populatePlpResultTables: Populate the PatientLevelPrediction results tables

In quinterpriest/PatientLevelPrediction: Developing patient level prediction using data in the OMOP Common Data Model

Populate the PatientLevelPrediction results tables

Description

This function formats and uploads results that have been generated via an ATLAS prediction package into a database

Usage

populatePlpResultTables(
  conn,
  resultSchema,
  stringAppendToTables = "",
  targetDialect = "postgresql",
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  packageName,
  studyJsonList,
  studyName = "",
  studyDescription = "",
  researcherName = "",
  researcherEmail = "",
  researcherOrg = "",
  databaseName = NULL,
  databaseAcronym = NULL,
  databaseVersion = 1,
  databaseDescription = NULL,
  databaseType = NULL,
  valDatabases = list(ccae = list(name = "CCAE", description = "", version = 1, type =
    "US Claims")),
  resultLocation = NULL,
  resultPattern = "",
  validationLocation = file.path(resultLocation, "Validation"),
  addInternalValidation = T,
  addExternalValidation = T,
  gsubVal = NULL,
  removePattern = NULL
)

Arguments

conn	A connection to a database created by using the function connect in the DatabaseConnector package.
resultSchema	(string) The name of the database schema with the result tables.
stringAppendToTables	(string) A string that appends to the PatientLevelPrediction result tables
targetDialect	(string) The database management system being used
tempEmulationSchema	(string) The temp schema used when the database management system is oracle
packageName	(string) The name of the ATLAS R package used to generate the results (this is used to extract cohort jsons)
studyJsonList	(list) A list of lists per cohort with the cohort_name, cohort_id and cohort_json
studyName	(string) A reference study name
studyDescription	(string) A description of the study
researcherName	(string) Name of the researcher who developed the study
researcherEmail	(string) Email of the researcher who developed the study
researcherOrg	(string) Organisation of the researcher who developed the study
databaseName	(string) name of the database used to develop the model/s
databaseAcronym	(string) acronym of the database used to develop the model/s
databaseVersion	(int) Version of the database used to develop the model/s
databaseDescription	(string) Description of the database used to develop the model/s
databaseType	(string) Type of the database used to develop the model/s (e.g., claims)
valDatabases	(list) A named list with details of the external validation databases. Needs to contain: name, description, version, type.
resultLocation	(string) location of directory where the main package results were saved
resultPattern	(string) A string to match to select models of interest
validationLocation	(string) location of directory where the validation package results were saved
addInternalValidation	(boolean) Whether the internval validation results should be uploaded
addExternalValidation	(boolean) Whether the externval validation results should be uploaded
gsubVal	(string) Remove patterns from the result name
removePattern	(string) Restrict to result names with this pattern

Details

This function can be used upload PatientLevelPrediction results into a database

Value

Returns NULL but uploads all the results in resultLocation to the PatientLevelPrediction result tables in resultSchema

quinterpriest/PatientLevelPrediction documentation built on April 20, 2022, 12:50 a.m.