Extract the outcome cohorts and where they are used in the analyses.

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

Usage

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

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')
targetId: An integer corresponding to the target cohort ID
getIncidenceInclusion: Whether to check usage of the cohort in incidence
getCharacterizationInclusion: Whether to check usage of the cohort in characterization
getPredictionInclusion: Whether to check usage of the cohort in prediction
getCohortMethodInclusion: Whether to check usage of the cohort in cohort method
getSccsInclusion: Whether to check usage of the cohort in SCCS
printTimes: whether to print the time it takes to run each SQL query

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
numDatabase number of databases with the cohort
databaseString all the names of the databases with the cohort
databaseIdString all the ids of the databases with the cohort
databaseStringCount all the names of the databases with the cohort plus their counts
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
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

Details

Specify the connectionHandler, the schema and the table prefixes

Examples

conDet <- getExampleConnectionDetails()

connectionHandler <- ResultModelManager::ConnectionHandler$new(conDet)
#> Connecting using SQLite driver

outcomeTable <- getOutcomeTable(
  connectionHandler = connectionHandler, 
  schema = 'main'
)
#> [1] "Extracting characterization outcomes took: 0.0684528350830078 secs"
#> [1] "-- Total time for extarcting outcome table: 0.219591617584229 secs"