OhdsiReportGenerator (version 2.0.2)

getTargetTable: Extract the target cohorts and where they are used in the analyses.

Description

This function extracts the target cohorts, the number of subjects/entries and where the cohort was used.

Usage

getTargetTable(
  connectionHandler,
  schema,
  cgTablePrefix = "cg_",
  cTablePrefix = "c_",
  ciTablePrefix = "ci_",
  cmTablePrefix = "cm_",
  sccsTablePrefix = "sccs_",
  plpTablePrefix = "plp_",
  databaseTable = "database_meta_data",
  getIncidenceInclusion = TRUE,
  getCharacterizationInclusion = TRUE,
  getPredictionInclusion = TRUE,
  getCohortMethodInclusion = TRUE,
  getSccsInclusion = TRUE,
  printTimes = FALSE
)

Value

Returns a data.frame with the columns:

• cohortId the number id for the target cohort

• cohortName the name of the cohort

• subsetParent the number id of the parent cohort

• subsetDefinitionId the number id of the subset

• subsetDefinitionJson the json of the subset

• subsetCohortIds the ids of any cohorts that are restricted to by the subset logic

• numDatabase number of databases with the cohort

• databaseString all the names of the databases with the cohort

• databaseCount all the names of the databases with the cohort and their sizes

• minSubjectCount number of subjects in databases with lowest count

• maxSubjectCount number of subjects in databases with highest count

• minEntryCount number of entries in databases with lowest count

• maxEntryCount number of entries in databases with highest count

• cohortIncidence whether the cohort was used in cohort incidence

• databaseComparator whether the cohort was used in database comparator

• cohortComparator whether the cohort was used in cohort comparator

• dechalRechal whether the cohort was used in dechallenge rechallenge

• riskFactors whether the cohort was used in risk factors

• caseSeries whether the cohort was used in case series analysis

• timeToEvent whether the cohort was used in time to event

• prediction whether the cohort was used in prediction

• cohortMethod whether the cohort was used in cohort method

• selfControlledCaseSeries whether the cohort was used in self controlled case series

Arguments

connectionHandler

A connection handler that connects to the database and extracts sql queries. Create a connection handler via `ResultModelManager::ConnectionHandler$new()`.

schema

The result database schema (e.g., 'main' for sqlite)

cgTablePrefix

The prefix used for the cohort generator results tables

cTablePrefix

The prefix used for the characterization results tables

ciTablePrefix

The prefix used for the cohort incidence results tables

cmTablePrefix

The prefix used for the cohort method results tables

sccsTablePrefix

The prefix used for the cohort generator results tables

plpTablePrefix

The prefix used for the patient level prediction results tables

databaseTable

The name of the table with the database details (default 'database_meta_data')

getIncidenceInclusion

Whether to check useage of the cohort in incidence

getCharacterizationInclusion

Whether to check useage of the cohort in characterization

getPredictionInclusion

Whether to check useage of the cohort in prediction

getCohortMethodInclusion

Whether to check useage of the cohort in cohort method

getSccsInclusion

Whether to check useage of the cohort in SCCS

printTimes

Whether to print how long each query took

Details

Specify the connectionHandler, the schema and the table prefixes

See Also

Other helper: addTarColumn(), formatBinaryCovariateName(), getExampleConnectionDetails(), getOutcomeTable(), kableDark(), printReactable(), removeSpaces()

Examples

conDet <- getExampleConnectionDetails()

connectionHandler <- ResultModelManager::ConnectionHandler$new(conDet)

targetTable <- getTargetTable(
  connectionHandler = connectionHandler, 
  schema = 'main'
)