runPheValuatorAnalyses: Run a list of analyses
In OHDSI/PheValuator: Rapid Phenotype Evaluation

runPheValuatorAnalyses

R Documentation

Run a list of analyses

Description

Run a list of analyses

Usage

runPheValuatorAnalyses(
  phenotype,
  cohortDefinitionSet = data.frame(),
  analysisName = "Main",
  runDateTime = format(Sys.time(), "%b %d %Y %X"),
  connectionDetails,
  oracleTempSchema = NULL,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  cdmDatabaseSchema,
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTable = "cohort",
  workDatabaseSchema = cdmDatabaseSchema,
  databaseId = cdmDatabaseSchema,
  cdmVersion = 5,
  outputFolder,
  priorModelToUse = NULL,
  pheValuatorAnalysisList
)

Arguments

`phenotype`	Name of the phenotype for analysis
`cohortDefinitionSet`	Data.frame of cohorts must include columns cohortId, cohortName, json, sql - should include all cohort definitions needed to replicate PheValuator analysis
`analysisName`	Name of the analysis
`runDateTime`	Starting date and time of the PheValuator run
`connectionDetails`	An R object of type `connectionDetails` created using the function `createConnectionDetails` in the `DatabaseConnector` package.
`oracleTempSchema`	DEPRECATED: use `tempEmulationSchema` instead.
`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.
`cdmDatabaseSchema`	The name of the database schema that contains the OMOP CDM instance. Requires read permissions to this database. On SQL Server, this should specifiy both the database and the schema, so for example 'cdm_instance.dbo'.
`cohortDatabaseSchema`	The name of the database schema that is the location where the cohort data used to define the at risk cohort is available. Requires read permissions to this database.
`cohortTable`	The tablename that contains the at risk cohort. The expectation is cohortTable has format of COHORT table: cohort_concept_id, SUBJECT_ID, COHORT_START_DATE, COHORT_END_DATE.
`workDatabaseSchema`	The name of the database schema that is the location where a table can be created and afterwards removed. Requires write permissions to this database.
`databaseId`	Name of the database in the analysis
`cdmVersion`	Define the OMOP CDM version used: currently supports "5".
`outputFolder`	Name of the folder where all the outputs will be written to.
`priorModelToUse`	folder where a previously developed model to use in analysis will be found
`pheValuatorAnalysisList`	A list of objects of type `pheValuatorAnalysis` as created using the `createPheValuatorAnalysis` function.