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Class for automating the creation of bulk cohorts

Source: R/TemplateCohorts.R
CohortTemplateDefinition.Rd

Class for automating the creation of bulk cohorts

Class for automating the creation of bulk cohorts

Details

This class provides a framework for automating the creation of bulk cohorts by defining template SQL queries and associated callbacks to execute them. This is useful when defining lots of exposure or outcomes for cohorts that are very general in nature. For example, all RxNorm ingredient cohorts, all ATC ingredient cohorts or all SNOMED condition occurrences with > x diagnosis codes.

These cohorts can then be subsetted with common cohort subset operations such as limiting to specific age, gender, or observation criteria, should this be excluded from the cohort definition. However, when applying operations in bulk it may be more efficient to include such definitions within the template sql itself.

This approach is also useful for cohorts that can not based on ATLAS/CirceDefinitions alone.

CURRENTLY NOT SUPPORTED: * Saving definitions that use runtime arguments on a per cdm basis. This creates a challenge for running the same cohort across different databases. Furthermore, saving information within the CDM schema in a shared OHDSI study is not desirable.

Active bindings

name

name for this template definition that describes the cohorts it creation

sqlArgs

optional arguments for sql

templateSql

sql template

translateSql

translate the sql for different platforms

references

data.frame of name/id references for cohort template that aligns with cohort set

Methods

Public methods

Method new()

Usage

CohortTemplateDefinition$new(settings)

Arguments

settings

Settings of object to load seealso createCohortTemplateDefinition To alter the execution, override this function in a subclass. This translates and executes the sql of the cohort definition Note that calling this function will generate the cohorts but will not do so in an incremental manner. Checksums and timestamps will, however, be added to the generation table ever want to call this function outside of a testing environment. It is best practice to always use the standard runCohortGeneration/generateCohortSet pipeline to ensure validity of execution steps.

Method executeTemplateSql()

Usage

CohortTemplateDefinition$executeTemplateSql(
  connection,
  cohortDatabaseSchema,
  cdmDatabaseSchema,
  cohortTableNames,
  vocabularyDatabaseSchema = cdmDatabaseSchema,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema")
)

Arguments

connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.

cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.

cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.

cdmDatabaseSchema

Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.

cohortTableNames

The names of the cohort tables. See getCohortTableNames for more details.

vocabularyDatabaseSchema

vocabulary database schema

tempEmulationSchema

cdm temp emulation schema get template references data.frame

Method getTemplateReferences()

Returns data.frame of references get the name of the definition

Usage

CohortTemplateDefinition$getTemplateReferences()

Method getName()

Name field get the generated id of the template definition

Usage

CohortTemplateDefinition$getName()

Method getId()

this is not the cohort ids and is based off of the checksum of the template definition get checksum

Usage

CohortTemplateDefinition$getId()

Method getChecksum()

Get the hash of the definition (generated when class is instantiated) to list

Usage

CohortTemplateDefinition$getChecksum()

Method toList()

Used for serializing the definition to json

Usage

CohortTemplateDefinition$toList()

Method toJson()

json serialized form of the template definition save to disk

Usage

CohortTemplateDefinition$toJson()

Method saveTemplate()

Save object to specified json path

Usage

CohortTemplateDefinition$saveTemplate(filePath)

Arguments

filePath

File path to save json serialized from

Method clone()

The objects of this class are cloneable with this method.

Usage

CohortTemplateDefinition$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.