getNotenlpCovariateData: getNotenlpCovariateData

In mi-erasmusmc/Triton: Generating Text Representation Features for a Cohort in the OMOP CDM

Description

This covariate builder creates text representation (Triton) covariates from a cohort in the OMOP cdm

Usage

getNotenlpCovariateData(
  connection,
  oracleTempSchema = NULL,
  cdmDatabaseSchema,
  cohortTable,
  cohortId,
  cdmVersion = "5",
  rowIdField,
  covariateSettings,
  aggregated = FALSE
)

Arguments

connection	A connection to the server containing the schema as created using the connect function in the DatabaseConnector package.
oracleTempSchema	A schema where temp tables can be created in Oracle.
cdmDatabaseSchema	The name of the database schema that contains the OMOP CDM instance. Requires read permissions to this database. On SQL Server, this should specifiy both the database and the schema, so for example 'cdm_instance.dbo'.
cohortTable	Name of the table holding the cohort for which we want to construct covariates. If it is a temp table, the name should have a hash prefix, e.g. '#temp_table'. If it is a non-temp table, it should include the database schema, e.g. 'cdm_database.cohort'.
cohortId	For which cohort ID should covariates be constructed? If set to -1, covariates will be constructed for all cohorts in the specified cohort table.
cdmVersion	The version of the Common Data Model used. Currently only cdmVersion = "5" is supported.
rowIdField	The name of the field in the cohort temp table that is to be used as the row_id field in the output table. This can be especially usefull if there is more than one period per person.
covariateSettings	An object of type covariateSettings as created using the createTextRepCovariateSettings function.
aggregated	Should aggregate statistics be computed instead of covariates per cohort entry?

Value

a covariateData object that can be used my other cdm framework functions.

mi-erasmusmc/Triton documentation built on Feb. 15, 2022, 10:37 a.m.