performConceptSetDiagnostics: given a search string (s) perform concept set diagnostics
In OHDSI/ConceptSetDiagnostics: Concept Set Diagnostics

View source: R/PerformConceptSetDiagnostics.R

performConceptSetDiagnostics

R Documentation

given a search string (s) perform concept set diagnostics

Description

given an array of comma separated quoted search string (s), this function will perform a series of operations that provides a recommended concept set expression, along with potentially more recommended and orphan concepts.

Usage

performConceptSetDiagnostics(
  searchPhrases,
  connection = NULL,
  connectionDetails = NULL,
  conceptPrevalenceSchema = NULL,
  runPhoebeRecommendation = TRUE,
  runOrphan = FALSE,
  locationForResults = NULL,
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  vocabularyDatabaseSchema = "vocabulary",
  vocabularyIdOfInterest = c("SNOMED", "HCPCS", "ICD10CM", "ICD10", "ICD9CM", "ICD9",
    "Read"),
  domainIdOfInterest = c("Condition", "Procedure", "Observation")
)

Arguments

`searchPhrases`	An array of text-phrases within quotations that are separated by commas.
`connection`	An object of type `connection` as created using the `connect` function in the DatabaseConnector package. Can be left NULL if `connectionDetails` is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.
`connectionDetails`	An object of type `connectionDetails` as created using the `createConnectionDetails` function in the DatabaseConnector package. Can be left NULL if `connection` is provided.
`conceptPrevalenceSchema`	The schema name that has the concept prevalence table. The following tables are expected to be present. recommender_set, cp_master, recommended_blacklist.
`runPhoebeRecommendation`	Do you want to run Concept Recommendation using PHOEBE?
`runOrphan`	Do you want to run Orphan Concept text search? This may take time.
`locationForResults`	If you want to export results, please provide disk drive location
`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.
`vocabularyDatabaseSchema`	The schema name of containing the vocabulary tables.
`vocabularyIdOfInterest`	A list of vocabulary ids to filter the results.
`domainIdOfInterest`	A list of domain ids to filter the results.