aou-dq-cohorts's Introduction

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:

Copy/download the examplePackage folder. For example, download the Zip file here, open it, and locate the examplePackage folder and extract it.
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.
Open the R project in R studio (e.g. by double-clicking on the .Rproj file).
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.

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.

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