PatientLevelPrediction

Introduction

An R package for building patient level predictive models using data in Common Data Model format.

Features

Takes a cohort and outcome of interest as input.
Extracts the necessary data from a database in OMOP Common Data Model format.
Uses a large set of covariates including for example all drugs, diagnoses, procedures, as well as age, comorbidity indexes, etc.
Various machine learning algorithms can be used to develop predictive models.
Includes function for evaluating predictive models
Includes functions to plot and explore model performance (ROC + Calibration)
Supported outcome models are l1 logistic regression, Random forest, Gradient boosting machines, Naive Bayes, KNN and MLP.

Screenshots


Calibration plot	ROC plot

Technology

PatientLevelPrediction is an R package, with some functions implemented in C++ and python.

System Requirements

Requires R (version 3.3.0 or higher). Installation on Windows requires RTools. Libraries used in PatientLevelPrediction require Java and Python.

The python installation is required for some of the machine learning algorithms. We advise to install Python 2.7 using Anaconda (https://www.continuum.io/downloads)

Dependencies

Cyclops
DatabaseConnector
SqlRender
FeatureExtraction
BigKnn

Getting Started

On Windows, make sure RTools is installed.
The DatabaseConnector and SqlRender packages require Java. Java can be downloaded from http://www.java.com.
Random forest, Naive Bayes and MLP require python 2.7. Python 2.7 can be downloaded from: https://www.continuum.io/downloads.
In R, use the following commands to download and install PatientLevelPrediction:

install.packages("drat")
drat::addRepo("OHDSI")
install.packages("PatientLevelPrediction")

Have a look at the video below for a demo of the package.

Getting Involved

Vignette: Building patient-level predictive models
Developer questions/comments/feedback: OHDSI Forum
We use the GitHub issue tracker for all bugs/issues/enhancements

License

PatientLevelPrediction is licensed under Apache License 2.0

Development

PatientLevelPrediction is being developed in R Studio.

Development status

Beta

Acknowledgements

This project is supported in part through the National Science Foundation grant IIS 1251151.

clairblacketer/PatientLevelPrediction