assessPhenotypes: Assess propensity models

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

Assess propensity models

Description

Assess propensity models

Usage

assessPhenotypes(
  connectionDetails,
  cdmDatabaseSchema,
  vocabularyDatabaseSchema = cdmDatabaseSchema,
  cohortDatabaseSchema,
  tablePrefix = "legend_t2dm",
  indicationId = "class",
  oracleTempSchema,
  outputFolder,
  sampleSize = 1e+05,
  minCellCount = 5,
  databaseId,
  databaseName = databaseId,
  databaseDescription = databaseId,
  createExposureCohorts = TRUE,
  runExposureCohortDiagnostics = TRUE,
  createOutcomeCohorts = TRUE,
  runOutcomeCohortDiagnostics = TRUE,
  filterExposureCohorts = NULL,
  filterOutcomeCohorts = NULL
)

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'.
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'.
tablePrefix	A prefix to be used for all table names created for this study.
indicationId	A string denoting the indicationId for which the exposure cohorts should be created; should be 'class' or 'drug'
oracleTempSchema	Should be used in Oracle to specify a schema where the user has write priviliges for storing temporary tables.
outputFolder	Name of local folder to place results; make sure to use forward slashes (/)
sampleSize	What is the maximum sample size across exposure cohorts?
minCellCount	The minimum cell count for fields contains person counts or fractions.
databaseId	A short string for identifying the database (e.g. 'Synpuf').
databaseName	Full name for the database.
databaseDescription	Brief description of population in database
createExposureCohorts	Boolean: execute exposure cohort instantiation? FALSE will attempt to re-use the cohort table in cohortDatabaseSchema
runExposureCohortDiagnostics	Boolean: execute cohort diagnostics on exposure cohorts?
createOutcomeCohorts	Boolean: execute outcome cohort instantiation? FALSE will attempt to re-use the cohort table in cohortDatabaseSchema
runOutcomeCohortDiagnostics	Boolean: execute cohort diagnostics on outcome cohorts?
filterExposureCohorts	Optional subset of exposure cohorts to use; NULL implies all.
filterOutcomeCohorts	Options subset of outcome cohorts to use; NULL implies all.

Details

This function will sample the exposure cohorts, and fit propensity models to identify issues. Assumes the exposure and outcome cohorts have already been created.

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