Example Package

This study package demonstrates how to currently use CohortDiagnostics in a package. The package only contains code to run StudyDiagnostics.

To modify the package to include the cohorts of interest, take these steps:

1. Copy/download the examplePackage folder. For example, download the Zip file here, open it, and locate the examplePackage folder and extract it.

2. Change the package name as needed. Most importantly:

   • Change the Package: field in the DESCRIPTION file,
   • The packageName argument in the R/CohortDiagnostics file, and
   • The library() call at the top of extras/CodeToRun.R
   • The name of the .Rproj file.

3. Open the R project in R studio (e.g. by double-clicking on the .Rproj file).

4. Modify inst/settings/CohortsToCreate.csv to include only those cohorts you are interested in. Fill in each of the four columns:

   • atlasId: The cohort ID in ATLAS.
   • atlasName: The full name of the cohort. This will be shown in the Shiny app.
   • cohortId: The cohort ID to use in the package. USually the same as the cohort ID in ATLAS.
   • name: A short name for the cohort, to use to create file names. do not use special characters.

5. Run this code (note, this can also be found in extras/PackageMaintenance.R):

   # If ROhdsiWebApi is not yet installed:
   install.packages("devtools")
   devtools::install_github("ROhdsiWebApi")
   
   ROhdsiWebApi::insertCohortDefinitionSetInPackage(fileName = "inst/settings/CohortsToCreate.csv",
                                                    baseUrl = <baseUrl>,
                                                    insertTableSql = TRUE,
                                                    insertCohortCreationR = TRUE,
                                                    generateStats = TRUE,
                                                    packageName = <package name>)

   Where <baseUrl> is the base URL for the WebApi instance, for example: "http://server.org:80/WebAPI", and <package name> is the name of your new package.

You can now build your package. See extras/CodeToRun.R on how to run the package.