Learn R Programming
omophub (version 1.4.0)

VocabulariesResource: Vocabularies Resource

Description

R6 class providing access to vocabulary operations.

Arguments

Value

Paginated vocabulary list.

Vocabulary details including vocabulary_id, vocabulary_name, vocabulary_reference, vocabulary_version, vocabulary_concept_id.

Vocabulary statistics.

Domain statistics including concept counts and class breakdown.

List of all available domains with domain_id, domain_name, and description.

List of all available concept classes with concept_class_id, concept_class_name, and concept_class_concept_id.

Paginated concepts.

Methods

Method new()

Create a new VocabulariesResource.

Usage

VocabulariesResource$new(base_req)

Arguments

base_req

Base httr2 request object.

Method list()

List all vocabularies.

Usage

VocabulariesResource$list(
  include_stats = FALSE,
  include_inactive = FALSE,
  sort_by = "name",
  sort_order = "asc",
  page = 1,
  page_size = 100
)

Arguments

include_stats

Include vocabulary statistics. Default FALSE.

include_inactive

Include inactive vocabularies. Default FALSE.

sort_by

Sort field ("name", "priority", "updated"). Default "name".

sort_order

Sort order ("asc" or "desc"). Default "asc".

page

Page number. Default 1.

page_size

Results per page. Default 100.

Method get()

Get vocabulary details.

Usage

VocabulariesResource$get(vocabulary_id)

Arguments

vocabulary_id

The vocabulary ID.

Method stats()

Get vocabulary statistics.

Usage

VocabulariesResource$stats(vocabulary_id)

Arguments

vocabulary_id

The vocabulary ID.

Method domain_stats()

Get statistics for a specific domain within a vocabulary.

Usage

VocabulariesResource$domain_stats(vocabulary_id, domain_id)

Arguments

vocabulary_id

The vocabulary ID (e.g., "SNOMED", "ICD10CM").

domain_id

The domain ID (e.g., "Condition", "Drug", "Procedure").

Method domains()

Get all standard OHDSI domains.

Usage

VocabulariesResource$domains()

Method concept_classes()

Get all concept classes.

Usage

VocabulariesResource$concept_classes()

Method concepts()

Get concepts in a vocabulary.

Usage

VocabulariesResource$concepts(
  vocabulary_id,
  search = NULL,
  standard_concept = "all",
  include_invalid = FALSE,
  include_relationships = FALSE,
  include_synonyms = FALSE,
  sort_by = "name",
  sort_order = "asc",
  page = 1,
  page_size = 20
)

Arguments

vocabulary_id

The vocabulary ID.

search

Search term to filter concepts by name or code.

standard_concept

Filter by standard concept status ('S', 'C', 'all'). Default "all".

include_invalid

Include invalid or deprecated concepts. Default FALSE.

include_relationships

Include concept relationships. Default FALSE.

include_synonyms

Include concept synonyms. Default FALSE.

sort_by

Sort field ('name', 'concept_id', 'concept_code'). Default "name".

sort_order

Sort order ('asc' or 'desc'). Default "asc".

page

Page number. Default 1.

page_size

Results per page (max 1000). Default 20.

Method print()

Print resource information.

Usage

VocabulariesResource$print()

Method clone()

The objects of this class are cloneable with this method.

Usage

VocabulariesResource$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.