armanmoztar/hyperthyroid-disease-classification

Term project for DSCI 310: Reproducible and Trustworthy Workflows for Data Science

Hyperthyroid Disease Classification

Authors: Arman Moztarzadeh, Eric Liu, Ryan Lee, Matthew Gillies

About

Hyperthyroidism is an issue that occurs when the thyroid gland makes more thyroid hormones than the body needs (De Leo et al., 2016). The body manages its energy by using thyroid hormones. By having an excessive amount, bodily functions may increase in speed resulting in weight loss, rapid heartbeat, fatigue, shaky hands, sweating, and more (U.S. Department of Health and Human Services, n.d.). The goal of our project is to create a tool to help predict the presence of hyperthyroidism using varying attributes such as age, sex, prior treatment for thyroid disease, and amount of thyroid hormones in the body.

Report

The JupyterLab analysis for Milestone 1 can be found here
The JupyterBook analysis for Milestone 3 can be found by running make all and is located at dsci-310-group-17/jbook/_build/html/index.html

Usage - Running with Docker

1. Clone this GitHub repository onto your local computer using the command: git clone <url>
2. Open your terminal and navigate to the root of this repository using the command cd <folder name or path to project>
3. Ensure that Docker is installed on your computer and running. If not, follow the instructions here.
4. Run the following commands:

docker pull erliuu/dsci-310-group-17

docker run --rm -p 8888:8888 \
    -v /$(pwd):/home/joyvan/dsci-310-group-17 \
    erliuu/dsci-310-group-17:latest

• Note: Sometimes ${pwd} does not work. Simply replace with the full path to the repository directory. Ex. /home/eric1126/DSCI_310/test-dsci-310-group-17

The first command first pulls the image from DockerHub, then the second creates and starts a new container from the downloaded image.

4. Once you have run the commands, copy the URL that will come up that looks something like http://127.0.0.1:8888/lab?token= into your web browser.
5. Once in JupyterLab, there are different versions of the analysis you can view and run
   • To run the jupyter-book (Main Report copy):
     • Navigate to the root of the repository and run enter make all onto the command line. This will generate the report in publication quality in HTML.
     • The HTML will be located at jbook/_build/analysis_jbook.html
     • All generated files will be located in the results/ directory
     • To remove all files in the results/ directory in order to reset the analysis, run make clean on the command line
6. Make sure to navigate to Kernel and click "Restart Kernal and Run All Cells" to ensure reproducibility.

PyTest

To confirm that functions run as intended run the following command on the terminal:

python3 -m pytest 

Dependencies

R version 4.2.2 & Jupyterlab 3.6.1

Docker Base Image: jupyter/scipy-notebook:ubuntu-22.04

Our list of dependencies with the package and version number can be found below:

Package	Version
matplotlib	3.7.1
numpy	1.24.2
pandas	1.5
seaborn	0.12.2
jupyter-book	0.12.1
py-test	7.2.2
group17pkg	0.0.0

Contributions

For contribution guidelines, please refer to the guidlines listed in this document here.

License

This project uses the MIT license for its code and the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) license for the analysis.