Tools for Healthcare Machine Learning

A machine learning toolbox tailored to healthcare data. Aids in data cleaning, model development, hyperparameter tuning, and model deployment in a production 'SQL' environment. Algorithms currently supported are Lasso, Random Forest, Extreme Gradient Boosting, K-means clustering, and Linear Mixed Modeling.


Build status Travis-CI Build Status License: MIT CRAN_Status_Badge DOI

The aim of healthcareai is to make machine learning easy on healthcare data. The package has two main goals:

  • Allow one to easily develop and compare models based on tabular data, and deploy a best model that pushes predictions to either databases or flat files.

  • Provide tools related to data cleaning, manipulation, and imputation.

For those starting out

  • If you haven't, install R version >= 3.2.3 and RStudio

Note: if you're setting up R on an ETL server, don't download RStudio--simply open up RGui

Install the latest release on Windows

Open RStudio and work in the console

install.packages('healthcareai')

If install.packages('healthcareai') or library(healthcareai) fails

If you don't have admin rights on the machine you are working on, you may need to set a custom location for your R libraries. Here's how to do that:

  1. Create a folder to hold your R packages. You'll generally have write access to your Documents folder, so you might create a new directory: C:\Users\your.name\Documents\R\R_library. Shift-right click on that folder and copy its path.
  2. Define a system variable with that folder location. Open the Control Panel and click through User Accounts -> User Accounts -> Change my environment variables, and add a variable called R_LIBS_USER, and paste the folder path (C:\Users\your.name\Documents\R\R_library) into the value field. Make sure the path is not surrounded by "s.
  3. Tell R to use that location. Restart R Studio, run install.packages('healthcareai'), and if asked whether you want to use a custom library location choose yes, which may be sufficient. If not, click into the Console in R Studio, type .libPaths(), paste the path to your new library folder inside the (), and change the \s to /. You should end up with a line that looks like: .libPaths("C:/Users/your.name/Documents/R/R_library"). Press enter to run that.
  4. Try again. Run install.packages('healthcareai') and library(healthcareai) again and all should be well!

How to install the latest version on macOS

Open RStudio and work in the console

install.packages('healthcareai')

How to install latest version on Ubuntu (Linux)

  • An Ubuntu 14.04 Droplet with at least 1 GB of RAM is required for the installation.
  • Follow steps 1 and 2 here to install R
  • Run sudo apt-get install libiodbc2-dev
  • Run sudo apt-get install unixodbc unixodbc-dev
  • After typing R run install.packages('healthcareai')

Install the bleeding edge version (for folks providing contributions)

Open RStudio and work in the console

library(devtools)
devtools::install_github(repo='HealthCatalyst/healthcareai-r')

Tips on getting started

Built-in examples

Load the package you just installed and read the built-in docs

library(healthcareai)
?healthcareai

Website examples

See our docs website

Join the community

Read the blog and join the slack channel at healthcare.ai

What's new?

The CRAN 1.0.0 release features:

  • Added:
    • Kmeans clustering
    • XGBoost multiclass support
    • findingVariation family of functions
  • Changed:
    • Develop step trains and saves models
    • Deploy no longer trains. Loads and predicts on all rows.
    • SQL uses a DBI back end
  • Removed:
    • testWindowCol is no longer a param.
    • SQL reading/writing is outside model deployment.

For issues

  • Double check that the code follows the examples in the built-in docs
library(healthcareai)
?healthcareai
  • Make sure you've thoroughly read the descriptions found here

  • If you're still seeing an error, file an issue on Stack Overflow using the healthcare-ai tag. Please provide

    • Details on your environment (OS, database type, R vs Py)
    • Goals (ie, what are you trying to accomplish)
    • Crystal clear steps for reproducing the error

Contributing

You want to help? Woohoo! We welcome that and are willing to help newbies get started.

First, see here for instructions on setting up your development environment and how to contribute.

News

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("healthcareai")

1.2.4 by Michael Levy, 9 days ago


http://healthcareai-r.readthedocs.io


Report a bug at https://github.com/HealthCatalyst/healthcareai-r/issues


Browse source code at https://github.com/cran/healthcareai


Authors: Levi Thatcher [aut], Michael Levy [aut, cre], Mike Mastanduno [aut], Taylor Larsen [aut], Taylor Miller [aut]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports caret, data.table, DBI, doParallel, dplyr, e1071, ggplot2, grpreg, lme4, methods, odbc, pROC, R6, ranger, ROCR, RSQLite, xgboost

Suggests testthat


See at CRAN