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Covid19IncidenceAlphaBlockers

Requirements

  • A database in Common Data Model version 5 in one of these platforms: SQL Server, Oracle, PostgreSQL, IBM Netezza, Apache Impala, Amazon RedShift, Google BigQuery, or Microsoft APS.
  • R version 3.5.0 or newer
  • On Windows: RTools
  • Java
  • 25 GB of free disk space

See these instructions on how to set up the R environment on Windows.

How to run

  1. In R, use the following code to install the dependencies:

    install.packages("devtools")
library(devtools)
install_github("ohdsi/ParallelLogger", ref = "v1.1.1")
install_github("ohdsi/SqlRender", ref = "v1.6.3")
install_github("ohdsi/DatabaseConnector", ref = "v2.4.1")
install_github("ohdsi/OhdsiSharing", ref = "v0.1.3")
install_github("ohdsi/FeatureExtraction", ref = "v2.2.5")
install_github("ohdsi/CohortMethod", ref = "develop")
install_github("ohdsi/EmpiricalCalibration", ref = "v2.0.0")
install_github("ohdsi/MethodEvaluation", ref = "v1.1.0")

    If you experience problems on Windows where rJava can't find Java, one solution may be to add args = "--no-multiarch" to each install_github call, for example:

    install_github("ohdsi/SqlRender", args = "--no-multiarch")

    Alternatively, ensure that you have installed only the 64-bit versions of R and Java, as described in the Book of OHDSI

  2. In R, use the following devtools command to install the Covid19IncidenceAlphaBlockers package:

    install() # Note: it is ok to delete inst/doc

  3. Once installed, you can execute the study by modifying and using the code below. For your convenience, this code is also provided under extras/CodeToRun.R:

    library(Covid19IncidenceAlphaBlockers)

# Maximum number of cores to be used:
maxCores <- parallel::detectCores()

# Minimum cell count when exporting data:
minCellCount <- 5

# The folder where the study intermediate and result files will be written:
outputFolder <- "c:/Covid19IncidenceAlphaBlockers"

# Details for connecting to the server:
# See ?DatabaseConnector::createConnectionDetails for help
connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "postgresql",
								server = "some.server.com/ohdsi",
								user = "joe",
								password = "secret")

# The name of the database schema where the CDM data can be found:
cdmDatabaseSchema <- "cdm_synpuf"

# The name of the database schema and table where the study-specific cohorts will be instantiated:
cohortDatabaseSchema <- "scratch.dbo"
cohortTable <- "my_study_cohorts"

# Some meta-information that will be used by the export function:
databaseId <- "Synpuf"
databaseName <- "Medicare Claims Synthetic Public Use Files (SynPUFs)"
databaseDescription <- "Medicare Claims Synthetic Public Use Files (SynPUFs) were created to allow interested parties to gain familiarity using Medicare claims data while protecting beneficiary privacy. These files are intended to promote development of software and applications that utilize files in this format, train researchers on the use and complexities of Centers for Medicare and Medicaid Services (CMS) claims, and support safe data mining innovations. The SynPUFs were created by combining randomized information from multiple unique beneficiaries and changing variable values. This randomization and combining of beneficiary information ensures privacy of health information."

# For Oracle: define a schema that can be used to emulate temp tables:
oracleTempSchema <- NULL

execute(connectionDetails = connectionDetails,
        cdmDatabaseSchema = cdmDatabaseSchema,
        cohortDatabaseSchema = cohortDatabaseSchema,
        cohortTable = cohortTable,
        oracleTempSchema = oracleTempSchema,
        outputFolder = outputFolder,
        databaseId = databaseId,
        databaseName = databaseName,
        databaseDescription = databaseDescription,
        createCohorts = TRUE,
        synthesizePositiveControls = TRUE,
        runAnalyses = TRUE,
        runDiagnostics = TRUE,
        packageResults = TRUE,
        maxCores = maxCores)

Note: If you experience an issue while running the code, please report this via the Issues tab above. Where possible, please include a snippet of the error message and any relevant information about your R environment / data layer (e.g. SQL Server, RedShift, Google BigQuery). Issues will be debugged and code will be updated accordingly.

  1. Upload the file export/Results<DatabaseId>.zip in the output folder to the study coordinator:

    submitResults("export/Results<DatabaseId>.zip", key = "<key>", secret = "<secret>")

    Where key and secret are the credentials provided to you personally by the study coordinator.

  2. To view the results, use the Shiny app:

    prepareForEvidenceExplorer("Result<databaseId>.zip", "/shinyData")
launchEvidenceExplorer("/shinyData", blind = TRUE)

Note that you can save plots from within the Shiny app. It is possible to view results from more than one database by applying prepareForEvidenceExplorer to the Results file from each database, and using the same data folder. Set blind = FALSE if you wish to be unblinded to the final results.

License

The Covid19IncidenceAlphaBlockers package is licensed under Apache License 2.0

Development

Covid19IncidenceAlphaBlockers was developed in ATLAS and R Studio.

Development status

Unknown