Generating Features for a Cohort

An R interface for generating features for a cohort using data in the Common Data Model. Features can be constructed using default or custom made feature definitions. Furthermore it's possible to aggregate features and get the summary statistics.

FeatureExtraction

FeatureExtraction is part of HADES.

Introduction

An R package for generating features (covariates) for a cohort using data in the Common Data Model.

Features

• Takes a cohort as input.
• Generates baseline features for that cohort.
• Default covariates include all drugs, diagnoses, procedures, as well as age, comorbidity indexes, etc.
• Support for creating custom covariates.
• Generate paper-ready summary table of select population characteristics.

Technology

FeatureExtraction is an R package, with some functions implemented in C++.

System Requirements

Requires R (version 3.2.2 or higher). Installation on Windows requires RTools. FeatureExtraction require Java.

Getting Started

1. See the instructions here for configuring your R environment, including RTools and Java.

2. In R, use the following commands to download and install FeatureExtraction:

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

User Documentation

The documentation website can be found at https://ohdsi.github.io/FeatureExtraction/. PDF versions of the vignettes and package manual are here:

• Vignette: Using FeatureExtraction
• Vignette: Creating covariates using cohort attributes
• Vignette: Creating custom covariate builders
• Vignette: Creating covariates based on other cohorts
• Package manual: FeatureExtraction manual

These vignettes are also available in Korean:

• Vignette: Using FeatureExtraction
• Vignette: Creating custom covariate builders

Support

• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

Contributing

Read here how you can contribute to this package.

License

FeatureExtraction is licensed under Apache License 2.0

Development

FeatureExtraction is being developed in R Studio.

Development status

Ready for use

Acknowledgements

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