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Characterization Package Specification

Introduction

Purpose

To create an R package that provide users with a basic understanding of R and the OMOP CDM a user-friendly R interface for running large-scale characterization studies.

Intended Audience

Users with basic R knowledge and basic knowledge of the OMOP CDM.

Intended Use

Perform characterization studies at scale for a set of cohort(s) and characterization specifications.

Scope

To perform aggregate feature extraction, time-to-event and dechallenge/rechallenge characterizations with an R interface.

Needs to be able to generate/save/load json specifications (corresponding to the R analysis specification) and save results into csv and into a database result schema.

Requires shiny modules for interactively exploring results in a database (will be put in OhdsiShinyModules) and rmarkdown templates for generating human readable protocols for the specification.

Definitions and Acronyms

Overall Description

User Needs

Researchers will use the R package by specifying the types of characterization studies they wish to run, the analysis settings and then provide the R connection to a database with OMOP CDM data and the database settings.

Version 1.0.0 of the package will enable users to perform aggregate descriptions via FeatureExtraction, time-to-event and dechallenge/rechallenge studies for a set of user supplied cohorts and user specified analysis settings.

Assumptions and Dependencies

Assumptions:

• Access to data in the OMOP CDM format
• Database in a management system supported by OHDSI

Dependencies:

• R (minimum version?) installed
• Java runtime installed (until DBI is used in DatabaseConnector)
• R packages installed:
  • FeatureExtraction
  • DatabaseConnector
  • SqlRender
  • OhdsiShinyModules
  • Andromeda
  • ParallelLogger

System Features and Requirements

Functional Requirements

The package needs to have functions to create study settings, create database results tables, execute each study type, generate plots of tables of results, save results as csv files or to a database.

Name	Description	Input	Output
createTimeToEventSettings	Create a setting object for the time to event analysis	targetIds, outcomeIds	List of class ‘timeToEventSettings’ with pair grid of all target and outcome combinations

In OhdsiShinyModules we will create shiny modules for viewing the results and contain the rmarkdown templates for generating the protocol.

External Interface Requirements

An interface such as ATLAS may be used to generate the json specification for the characterization execute(). CohortGenerator (or manual SQL execution) will be required to create the cohorts used in this package. Cohort creation is out of scope in this package.

A module wrapper around the characterization package will be created to run characterization inside of strategus. This will contain a script for executing the characterization given a valid json spec, code to exporting to csv and the renv containing the package and dependencies.

System Features

Mac/Windows/Linux with R installed

Nonfunctional Requirements

1. Performance: Code needs to run efficiently at scale (thousands of cohorts + study setting combination)
2. Quality: Unit tests must be >80% coverage and passing.