runCohortTimeSeriesDiagnostics: Given a set of instantiated cohorts get time series for the...
In OHDSI/StudyDiagnostics: Diagnostics for OHDSI Cohorts

runCohortTimeSeriesDiagnostics

R Documentation

Given a set of instantiated cohorts get time series for the cohorts.

Description

This function first generates a calendar period table, that has calendar intervals between the timeSeriesMinDate and timeSeriesMaxDate. Calendar Month, Quarter and year are supported. For each of the calendar interval, time series data are computed. The returned object is a R dataframe that will need to be converted to a time series object to perform time series analysis.

Data Source time series: computes time series at the data source level i.e. observation period table. This output is NOT limited to individuals in the cohort table but is for ALL people in the datasource (i.e. present in observation period table)

Usage

runCohortTimeSeriesDiagnostics(
  connectionDetails = NULL,
  connection = NULL,
  tempEmulationSchema = NULL,
  cdmDatabaseSchema,
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTable = "cohort",
  runCohortTimeSeries = TRUE,
  runDataSourceTimeSeries = FALSE,
  timeSeriesMinDate = as.Date("1980-01-01"),
  timeSeriesMaxDate = as.Date(Sys.Date()),
  stratifyByGender = TRUE,
  stratifyByAgeGroup = TRUE,
  cohortIds = NULL
)

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.
`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.
`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'.
`cohortDatabaseSchema`	Schema name where your cohort table resides. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.
`cohortTable`	Name of the cohort table.
`runCohortTimeSeries`	Generate and export the cohort level time series?
`runDataSourceTimeSeries`	Generate and export the Data source level time series? i.e. using all persons found in observation period table.
`timeSeriesMinDate`	(optional) Minimum date for time series. Default value January 1st 1980.
`timeSeriesMaxDate`	(optional) Maximum date for time series. Default value System date.
`stratifyByGender`	Do you want to stratify by Gender
`stratifyByAgeGroup`	Do you want to stratify by Age group
`cohortIds`	A vector of one or more Cohort Ids to compute time distribution for.