Final Project

Introduction

The dataset used in this analysis includes data on patient visits at an STI clinic in Boston from January 1st, 2020 to December 31st, 2023. The data includes the patient's ID, the date of the clinic visit, an indicator variable for if the patient received a gonorrhea test, an indicator variable for if the patient received a chlamydia test, and an indicator variable for if the patient received an HIV test at the visit. The purpose of this analysis is to identify the average number of STI tests an individual has taken stratified by test type. We also aim to visualize the total number of STI tests stratified by test type through a bar chart. This descriptive analysis will provide an understanding of the extent of the utilization of STI screening services within the clinic from 2020 to 2023.

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Instructions for Generating Final Report using Image on DockerHub (Automated Version of Image)

1. Fork and clone the repository from GitHub to your local machine.
2. Make sure the current working directory of the terminal and console is set to the folder that contains the cloned repository.
3. Open the final_project2.Rproj from the project directory.
4. To use the image from DockerHub, run docker pull nehavm123/project_image1:latest in the terminal.
5. If you have a Windows operating system, run make report-windows in the terminal to generate the report. If you have a Mac operating system, run make report-mac in the terminal to generate the report.
6. The final report will be generated in the report/ folder on your local machine.

Link to DockerHub image: https://hub.docker.com/repository/docker/nehavm123/project_image1/general

Instructions for Building the Image Locally

If you would like to build the image locally instead of using the one on DockerHub, use the following instructions.

1. Fork and clone the repository from GitHub to your local machine.
2. Make sure the current working directory of the terminal and console is set to the folder that contains the cloned repository.
3. Open the final_project2.Rproj from the project directory.
4. Run make project-image in the terminal to build the image locally.

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Code Structure

code/01_make_table.R

• Reads in final_project_data.rds and creates wide dataset for the sum of tests at the individual level
• Adds labels to variables representing the number of STI tests specific to each disease
• Creates a table using the table1 package with the mean and standard deviation of the number of STI tests specific to each disease

code/02_make_figure.R

• Reads in final_project_data.rds and creates wide dataset for the sum of tests at the individual level
• Creates a dataset with the total number of disease-specific tests in the dataset
• Creates a figure using the ggplot2 package with the total number of disease-specific tests in the dataset

code/03_render_report.R

• Renders the final report (report.Rmd) and outputs report.html

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The Makefile, Rmarkdown (report.Rmd), and HTML report will be in the root directory of the project. The Rmarkdown will contain the table and figure produced in the analysis.