ConceptSetDef R6 Class

ConceptSetDef R6 Class

ConceptSetDef R6 Class

Details

An R6 class that stores key information about OHDSI CIRCE concept sets that need to be managed in a study.

The ConceptSetDef class manages concept set metadata, JSON definitions, and domain information. Upon initialization, it loads and validates concept set definitions from CIRCE JSON files, creates a hash to uniquely identify the generated JSON, and stores domain and source concept information.

Active bindings

label

character to set the label to. If missing, returns the current label.

tags

list of the values to set the tags to. If missing, returns the current tags.

Methods

Public methods

• ConceptSetDef$new()

• ConceptSetDef$getFilePath()

• ConceptSetDef$getJson()

• ConceptSetDef$getHash()

• ConceptSetDef$getId()

• ConceptSetDef$setId()

• ConceptSetDef$formatTagsAsString()

• ConceptSetDef$clone()

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Method new()

Initialize a new ConceptSetDef

Usage

ConceptSetDef$new(label, tags = list(), filePath, domain = "init")

Arguments

label

Character. The common name of the concept set.

tags

List. A named list of tags that give metadata about the concept set.

filePath

Character. Path to the concept set JSON file in inputs/conceptSet folder.

domain

Character. The OMOP CDM clinical domain for this concept set. Valid values: "drug_exposure", "condition_occurrence", "measurement", "procedure", "observation", "device_exposure", "visit_occurrence", "init". Get the file path

sourceCode

Logical. Whether the concept set uses source concepts (TRUE) or standard concepts (FALSE).

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Method getFilePath()

Usage

ConceptSetDef$getFilePath()

Returns

Character. Relative path to the concept set file. Get the concept set JSON

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Method getJson()

Usage

ConceptSetDef$getJson()

Returns

Character. The JSON definition of the concept set. Get the JSON hash

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Method getHash()

Usage

ConceptSetDef$getHash()

Returns

Character. MD5 hash of the current JSON definition. Get the concept set ID

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Method getId()

Usage

ConceptSetDef$getId()

Returns

Integer. The concept set ID, or NA_integer_ if not set. Set the concept set ID (internal use)

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Method setId()

Usage

ConceptSetDef$setId(id)

Arguments

id

Integer. The concept set ID to set. Format tags as string

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Method formatTagsAsString()

Usage

ConceptSetDef$formatTagsAsString()

Returns

Character. Tags formatted as "name: value | name: value".

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Method clone()

The objects of this class are cloneable with this method.

Usage

ConceptSetDef$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.