DATA 550: Final Project (Katelyn Chiang)

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Final Report Information

The final report can be generated using the contents of this directory:

• The Makefile contains rules for generating targets that culminate in the Final Report.
• The Dockerfile contains commands for building a container with the appropriate software and packages needed to run this analysis.
• The Code folder contains various R scripts for different aspects of the analysis.
• The Output folder contains various results from different analyses that will be included when building the final report.
• The Data folder contains the raw data that will be used in the analysis.

Instructions for Building the Image (For Final Project 8: docker)

To build the image locally on your computer:

1. Clone the contents of this repository onto your local machine.
2. Ensure you are in the correct working directory (project directory with appropriate project files).
3. In the terminal, run make project_image to build the image that will have the necessary software and packages to run the analyses for this final report.

Instructions for Generating the Final Report (For Final Project 8: docker)

There are 2 options for generating the final report. You can either pull or download the image from DockerHub and then use that image to run the container to automatically generate the final report. Alternatively, you can use the included Dockerfile found in this GitHub repository to build the image on your local machine before using that image to run the container and automatically generate the final report.

Option 1: Use the Image from DockerHub and Run

If you are using a Mac or Linux operating system:

1. Clone the contents of this repository onto your local machine.
2. Ensure you are in the appropriate working directory (project directory with appropriate project files).
3. In the terminal, run make pull_project_image to pull the image from DockerHub that has the necessary software and packages to run the analysis. This is an optional step and is not necessary.
4. In the terminal, run make mac_docker_image/report.html to run the container and automatically generate the final report. You will find the final report .html file inside the "report" folder in the working directory on your local machine.

If you are using a Windows operating system:

1. Clone the contents of this repository onto your local machine.
2. Ensure you are in the appropriate working directory (project directory with appropriate project files).
3. In the terminal, run make pull_project_image to pull the image from DockerHub that has the necessary software and packages to run the analysis. This is an optional step and is not necessary.
4. In the terminal, run make windows_docker_image/report.html to run the container and automatically generate the final report. You will find the final report .html file inside the "report" folder in the working directory on your local machine.

Link to image on DockerHub

Option 2: Build the Image Locally and Run

If you are using a Mac or Linux operating system:

1. Clone the contents of this repository onto your local machine.
2. Ensure you are in the correct working directory (project directory with appropriate project files).
3. In the terminal, run make project_image to build the image that will have the necessary software and packages to run the analyses.
4. In the terminal, run make mac_report/report.html to run the container and automatically generate the final report. You will find the final report .html file inside the "report" folder in the project directory on your local machine.

If you are using a Windows operating system:

1. Clone the contents of this repository onto your local machine.
2. Ensure you are in the correct working directory (project directory with appropriate project files).
3. In the terminal, run make project_image to build the container that will have the necessary software and packages to run the analyses.
4. In the terminal, run make windows_report/report.html to run the container and automatically generate the final report. You will find the final report .html file inside the "report" folder in the project directory on your local machine.

Instructions for Generating the Final Report (For Final Project 6: renv)

1. Ensure you are in the correct working directory.
2. Ensure you have the renv package installed on your computer.
3. In the terminal, run make install to install necessary packages. As of April 29, this rule has been commented out of the Makefile to ease local image building. This rule will no longer work as of April 29.
4. In the terminal, run make report.html to create the final report.

Code Description

Code/01_Calculate_Obesity_Prevalence.R

• Calculates the prevalence of obesity among Local Pediatric Primary Care Clinic patients for each year (2016-2023).
• Saves prevalence information as an .rds object in the Output/ folder.
• Calculated prevalence information is later used to create Figure 1.

Code/02_Make_Table1.R

• Creates Table 1 which displays weight status of various sociodemographic groups in the Local Pediatric Primary Care Clinic patient population in 2023. The table displays the number (and row percents) of patients in each weight status category in various groups.
• Saves table information as an .rds object in the Output/ folder.

Code/03_Make_Figure1.R

• Creates Figure 1 which displays prevalence of obesity in the Local Pediatric Primary Care Clinic for each year 2016-2023.
• Saves figure information as an .rds object in the Output/ folder.

Code/04_Render_Report.R

• Creates the Final Report which includes introductory information and the results (Table 1 and Figure 1).
• Rendered report is saved as an .html file in the main folder.

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