Uses one or several covariate builder functions to construct covariates.

getDbCovariateData(
  connectionDetails = NULL,
  connection = NULL,
  oracleTempSchema = NULL,
  cdmDatabaseSchema,
  cdmVersion = "5",
  cohortTable = "cohort",
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTableIsTemp = FALSE,
  cohortId = -1,
  cohortIds = c(-1),
  rowIdField = "subject_id",
  covariateSettings,
  aggregated = FALSE,
  minCharacterizationMean = 0
)

Arguments

connectionDetails

An R object of type connectionDetails created using the function createConnectionDetails in the DatabaseConnector package. Either the connection or connectionDetails argument should be specified.

connection

A connection to the server containing the schema as created using the connect function in the DatabaseConnector package. Either the connection or connectionDetails argument should be specified.

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 specify both the database and the schema, so for example 'cdm_instance.dbo'.

cdmVersion

Define the OMOP CDM version used: currently supported is "5".

cohortTable

Name of the (temp) table holding the cohort for which we want to construct covariates

cohortDatabaseSchema

If the cohort table is not a temp table, specify the database schema where the cohort table can be found. On SQL Server, this should specify both the database and the schema, so for example 'cdm_instance.dbo'.

cohortTableIsTemp

Is the cohort table a temp table?

cohortId

DEPRECATED:For which cohort ID(s) should covariates be constructed? If set to -1, covariates will be constructed for all cohorts in the specified cohort table.

cohortIds

For which cohort ID(s) should covariates be constructed? If set to c(-1), covariates will be constructed for all cohorts in the specified cohort table.

rowIdField

The name of the field in the cohort 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

Either an object of type covariateSettings as created using one of the createCovariate functions, or a list of such objects.

aggregated

Should aggregate statistics be computed instead of covariates per cohort entry? If aggregated is set to FALSE, the results returned will be based on each subject_id and cohort_start_date in your cohort table. If your cohort contains multiple entries for the same subject_id (due to different cohort_start_date values), you must carefully set the rowIdField so you can identify the patients properly. See issue #229 for more discussion on this parameter.

minCharacterizationMean

The minimum mean value for characterization output. Values below this will be cut off from output. This will help reduce the file size of the characterization output, but will remove information on covariates that have very low values. The default is 0.

Value

Returns an object of type covariateData, containing information on the covariates.

Details

This function uses the data in the CDM to construct a large set of covariates for the provided cohort. The cohort is assumed to be in an existing table with these fields: 'subject_id', 'cohort_definition_id', 'cohort_start_date'. Optionally, an extra field can be added containing the unique identifier that will be used as rowID in the output.

Examples

# \donttest{
eunomiaConnectionDetails <- Eunomia::getEunomiaConnectionDetails()
#> attempting to download GiBleed
#> attempting to extract and load: /Users/ginberg/Data/eunomia/GiBleed_5.3.zip to: /Users/ginberg/Data/eunomia/GiBleed_5.3.sqlite
covSettings <- createDefaultCovariateSettings()
Eunomia::createCohorts(
  connectionDetails = eunomiaConnectionDetails,
  cdmDatabaseSchema = "main",
  cohortDatabaseSchema = "main",
  cohortTable = "cohort"
)
#> Cohorts created in table main.cohort
#>   cohortId       name
#> 1        1  Celecoxib
#> 2        2 Diclofenac
#> 3        3    GiBleed
#> 4        4     NSAIDs
#>                                                                                        description
#> 1    A simplified cohort definition for new users of celecoxib, designed specifically for Eunomia.
#> 2    A simplified cohort definition for new users ofdiclofenac, designed specifically for Eunomia.
#> 3 A simplified cohort definition for gastrointestinal bleeding, designed specifically for Eunomia.
#> 4       A simplified cohort definition for new users of NSAIDs, designed specifically for Eunomia.
#>   count
#> 1  1844
#> 2   850
#> 3   479
#> 4  2694
covData <- getDbCovariateData(
  connectionDetails = eunomiaConnectionDetails,
  oracleTempSchema = NULL,
  cdmDatabaseSchema = "main",
  cdmVersion = "5",
  cohortTable = "cohort",
  cohortDatabaseSchema = "main",
  cohortTableIsTemp = FALSE,
  cohortIds = -1,
  rowIdField = "subject_id",
  covariateSettings = covSettings,
  aggregated = FALSE
)
#> Connecting using SQLite driver
#> Constructing features on server
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#> Executing SQL took 1.36 secs
#> Fetching data from server
#> Fetching data took 0.0831 secs
# }