testPhenotypeAlgorithm: Test phenotype algorithms

In OHDSI/PheValuator: Rapid Phenotype Evaluation

Test phenotype algorithms

Description

Test phenotype algorithms

Usage

testPhenotypeAlgorithm(
  phenotype,
  analysisName,
  runDateTime,
  connectionDetails,
  cutPoints = c("EV"),
  outFolder,
  exportFolder,
  evaluationCohortId = "main",
  phenotypeCohortId,
  cdmDatabaseSchema,
  databaseId,
  cohortDatabaseSchema,
  cohortTable,
  washoutPeriod = 0,
  splayPrior = 7,
  splayPost = 7
)

Arguments

phenotype	Name of the phenotype for analysis
analysisName	Name of the analysis
runDateTime	Starting date and time of the PheValuator run
connectionDetails	ConnectionDetails created using the function createConnectionDetails in the DatabaseConnector package.
cutPoints	A list of threshold predictions for the evaluations. Include "EV" for the expected value
outFolder	The folder where the cohort evaluation output files are written
exportFolder	The folder where the csv output files will be written.
evaluationCohortId	A string used to generate the file names for the evaluation cohort.
phenotypeCohortId	The ID of the cohort to evaluate in the specified cohort table.
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'.
databaseId	Name of the database in the analysis
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.
washoutPeriod	The mininum required continuous observation time prior to index date for subjects within the cohort to test (Default = 0).
splayPrior	The number of days to allow for test phenotype visit date prior to evaluation date
splayPost	The number of days to allow for test phenotype visit date after evaluation date

Details

This function will perform the phenotype algorithm evaluation using the evaluation cohort returned from createEvalCohort and the phenotype algorithm cohort specified

Value

A dataframe with the results from the phenotype algorithm evaluation.

If 0.5 is included as a cutpoint, the data frame will have an attribute called 'misses', a dataframe with a sample of subject ids for TPs, FPs, TNs, and FNs for the 50 percent and over prediction threshold.

OHDSI/PheValuator documentation built on Jan. 28, 2024, 4:05 a.m.