Software Tools for Data Analysis
STA 9750
Michael Weylandt
Week 2 – Thursday 2026-02-05
Last Updated: 2026-02-05

STA 9750 Week 2

Today: Lecture #02: Tools for Reproducible Research

These slides can be found online at:

https://michael-weylandt.com/STA9750/slides/slides02.html

In-class activities (if any) can be found at:

https://michael-weylandt.com/STA9750/labs/lab02.html

Upcoming TODO

Upcoming student responsibilities:

Date Time Details
2026-02-12 11:59pm ET Syllabus Quiz / Verification of Enrollment
2026-02-12 NA Classes Cancelled (Lincoln’s Birthday)
2026-02-19 6:00pm ET Pre-Assignment #03 Due
2026-02-19 11:59pm ET Team Roster Submission
2026-02-20 11:59pm ET Mini-Project #00 Due
2026-02-26 6:00pm ET Team Contract Due
2026-02-26 6:00pm ET Project Proposal Presentation Slides Due
2026-03-01 11:59pm ET Mini-Project Peer Feedback #00 Due
2026-03-05 6:00pm ET Pre-Assignment #05 Due

Course Enrollment

Final enrollment: 24

  • \(\approx\) 5 final project teams (4-6 each)
  • 3-4 MPs to review per peer-feedback cycle

Course Project

Course project description is now online

Detailed discussion of:

  • Project structure
  • Key deadlines
  • Grading rubrics

Please send me questions!

First step: by 2026-02-19, email me your group members.

Special presentation next week on finding good data sources

Piazza

  • 12 sign-ups:
    • 12 still sneed to sign up
  • Post #05 - Search for Teammates

Instructor Tip: Before committing to a team with someone, you can look up their GitHub and see how they did MP#00 (how early, how technical). This might be helpful to find teammates whose work patterns are calibrated to your own.

Pre-Assignments

Pre-Assignment #02

  • I sometimes give feedback through Brightspace, so check ‘feedback’ if you are alerted to any
  • Settings tweaked to only re-display questions you got wrong on re-attempts

Pre-Assignment #03

  • Day before class by 6:00pm each week
  • Available on course website + Brightspace after 9:00pm

Mini-Project #00

Mini-Project #00

  • Due (just after) our next class
    • Friday, February 20
  • Possible tech issues, so start early

Optional DataCamp

New optional DataCamp course:

  • Reporting with R Markdown

R Markdown is proto-Quarto:

Today

  • Introduction to Markdown and Quarto
  • Review of Questions from Pre-Assign #02
  • Introduction to Git and GitHub pages
  • How to ask for help

Introduction to Markdown and Quarto

Markdown

Markdown:

  • Initially developed to replace complex mark-up languages (HTML, XML)
  • Simple syntax:
    • Can be read as plain text
    • Easy to translate to HTML
  • Now ubiquitous (even in ChatGPT!)
  • Can be used for more than just web pages
  • Standardized as CommonMark

Markdown

Source code:

This is what Markdown looks like!

I can write in *italics* or **bold**. 

Lists are easy: 

1. First
1. Second
1. Third

as are links to [helpful info](https://commonmark.org).

Markdown

Output:

This is what Markdown looks like!

I can write in italics or bold.

Lists are easy:

  1. First
  2. Second
  3. Third

as are links to helpful info.

Rendering Markdown

Markdown is just a language:

  • Software needed to render from plain text to output formats
  • Most popular (behind the scenes) is Pandoc

Rendering Markdown

Pandoc can essentially convert anything to anything:

Markdown - WYSIWYM

Markdown is a WYSIWYM format:

  • What You See is What Y Mean
  • Not WYSIWYG: What You See is What Y Get

Extensions allow finer control of formatting

  • Provide templates to pandoc for finer control (not in this class)

Markdown and Quarto

  • Quarto implements Markdown with data-analytic extensions
  • Seamless (ideally!) integration of code and text
  • No more copy and paste

Markdown and Quarto

In this class, web sites:

  • Each qmd document becomes a single html file (page)
  • All files in directory collectively make a web site
    • GitHub project \(\implies\) your website in MP#00

Resources:

RStudio - A Useful IDE

Official Cheat Sheets:

Data Camp RStudio Tutorial (Free)

  • For today, first ~half

RStudio has native Quarto support: just hit “Render”

FAQs from PA#02

Q1

What is Markdown?

