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,
tempEmulationSchema = NULL
)Arguments
- connectionDetails
An R object of type
connectionDetailscreated using the functioncreateConnectionDetailsin theDatabaseConnectorpackage. Either theconnectionorconnectionDetailsargument should be specified.- connection
A connection to the server containing the schema as created using the
connectfunction in theDatabaseConnectorpackage. Either theconnectionorconnectionDetailsargument should be specified.- oracleTempSchema
DEPRECATED: use
tempEmulationSchemainstead.- 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
covariateSettingsas 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.
- tempEmulationSchema
Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
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()
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,
tempEmulationSchema = 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 1.38 secs
#> Fetching data from server
#> Fetching data took 0.0882 secs
# }