execute: Execute OHDSI LEGEND study

In ohdsi-studies/LegendT2dm: Large-Scale Evidence Generation and Evaluation in a Network of Databases

Execute OHDSI LEGEND study

Description

Execute OHDSI LEGEND study

Usage

execute(
  connectionDetails,
  cdmDatabaseSchema,
  vocabularyDatabaseSchema = cdmDatabaseSchema,
  oracleTempSchema,
  cohortDatabaseSchema,
  outputFolder,
  indicationId = "class",
  tablePrefix = "legendt2dm",
  databaseId = "Unknown",
  databaseName = "Unknown",
  databaseDescription = "Unknown",
  minCohortSize = 1000,
  minCellCount = 5,
  imputeExposureLengthWhenMissing = FALSE,
  studyEndDate = "",
  createExposureCohorts = TRUE,
  createOutcomeCohorts = TRUE,
  createPairedExposureSummary = TRUE,
  fetchAllDataFromServer = TRUE,
  synthesizePositiveControls = FALSE,
  generateAllCohortMethodDataObjects = TRUE,
  runCohortMethod = TRUE,
  runSections = c(1:7),
  computeCovariateBalance = TRUE,
  exportToCsv = TRUE,
  exportSettings = createExportSettings(),
  filterExposureCohorts = NULL,
  filterOutcomeCohorts = NULL,
  maxCores = 4
)

Arguments

connectionDetails	An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package.
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'.
vocabularyDatabaseSchema	Schema name where your vocabulary tables in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
oracleTempSchema	Should be used in Oracle to specify a schema where the user has write priviliges for storing temporary tables.
cohortDatabaseSchema	Schema name where intermediate data can be stored. You will need to have write priviliges in this schema. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
outputFolder	Name of local folder to place results; make sure to use forward slashes (/). Do not use a folder on a network drive since this greatly impacts performance.
indicationId	A string denoting the indicationId.
tablePrefix	A prefix to be used for all table names created for this study.
databaseId	A short string for identifying the database (e.g. 'Synpuf').
databaseName	The full name of the database (e.g. 'Medicare Claims Synthetic Public Use Files (SynPUFs)').
databaseDescription	A short description (several sentences) of the database.
minCellCount	The minimum cell count for fields contains person counts or fractions when exporting to CSV.
imputeExposureLengthWhenMissing	For OptumEHR: impute length of drug exposures when the length is missing?
studyEndDate	Optional study end date for EHRs
createExposureCohorts	Create the tables with the exposure cohorts?
createOutcomeCohorts	Create the tables with the outcome cohorts?
createPairedExposureSummary	Create local fils with paired exposure summary?
fetchAllDataFromServer	Fetch all relevant data from the server?
synthesizePositiveControls	Inject signals to create synthetic controls?
generateAllCohortMethodDataObjects	Create the cohortMethodData objects from the fetched data and injected signals?
runCohortMethod	Run the CohortMethod package to produce the outcome models?
runSections	Run specific sections through CohortMethod
computeCovariateBalance	Report covariate balance statistics across comparisons?
exportToCsv	Export all results to CSV files?
exportSettings	Settings to optionalize restuls export; see 'createExportSettings()'.
filterExposureCohorts	Optional subset of exposure cohorts to use; NULL implies all.
filterOutcomeCohorts	Options subset of outcome cohorts to use; NULL implies all.
maxCores	How many parallel cores should be used? If more cores are made available this can speed up the analyses.

Details

This function executes the OHDSI LEGEND study.

ohdsi-studies/LegendT2dm documentation built on July 4, 2025, 8:25 p.m.