CohortDef R6 Class

CohortDef R6 Class

CohortDef R6 Class

Details

An R6 class that stores key information about CIRCE cohorts that need to be generated for a study.

The CohortDef class manages cohort metadata and SQL generation. Upon initialization, it loads and validates cohort definitions from either JSON (CIRCE format) or SQL files, and creates a hash to uniquely identify the generated SQL.

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 label.

Methods

Public methods

• CohortDef$new()

• CohortDef$getFilePath()

• CohortDef$getSql()

• CohortDef$getHash()

• CohortDef$getId()

• CohortDef$setId()

• CohortDef$formatTagsAsString()

• CohortDef$getCohortType()

• CohortDef$setCohortType()

• CohortDef$getDependencies()

• CohortDef$setDependencies()

• CohortDef$getDependencyHash()

• CohortDef$setDependencyHash()

• CohortDef$clone()

---

Method new()

Initialize a new CohortDef

Usage

CohortDef$new(label, tags = list(), filePath)

Arguments

label

Character. The common name of the cohort.

tags

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

filePath

Character. Path to the cohort file in inputs/cohorts folder (can be .json or .sql). Get the file path

---

Method getFilePath()

Usage

CohortDef$getFilePath()

Returns

Character. Relative path to the cohort file. Get the generated SQL

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Method getSql()

Usage

CohortDef$getSql()

Returns

Character. The SQL definition of the cohort. Get the SQL hash

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Method getHash()

Usage

CohortDef$getHash()

Returns

Character. MD5 hash of the current SQL definition. Get the cohort ID

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Method getId()

Usage

CohortDef$getId()

Returns

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

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Method setId()

Usage

CohortDef$setId(id)

Arguments

id

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

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Method formatTagsAsString()

Usage

CohortDef$formatTagsAsString()

Returns

Character. Tags formatted as "name: value | name: value". Get the cohort type

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Method getCohortType()

Usage

CohortDef$getCohortType()

Returns

Character. One of 'source', 'subset', 'union', 'complement'. Default: 'source'. Set the cohort type (internal use)

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Method setCohortType()

Usage

CohortDef$setCohortType(cohortType)

Arguments

cohortType

Character. One of 'circe', 'subset', 'union', 'complement'. Get dependency information

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Method getDependencies()

Usage

CohortDef$getDependencies()

Returns

List with elements: cohort_ids (integer vector), rule (list of parameters). Set dependency information (internal use)

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Method setDependencies()

Usage

CohortDef$setDependencies(dependsOnCohortIds, dependencyRule)

Arguments

dependsOnCohortIds

Integer vector of parent cohort IDs.

dependencyRule

List of dependency parameters. Get the dependency hash

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Method getDependencyHash()

Usage

CohortDef$getDependencyHash()

Returns

Character. Hash of dependencies for change detection, or NULL if none. Set the dependency hash (internal use)

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Method setDependencyHash()

Usage

CohortDef$setDependencyHash(depHash)

Arguments

depHash

Character. Hash to set.

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Method clone()

The objects of this class are cloneable with this method.

Usage

CohortDef$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.