Constructs the set of covariates for one or more cohorts using data in the CDM schema. This implements the covariates typically used in the HDPS algorithm.
getDbHdpsCovariateData(connection, oracleTempSchema = NULL, cdmDatabaseSchema, cohortTable = "cohort_person", cohortId = -1, cdmVersion = "5", rowIdField = "subject_id", covariateSettings, aggregated = FALSE)
A connection to the server containing the schema as created using the
A schema where temp tables can be created in Oracle.
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'.
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'.
For which cohort ID should covariates be constructed? If set to -1, covariates will be constructed for all cohorts in the specified cohort table.
The version of the Common Data Model used. Currently only
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.
An object of type
Should aggregate statistics be computed instead of covariates per cohort entry?
Returns an object of type
covariateData, 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:
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.
An ffdf object describing the covariates that have been extracted.
A list of objects with information on how the covariateData object was constructed.
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.