execute: Execute the Study

In ohdsi-studies/Covid19VaccinePrediction: COVID-19 vaccination prediction methoods research and model development

Execute the Study

Description

Execute the Study

Usage

execute(
  connectionDetails,
  cdmDatabaseSchemas,
  cdmDatabaseNames = "friendly database name",
  cohortDatabaseSchemas = cdmDatabaseSchema,
  cohortTables = "cohort",
  oracleTempSchema = cohortDatabaseSchema,
  outputFolder,
  createCohorts = F,
  fetchData = F,
  runDevelopment = F,
  runValidate = F,
  sampleSize = NULL,
  verbosity = "INFO",
  cdmVersion = 5,
  cores = 4
)

Arguments

connectionDetails	An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package.
cdmDatabaseSchemas	Schema name where your patient-level data in OMOP CDM format resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
cdmDatabaseNames	Shareable name of the database
cohortDatabaseSchemas	Schema name where intermediate data can be stored. You will need to have write priviliges in this schema. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
cohortTables	The name of the table that will be created in the work database schema. This table will hold the target population cohorts used in this study.
oracleTempSchema	Should be used in Oracle to specify a schema where the user has write priviliges for storing temporary tables.
outputFolder	Name of local folder to place results; make sure to use forward slashes (/). Do not use a folder on a network drive since this greatly impacts performance.
createCohorts	Create the cohortTable table with the target population and outcome cohorts?
fetchData	Only fetch data for the analyses without fitting models. Setting this flag will overwrite your input provided to the runAnalyses and createCohorts parameters.
runDevelopment	Run the model development
runValidate	Run the model validation
sampleSize	The number of patients in the target cohort to sample (if NULL uses all patients)
verbosity	Sets the level of the verbosity. If the log level is at or higher in priority than the logger threshold, a message will print. The levels are: DEBUGHighest verbosity showing all debug statements TRACEShowing information about start and end of steps INFOShow informative information (Default) WARNShow warning messages ERRORShow error messages FATALBe silent except for fatal errors
cdmVersion	The version of the common data model
cores	The number of threads to use when developing the models
createProtocol	Creates a protocol based on the analyses specification

Details

This function executes the CovidVaccinePrediction Study.

Examples

## Not run: 
connectionDetails <- createConnectionDetails(dbms = "postgresql",
                                             user = "joe",
                                             password = "secret",
                                             server = "myserver")

execute(connectionDetails,
        cdmDatabaseSchemas = "cdm_data",
        cdmDatabaseNames = 'shareable name of the database'
        cohortDatabaseSchemas = "study_results",
        cohortTables = "cohort",
        oracleTempSchema = NULL,
        outputFolder = "c:/temp/study_results", 
        createCohorts = T,
        fetchData = T,
        runDevelopment = T,
        sampleSize = 10000,
        verbosity = "INFO",
        cdmVersion = 5)

## End(Not run)

ohdsi-studies/Covid19VaccinePrediction documentation built on Jan. 16, 2025, 1:02 a.m.