executePhenotyeLibraryDiagnostics: Execute the cohort diagnostics

In ohdsi-studies/PhenotypeLibraryDiagnostics: Generating Cohort Diagnostics for the OHDSI Phenotype Library

Execute the cohort diagnostics

Description

Execute the cohort diagnostics

Usage

executePhenotyeLibraryDiagnostics(
  connectionDetails,
  cdmDatabaseSchema,
  vocabularyDatabaseSchema = cdmDatabaseSchema,
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTable = "cohort",
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  verifyDependencies = TRUE,
  outputFolder,
  cohortIds = NULL,
  incrementalFolder = file.path(outputFolder, "incrementalFolder"),
  databaseId = "Unknown",
  databaseName = databaseId,
  databaseDescription = databaseId,
  extraLog = 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 OMOP vocabulary data resides. This is commonly the same as cdmDatabaseSchema. Note that for SQL Server, this should include both the database and schema name, for example 'vocabulary.dbo'.
cohortDatabaseSchema	Schema name where intermediate data can be stored. You will need to have write privileges in this schema. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
cohortTable	The name of the table that will be created in the work database schema. This table will hold the exposure and outcome cohorts used in this study.
tempEmulationSchema	Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
verifyDependencies	Check whether correct package versions are installed?
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.
cohortIds	An optional parameter to filter the cohortIds in OHDSI Phenotype library to run. By Default all cohorts will be run.
incrementalFolder	Name of local folder to hold the logs for incremental run; make sure to use forward slashes (/). Do not use a folder on a network drive since this greatly impacts performance.
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.
extraLog	Do you want to add anything extra into the log?

Details

This function executes the cohort diagnostics.

ohdsi-studies/PhenotypeLibraryDiagnostics documentation built on Oct. 24, 2023, 7:29 p.m.