execute: Execute the Study
In ohdsi-studies/PredictionCovariateLookback: Investigating Covariate Lookback

Description Usage Arguments Details Examples

View source: R/Main.R

Execute the Study

execute(
  connectionDetails,
  cdmDatabaseSchema,
  cdmDatabaseName = "friendly database name",
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTable = "cohort",
  oracleTempSchema = cohortDatabaseSchema,
  outputFolder,
  sampleSize = NULL,
  repeats = 5,
  studyStartDate = "20160101",
  studyEndDate = "",
  createCohorts = T,
  runAnalyses = T,
  externalValidate = F,
  modelDatabaseName,
  summarizeResults,
  minCellCount = 5,
  verbosity = "INFO",
  cdmVersion = 5,
  requiredPriorObservation = 365
)

`connectionDetails`	An object of type `connectionDetails` as created using the `createConnectionDetails` function in the DatabaseConnector package.
`cdmDatabaseSchema`	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'.
`cdmDatabaseName`	Shareable name of the database
`cohortDatabaseSchema`	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'.
`cohortTable`	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.
`sampleSize`	The number of patients in the target population to sample
`repeats`	How many test/train splits to run
`studyStartDate`	Only cohort start dates after this date are included
`studyEndDate`	Only cohort end dates before this date are included
`createCohorts`	Create the cohortTable table with the target population and outcome cohorts?
`runAnalyses`	Run the model development
`summarizeResults`	Summarise the results in the outputFolder for the cdmDatabaseName models
`minCellCount`	The minimum number of subjects contributing to a count before it can be included in packaged results.
`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
`requiredPriorObservation`	A sensitivity parameter (default is 365 days)
`externalValdiate`	Externally validate the models you developed

This function executes the PredictionCovariateLookback Study.

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

execute(connectionDetails,
        cdmDatabaseSchema = "cdm_data",
        cdmDatabaseName = 'shareable name of the database'
        cohortDatabaseSchema = "study_results",
        cohortTable = "cohort",
        oracleTempSchema = NULL,
        outputFolder = "c:/temp/study_results", 
        createCohorts = T,
        runAnalyses = T,
        minCellCount = 5,
        verbosity = "INFO",
        cdmVersion = 5,
        requiredPriorObservation = 365)

## End(Not run)