execute: Execute the Study

In ohdsi-studies/dGEMcovid: A Skeleton for running distributed model studies

Execute the Study

Description

Execute the Study

Usage

execute(
  databaseDetails,
  siteId = "site_name",
  outputFolder,
  createCohorts = F,
  createData = F,
  createPlot = createData,
  sampleSize = NULL,
  createControl = F,
  siteIds = "",
  leadSiteNextStep = F,
  runInitialize = F,
  runDerive = F,
  runEstimate = F,
  runSynthesize = F,
  verbosity = "INFO",
  alphaStart = "20201101",
  alphaEnd = "20210201",
  deltaStart = "20210701",
  deltaEnd = "20211001"
)

Arguments

databaseDetails	The connection details and OMOP CDM details. Created using PatientLevelPrediction::createDatabaseDetails.
siteId	The name of your site (can be the university name, site with a number, etc.) tnis needs to be shared with the study administrator
outputFolder	Name of local folder to place results - make sure control is in here; 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?
createData	Create the labelled data set (this is required before runAnalysis)
createPlot	Plot the number of covid hospitalizations by month
sampleSize	The number of patients in the target cohort to sample (if NULL uses all patients)
createControl	(for the lead site only) Run this code to create the study control
siteIds	(for the lead site only) vector with the names of all the sites contributing to the study. Required when createControl = TRUE
runInitialize	Runs the initialization step - this require downloading the json control from https://pda-ota.pdamethods.org/
runDerive	Runs the derive step - this require downloading the updated json control from https://pda-ota.pdamethods.org/
runEstimate	Runs the estimate step - this require downloading the updated json control from https://pda-ota.pdamethods.org/
runSynthesize	Once the site estimates are returned, it is now possible to apply each model to the data to calculate predictions. This step requires downloading the updated json control from https://pda-ota.pdamethods.org/
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 @param alphaStart The start date for the alpha wave in the data in "yyyymmdd" format @param alphaEnd The end date for the alpha wave in the data in "yyyymmdd" format @param deltaStart The start date for the delta wave in the data in "yyyymmdd" format @param deltaEnd The end date for the detla wave in the data in "yyyymmdd" format

Details

This function executes the dGEMcovid Study.

Examples

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

execute(databaseDetails,
        siteId = 'site_1',
        outputFolder = "c:/temp/study_results", 
        createCohorts = T,
        createData = T,
        sampleSize = 10000,
        createControl = F,
        siteIds = c('site_1', 'site_2'),
        leadSiteNextStep = F,
        runAnalysis = F,
        runSynthesize = F,
        verbosity = "INFO"
        )

## End(Not run)

ohdsi-studies/dGEMcovid documentation built on May 10, 2023, 3:38 a.m.