Run a list of analyses

Run a list of analyses

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.

Value

A data frame specifying where the constructed evaluation cohort and phenotype evaluation results can be found in the local file system.

Details

Run a list of analyses.