Get default covariate information from the database
Source:R/GetDefaultCovariates.R
getDbDefaultCovariateData.RdConstructs a large default set of covariates for one or more cohorts using data in the CDM schema. Includes covariates for all drugs, drug classes, condition, condition classes, procedures, observations, etc.
getDbDefaultCovariateData(
connection,
oracleTempSchema = NULL,
cdmDatabaseSchema,
cohortTable = "#cohort_person",
cohortId = -1,
cohortIds = c(-1),
cdmVersion = "5",
rowIdField = "subject_id",
covariateSettings,
targetDatabaseSchema,
targetCovariateTable,
targetCovariateRefTable,
targetAnalysisRefTable,
aggregated = FALSE,
minCharacterizationMean = 0
)Arguments
- connection
A connection to the server containing the schema as created using the
connectfunction in theDatabaseConnectorpackage.- 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
DEPRECATED:For which cohort ID 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.
- 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
Either an object of type
covariateSettingsas created using one of the createCovariate functions, or a list of such objects.- targetDatabaseSchema
(Optional) The name of the database schema where the resulting covariates should be stored.
- targetCovariateTable
(Optional) The name of the table where the resulting covariates will be stored. If not provided, results will be fetched to R. The table can be a permanent table in the
targetDatabaseSchemaor a temp table. If it is a temp table, do not specifytargetDatabaseSchema.- targetCovariateRefTable
(Optional) The name of the table where the covariate reference will be stored.
- targetAnalysisRefTable
(Optional) The name of the table where the analysis reference will be stored.
- aggregated
Should aggregate statistics be computed instead of covariates per cohort entry?
- minCharacterizationMean
The minimum mean value for binary 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, which is an Andromeda object containing information on the baseline covariates.
Information about multiple outcomes can be captured at once for efficiency reasons. This object is
a list with the following components:
- covariates
An ffdf object listing the baseline covariates per person in the cohorts. This is done using a sparse representation: covariates with a value of 0 are omitted to save space. The covariates object will have three columns: rowId, covariateId, and covariateValue. The rowId is usually equal to the person_id, unless specified otherwise in the rowIdField argument.
- covariateRef
A table describing the covariates that have been extracted.
. The CovariateData object will also have a metaData attribute, a list of objects with
information on how the covariateData object was constructed.
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 temp 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. Typically, users don't call this
function directly but rather use the getDbCovariateData function instead.
Examples
# \donttest{
connectionDetails <- 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
Eunomia::createCohorts(
connectionDetails = connectionDetails,
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
connection <- DatabaseConnector::connect(connectionDetails)
#> Connecting using SQLite driver
results <- getDbDefaultCovariateData(
connection = connection,
cdmDatabaseSchema = "main",
cohortTable = "cohort",
covariateSettings = createDefaultCovariateSettings(),
targetDatabaseSchema = "main",
targetCovariateTable = "ut_cov"
)
#> Constructing features on server
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#> Executing SQL took 1.34 secs
#> Writing data to table
#> Writing data took0.015 secs
# }