execute: Execute the Study

In ohdsi-studies/PCE: A Package Skeleton for Replicating Published Prediction Models

Description

Execute the Study

Usage

execute(
  connectionDetails,
  cdmDatabaseSchema,
  cdmDatabaseName = "friendly database name",
  cohortDatabaseSchema = cdmDatabaseSchema,
  cohortTable = "cohort",
  oracleTempSchema = cohortDatabaseSchema,
  setting = NULL,
  sampleSize = NULL,
  recalibrate = F,
  recalibrateInterceptOnly = F,
  riskWindowStart = 1,
  startAnchor = "cohort start",
  riskWindowEnd = 365,
  endAnchor = "cohort start",
  firstExposureOnly = F,
  removeSubjectsWithPriorOutcome = F,
  priorOutcomeLookback = 99999,
  requireTimeAtRisk = F,
  minTimeAtRisk = 1,
  includeAllOutcomes = T,
  outputFolder,
  createCohorts = F,
  runAnalyses = F,
  aggregateCohorts = T,
  viewShiny = F,
  packageResults = F,
  minCellCount = 10,
  verbosity = "INFO",
  cdmVersion = 5
)

Arguments

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.
setting	A data.frame with the tId, oId, model triplets to run - if NULL it runs all possible combinations
sampleSize	How many patients to sample from the target population
recalibrate	Recalibrate the model intercept and slop
recalibrateInterceptOnly	Recalibrate the intercept only.
riskWindowStart	The start of the risk window (in days) relative to the startAnchor.
startAnchor	The anchor point for the start of the risk window. Can be "cohort start" or "cohort end".
riskWindowEnd	The end of the risk window (in days) relative to the endAnchor parameter
endAnchor	The anchor point for the end of the risk window. Can be "cohort start" or "cohort end".
firstExposureOnly	Should only the first exposure per subject be included? Note that this is typically done in the createStudyPopulation function,
removeSubjectsWithPriorOutcome	Remove subjects that have the outcome prior to the risk window start?
priorOutcomeLookback	How many days should we look back when identifying prior outcomes?
requireTimeAtRisk	Should subject without time at risk be removed?
minTimeAtRisk	The minimum number of days at risk required to be included
includeAllOutcomes	(binary) indicating whether to include people with outcomes who are not observed for the whole at risk period
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?
runAnalyses	Run the model development
aggregateCohorts	Run this after runAnalyses to calculate the performance for combination of males and females, black and non-black
viewShiny	View the results as a shiny app
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
standardCovariates	Use this to add standard covariates such as age/gender

Details

This function executes the PCE Study.

Examples

## 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",
        outcomeId = 1,
        oracleTempSchema = NULL,
        riskWindowStart = 1,
        startAnchor = 'cohort start',
        riskWindowEnd = 365,
        endAnchor = 'cohort start',
        outputFolder = "c:/temp/study_results", 
        createCohorts = T,
        runAnalyses = T,
        aggregateCohorts = T,
        viewShiny = F,
        packageResults = F,
        minCellCount = 10,
        verbosity = "INFO",
        cdmVersion = 5)

## End(Not run)

ohdsi-studies/PCE documentation built on Feb. 15, 2021, 6:33 a.m.