Final Project Alzheimer's Disease Analysis

Welcome~~ This repository contains the code and data for analyzing Alzheimer's disease data.

Dataset

• Since it is a rather big dataset file, Github doesn't allow me to upload it straight in CVS format.
  I upload the first 250 rows dataset file, it might alter the result from the word summary.

OR

• You can download it straight from the Kaggle website:
  https://www.kaggle.com/datasets/amitvkulkarni/aging-and-memory-alzheimers-statistics?resource=download

Installation

To set up the R package environment, you need to restore the package state with renv to ensure reproducibility. Here’s how to do it:

1. Ensure you have R and renv installed on your system. If renv is not installed, you can install it by running install.packages("renv") in R.

2. Run the following command in the terminal within the project directory:

   make install

This command uses renv to install all necessary packages as specified in the renv.lock file.

Building the Docker Image

To build the Docker image, you need to have Docker installed on your machine. Once installed, you can build the image by running the following command from the root directory of this project:

docker build -t sabrinayan0229/data550_final .

Generating the Report Using Docker Container

The report is generated by running the Docker container, which executes an R script to analyze data and produce a report. To run this process, use the make command specified in the Makefile:

make run-report

run-report:
    docker run -v $(PWD)/report:/usr/src/app/report sabrinayan0229/data550_final

Contents

• data/: Contains the dataset file Alzheimers_Disease_Healthy_Aging_data.csv.
• code/: Contains the R scripts for analysis, generating tables, and figures.
  • analysis.R: Main analysis script.
  • table.R: Script for generating the required table.
  • figure.R: Script for generating the required figure.
• report/: Contains the R Markdown file for the final report.
• Makefile: Contains rules for building the final report and managing dependencies with renv.
• Dockerfile: Contains all commands needed to build the Docker image.

Generating the Report

To generate the final report, follow these steps:

1. Clone the repository.
2. Open a terminal and navigate to the project directory.
3. Run the command make all to execute the analysis and generate the report.
4. The generated report will be saved as report/report.html.

Table and Figure

• The code for creating the required table is located in code/table.R.
• The code for creating the required figure is located in code/figure.R.