usage

kgShortestPath(from, to, hub = NULL, max_depth = 5)

Arguments

from	Character; source entity name
to	Character; target entity name
hub	AnnotationHub object
max_depth	Integer; maximum search depth (default 5)

Value

List with path (entities), predicates, and depth

Examples

kgShortestPath("Trapezius", "External Occipital Protuberance")

---

Link a clinical instrument to its ICF categories

Description

Like [tagICF()] but returns a data frame with the ICF code and its title, suitable for annotating a clinical outcome measure.

Usage

linkInstrumentToICF(instrument_id, hub = NULL)

Arguments

instrument_id	A clinical instrument identifier (e.g. "berg", "fma_ue").
hub	Optional PhysioAnnotationHub.

Value

A data frame with instrument_id, icf_code, icf_title (zero rows, with a warning, if unmapped).

See Also

[tagICF()]

Examples

linkInstrumentToICF("berg")

---

Load the PhysioAnnotationHub

Description

Loads all annotation data into a cached environment for fast repeated queries.

Usage

loadAnnotationHub(reload = FALSE)

Arguments

reload

Logical; force reload even if cached (default FALSE)

Value

An AnnotationHub object (list) with muscle, bone, nerve, kg, clinical data

Examples

hub <- loadAnnotationHub()
hub

---

Print method for PhysioAnnotationHub

Description

Print method for PhysioAnnotationHub

Usage

## S3 method for class 'PhysioAnnotationHub'
print(x, ...)

Arguments

x	A PhysioAnnotationHub object
...	Additional arguments (ignored)

Value

Invisibly returns x

---

Query the Knowledge Graph by triple pattern

Description

Query the Knowledge Graph by triple pattern

Usage

queryKG(
  subject = NULL,
  predicate = NULL,
  object = NULL,
  hub = NULL,
  exact = FALSE
)

Arguments

subject	Character or NULL; entity name pattern (grep)
predicate	Character or NULL; relation type (exact or grep)
object	Character or NULL; target entity pattern (grep)
hub	AnnotationHub object (loaded if NULL)
exact	Logical; use exact matching instead of grep (default FALSE)

Value

data.frame of matching triples

Examples

# All triples with Trapezius as the subject:
head(queryKG(subject = "Trapezius"))

---

Tag a metric or instrument with ICF categories

Description

Returns the WHO ICF category codes linked to a physiological metric or clinical instrument, using the packaged metric-to-ICF map (built with the Cieza 2005 ICF linking rules). Matching is case-insensitive.

Usage

tagICF(metric, hub = NULL)

Arguments

metric	A metric / instrument identifier (e.g. "gait_speed", "FMA_UE", "HRV").
hub	Optional PhysioAnnotationHub (loaded on demand otherwise).

Value

A character vector of ICF codes (empty, with a warning, if unmapped).

References

WHO ICF; Cieza et al. 2005 (ICF linking rules).

See Also

[linkInstrumentToICF()], [getCoreSet()], [icfCategories()]

Examples

tagICF("gait_speed")
tagICF("FMA_UE")

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