reindexCohortsByDays {CohortAlgebra}

Reindex cohort(s) by relative days

Description

reindexCohort changes the cohort_start_date and/or cohort_end_date of one or more source cohorts based on a set of reindexing rules. The output is a one or more valid target cohorts.

Usage

reindexCohortsByDays(
  connectionDetails = NULL,
  connection = NULL,
  sourceCohortDatabaseSchema = NULL,
  sourceCohortTable = "cohort",
  sourceCohortIds,
  targetCohortDatabaseSchema = NULL,
  targetCohortTable,
  offsetStartAnchor = "cohort_start_date",
  offsetEndAnchor = "cohort_end_date",
  reindexRules,
  cdmDatabaseSchema = NULL,
  purgeConflicts = FALSE,
  isTempTable = FALSE,
  bulkLoad = Sys.getenv("DATABASE_CONNECTOR_BULK_UPLOAD"),
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema")
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.

connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.

sourceCohortDatabaseSchema

Schema name where your source cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.

sourceCohortTable

The name of the source cohort table.

sourceCohortIds

An array of one or more cohortIds in the source cohort table.

targetCohortDatabaseSchema

Schema name where your target cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.

targetCohortTable

The name of the target cohort table.

offsetStartAnchor

Determines the anchor point for the start of the reindexing. It can be either cohort_start_date or cohort_end_date of sourceCohort.

offsetEndAnchor

Determines the anchor point for the end of the reindexing. It can be either cohort_start_date or cohort_end_date of targetCohort.

reindexRules

A data frame specifying the reindexing rules. It should contain the following columns: 'offsetId' a unique key for identifying the newly generated cohorts. Each offsetId corresponds to a specific reindex rule and will be used to create new cohort id in targetCohort. 'offsetStartValue' is an integer value indicating the number of days to 'offsetStartAnchor'. A positive values will extend, while negative values will shorten the start date from the 'offsetStartAnchor'. offsetEndValue' An integer value indicating the number of days to offset the end date. Positive values will extend, while negative values will shorten the end date from the 'offsetEndAnchor'.

cdmDatabaseSchema

Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.

purgeConflicts

If there are conflicts in the target cohort table i.e. the target cohort table already has records with newCohortId, do you want to purge and replace them with transformed. By default - it will not be replaced, and an error message is thrown.

isTempTable

Is the output a temp table. If yes, a new temp table is created. This will required an active connection. Any old temp table is dropped and replaced.

bulkLoad

See 'insertTable' function in 'DatabaseConnector'.

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

If output is temp table, then the name of the temp table is returned.