Reproducible Workflows

Fundamentals of Data Science

MTH-391D | Spring 2025 | University of Portland

January 22, 2025

Objectives

Introduce R Markdown
Elaborate motivations for learning R in Data Science
Summarize expectations on assignment deliverables
Activity: Modify an RMarkdown document

Previously… (1/2)

R Script File Example

Previously… (2/2)

Running R Commands in Different Ways

RMarkdown, an Introduction

What is RMarkdown?

A tool for creating dynamic documents.
Combines plain text, code, and outputs (e.g., plots, tables).
RMarkdown is a file with extension “.Rmd”, and when executed, it outputs into HTML, PDF, Word, or Slides.

It support multiple programming languages.
It was created for the purpose of automating scientific reports and visualizations.
It is also professional, clean, and organized.

RMarkdown for Reproducibility

Why use RMarkdown?

Dynamic and Flexible Document Creation: Allows easy updates and ideal for iterative research processes.
Integration of Code and Results: Combine R and other programming languages in the same document. Automatically executes and displays code outputs (e.g., tables, plots).
Python Equivalent: Jupyter Notebook is similar to RMarkdown but it is primarily built for Python instead of R. We will explore more on this later.

Widely Used in Data Science: Popular in academia, industry, and reporting. Simplifies workflows for analysis, visualization, and documentation.
RMarkdown is required for this course’s project phase reports: All project reports must be completed in RMarkdown and submitted in both .Rmd and .html formats. This ensures that your work is detailed, well-organized, and clearly presented.

RMarkdown in R Studio

What does RMarkdown look like in R Studio?

RMarkdown Viewed in R Studio

Basic Parts of RMarkdown (1/2)

RMarkdown Basic Parts 1, 2, & 3

The YAML header: It is placed at the very beginning of the file with start and end syntax “---”. This header is required and the information that it contains can affect the entire output.
Levels of Headers: It provides titles to sections.
Basic Paragraph: Normal text that you can write where a new line means new paragraph.

Basic Parts of RMarkdown (2/2)

RMarkdown Basic Parts 4 & 5

Code Chunks: The heart of RMarkdown, where you can run codes and present it and its output clearly with the rest of the document. The start and end syntax is “```”.
Blocked Paragraph: A special paragraph that allows customization, such as changing the text color of its output.

Code Chunks in RMarkdown

Creating an R Code Chunk

Running Code Chunks

Running R on RMarkdown vs Knitting

\(\star\) Understanding this difference is key for fixing majority of errors and undesired outputs.

Transferable Skills

Why learn any of these things?

Data Science

Data processing and Analysis
Critical thinking and problem-solving
Data visualization and communication
Domain knowledge adaptability
Project management and team collaboration

R and Python

Logical reasoning
Automating repetitive tasks
Programming is an in-demand skill in both industry and academia
Learning R or Python is a gateway for more advanced programming languages
Learning how to code is a versatile skill and opens up opportunities

Expectations on Assignment Deliverables

Mini-Assignments

In-class activities and mini-assignments must be submitted either physically or through Moodle. Depending on the lesson, submission format will be in physical form, .pdf, .Rmd, or .html.

Project Phases

All project phase reports must be submitted in both .Rmd and .html files through Moodle.

\(\star\) Mini-assignments and the Project will have special R Studio spaces.

Tips for Success

How can I be successful in this class?

In-Class

Show up to class
Pay attention in class
Be respectful to your peers
Carefully read instructions and ask questions
Know that it’s okay to make mistakes

Assignments

Participate in class activities
Work on mini-assignments
Work on your project diligently
If there are significant errors, ask for help
Be responsible for your own learning

\(\star\) Help hours –walk-in and by appointment– exists!

Activity: Modify a RMarkdown document

The purpose of this activity is for you to get a sense of how mini-assignments and the project are done.

Log-in to Posit Cloud and open the R Studio assignment MA2: Modify a RMarkdown Document.
Make sure you are in the current working directory. Rename the .Rmd file by replacing [name] with your name using the format [First name][Last initial]. Then, open the .Rmd file.
Change the author in the YAML header.
Read the provided instructions.
Answer all exercise problems on the designated sections.