execute: Execute the Study
In ohdsi-studies/DistributedLMM: Predicting Length of Hopsital Stay for COVID-19

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,
  sampleSize = NULL,
  studyStartDate = "",
  studyEndDate = "",
  endDay = -1,
  outputFolder,
  createCohorts = T,
  useFluCohort = F,
  extractData = T,
  packageResults = T,
  minCellCount = 10,
  verbosity = "INFO",
  cdmVersion = 5
)

`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 the cohorts and covariates are created. 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, outcome and variable 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.
`sampleSize`	How many patients to sample from the target population
`studyStartDate`	Restrict to certain time period
`studyEndDate`	Restrict to certain time period
`endDay`	The end day relative to index for the custom covariates (default is -1)
`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 cohorts
`useFluCohort`	use to the test the package in flu data
`extractData`	Extract the data and create the components for the DLLM
`packageResults`	Should results be packaged for later sharing?
`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

This function executes the DLMM 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,
        sampleSize = NULL
        studyStartDate,
        studyEndDate,
        endDay = -1,
        outputFolder = "c:/temp/study_results",
        createCohorts = T,
        useFluCohort = F,
        extractData = T,
        packageResults = T,
        minCellCount = 10,
        verbosity = "INFO",
        cdmVersion = 5)

## End(Not run)