examplePackage/README.md

In OHDSI/PheValuator: Rapid Phenotype Evaluation

Example Package

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

To modify the package for your own phenotype evaluations, 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 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 need for PheValuator. These include the xSpec, xSens, as well as the cohort definitions to evaluate. This file has the following 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 to fetch the JSON and SQL for these cohort definitions, and insert them into the package (note, this can also be found in extras/PackageMaintenance.R):

   ```r

   If ROhdsiWebApi is not yet installed:

   install.packages("devtools") devtools::install_github("ROhdsiWebApi")

   ROhdsiWebApi::insertCohortDefinitionSetInPackage(fileName = "inst/settings/CohortsToCreate.csv", baseUrl = , insertTableSql = TRUE, insertCohortCreationR = TRUE, generateStats = FALSE, packageName = ) ```

   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.

6. Create your PheValuator analysis settings, and store them as inst/settings/pheValuatorAnalysisList.json. Note that example code for creating PheValuator settings can be found in extras/CreateAnalysisSettings.R.

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

OHDSI/PheValuator documentation built on Jan. 28, 2024, 4:05 a.m.