readme.md

In oxford-pharmacoepi/diagCovVaxExposures: A Package Skeleton for Cohort Diagnostics

diagCovVaxExposures: CohortDiagnostics package to assess Covid-19 vaccines

Running the analysis

1) Download this entire repository (you can download as a zip folder using Code -> Download ZIP, or you can use GitHub Desktop). If possible, avoid saving to a shared network drive as this can cause issues or in folders with a particularly long path. 2) Open the project diagCovVaxExposures/diagCovVaxExposures.Rproj in RStudio (when inside the project, you will see its name on the top-right of your RStudio session) 3) Open the diagCovVaxExposures/extras/CodeToRun.R file which should be the only file that you need to interact with

• First, build the package (build -> install and restart)
• Then run renv::activate() and renv::restore() to bring in the required packages to be used
• Next,
  • outputFolder <- "....": Add your database specific information
  • options(andromedaTempFolder = "C/andromedaTemp"): To specify andromedaTempFolder location
  • maxCores <- parallel::detectCores(): To specify how many cores to use
  • connectionDetails <- createConnectionDetails("........."): These are the connection details for the OHDSI DatabaseConnector package.Note, this is v4.0.0 of DatabaseConnector and so you will need to have downloaded the relevant drivers (see here for more details) and pass the pathToDriver argument to the createConnectionDetails command.
  • cdmDatabaseSchema <-".....": This is the name of the schema that contains the OMOP CDM with patient-level data
  • cohortDatabaseSchema <-".....": This is the name of the schema where a results table will be created
  • cohortTable <- "diagCovVaxExposuresCohorts": This is the name of the table that will be created in the results schema (which could be called "diagCovVaxExposuresCohorts" or something else - note, any existing table in your results schema with this name will be overwritten)
  • databaseId <-".....": This is the short name/ acronym for your database
  • databaseName <- "....": This is the full name of your database
  • databaseDescription <- "....": A brief description your database
  • After adding these details, you should then be able to run the line diagCovVaxExposures::runCohortDiagnostics(...) line which will run all of the required analyses. Once run, you can view you results by running the lines CohortDiagnostics::preMergeDiagnosticsFiles(file.path(outputFolder, "diagnosticsExport")) and CohortDiagnostics::launchDiagnosticsExplorer(file.path(outputFolder, "diagnosticsExport"))

  ### NOTE: The package may take a long time to run when the vaccinated cohorts are large.

oxford-pharmacoepi/diagCovVaxExposures documentation built on Dec. 22, 2021, 5:21 a.m.