execute: Execute OHDSI LEGEND study

Description Usage Arguments Details

View source: R/Main.R

Description

Execute OHDSI LEGEND study

Usage

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execute(connectionDetails, cdmDatabaseSchema, oracleTempSchema,
  cohortDatabaseSchema, outputFolder, indicationId = "Depression",
  tablePrefix = "legend", databaseId = "Unknown",
  databaseName = "Unknown", databaseDescription = "Unknown",
  minCellCount = 5, imputeExposureLengthWhenMissing = FALSE,
  createExposureCohorts = TRUE, createOutcomeCohorts = TRUE,
  fetchAllDataFromServer = TRUE, synthesizePositiveControls = TRUE,
  generateAllCohortMethodDataObjects = TRUE, runCohortMethod = TRUE,
  computeIncidence = TRUE, fetchChronographData = TRUE,
  computeCovariateBalance = TRUE, exportToCsv = TRUE, 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'.

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 PanTher: impute length of drug exposures when the length is missing?

createExposureCohorts

Create the tables with the exposure cohorts?

createOutcomeCohorts

Create the tables with the outcome cohorts?

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?

computeIncidence

Compute incidence rates?

fetchChronographData

Fetch the data for constructing chronographs?

computeCovariateBalance

Compute covariate balance?

exportToCsv

Export all results to CSV files?

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/Legend documentation built on Dec. 29, 2020, 3:52 a.m.