Description Usage Arguments Details
Execute OHDSI LEGEND study
1 2 3 4 5 6 7 8 9 10 | 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)
|
connectionDetails |
An object of type |
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. |
This function executes the OHDSI LEGEND study.
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