SkeletonPredictionValidationStudy

Introduction

This package contains code to externally validate models for the prediction quesiton developed on the database .

Features

  • Applies models developed using the OHDSI PatientLevelPrediction package
  • Evaluates the performance of the models on new data
  • Packages up the results (after removing sensitive date) to share with study owner

Technology

SkeletonPredictionValidationStudy is an R package.

System Requirements

  • Requires: OMOP CDM database and connection details
  • Requires: Java runtime enviroment (for the database connection)
  • Requires: R (version 3.3.0 or higher).
  • Sometimes required: Python

Dependencies

  • PatientLevelPrediction

Guide

A general guide for running a valdiation study package is available here: Skeleton Validation Study guide

A1. Installing the package from GitHub

# To install the package from github:
install.packages("devtools")
devtools::install_github("ohdsi-studies/SkeletonPredictionValidationStudy")

A2. Building the package inside RStudio

  1. Open the validation package project file (file ending in .Rproj)
  2. Build the package in RStudio by selecting the ‘Build’ option in the top right (the tabs contain ‘Environment’, ‘History’, ‘Connections’, ‘Build’, ‘Git’) and then clicking on the ‘Install and Restart’

B. Getting Started

  1. Make sure to have either: installed (A1) or built (A2) the package
  2. In R, run the code in ‘extras/codeToRun.R’ (see Skeleton Validation Study guide for guideance)

C. Example Code

library(SkeletonPredictionValidationStudy)

# add details of your database setting:
databaseName

License

SkeletonPredictionValidationStudy is licensed under Apache License 2.0

Development

SkeletonPredictionValidationStudy is being developed in R Studio.