Per Wikipedia: “Markdown is a light-weight, plain-text, markup language specification”

  • Light-weight: relatively simple, focus on content than formatting
  • Plain-text: accessible using almost any text editor (RStudio, GitHub, VS Code, etc)
    • Not locked into specific software (e.g., MS Word)
    • Easily incorporated into a variety of technologies

Q1

What is Markdown?

  • Markup language: a ‘mini-coding language’ for text documents
    • Other famous examples: HTML, XML
  • Specification:
    • CommonMark defines ‘standard’ Markdown
    • Some software allows extensions
    • Pandoc often powers under the hood

Q2

Other than text formatting, does Markdown have any other uses?

On its own, Markdown is just text formatting (but that’s a lot!)

We will use Quarto which augments markdown for reproducible research.

We can embed code-and its output-inside Markdown documents.

Q3

What uses Markdown?

So much! Used by Bitbucket, GitHub, OpenStreetMap, Reddit, Stack Exchange, Drupal, ChatGPT, Discord, MS Teams and many more!

Tools like Pandoc/Quarto render Markdown to:

  • HTML
  • PDF
  • Web Slides
  • EBooks
  • Research Papers
  • Word Documents
  • PowerPoint slides
  • and so much more!

Q4

What is the difference between a Code section and a Nested List? Are they just different ways of indenting?

No. Nested lists are ‘just’ text

Code formatting enables much more if rendering engine supports it:

library(tidyverse)
ggplot(txhousing, 
       aes(x=ym(year, month, 1), 
           y=sales, 
           color=city)) + 
    geom_point() + 
    geom_smooth() + 
    xlab("Date") + 
    ylab("Number of Sales")

Q5

How are we going to use Markdown?

All written work (mini-projects and final project) in this course will be submitted using Markdown (by way of Quarto).

Specifically:

  • Submission pages for 5 mini-projects
  • Individual reports for course project
  • Summary (team) report for final project

You are also encouraged (but not required) to use Markdown for presentation slides (like these!)

Q6

How can I create Tables in Markdown?

Markdown has two table syntaxes:

  • an easy one with minimal control
  • a hard one which allows fine grained control (alignment, column widths, etc.) - “pipe tables”

If you are making complex tables, I recommend using the list-table extension.

(See syllabus.qmd in course repo for examples.)

Q7

How to create images and links?

Basic hyperlinks look like this:

[link text](https://the.url/goes/here)

If you want to embed the contents of a link, prepend it with an exclamation point. This is most useful for images:

![Image Caption](https://the.url/goes/here.png)

You can even put a link inside an image to be fancy:

[![Elephant](elephant.png)](https://en.wikipedia.org/wiki/Elephant)

Q7

How to create images and links?

Quarto automatically embeds the results of plotting code:

Here, Quarto handles all the file creation and link targeting for us. If I change the code, the figure will change automatically.

Git and GitHub Pages

Git

git is the industry-standard tool for source code management (SCM)

  • SCM aka Version Control Systems (VCS) are used to manage code through the development process
  • Saves versions of your code and lets you access them whenever
  • Not automatic like Dropbox: you save a version when you intend
  • Powerful tools for parallel versions or multiple authors - we won’t be using these

Git

Courtesy of PhD Comics, this is what we want to avoid:

Git

Git tracks changes to files

  • A commit is both a set of changes & the result of all changes to that point
  • A branch name (like main) is just a stand-in for “latest commit”

The Cycle of Git

For this course, I like the mental model of a box:

  • git add: Commands to put changes in the box
  • git commit: Seal the box and put shipping info on the outside
  • git push: Send the box (to GitHub)

The Cycle of Git

From GitHub user @design-web-victo:

RStudio Git Integration

Once you create a project, RStudio has built-in git integration

  • Do the same commands with buttons instead of code

  • Uncheck Blue M are files that have been Modified since the last commit
  • Yellow ? are files I have never told git to track

RStudio Git Integration

Check box next to a file name to stage (or add) it in git

  • Load it in the box
  • Getting ready to save it

RStudio Git Integration

Create a commit with the Commit button

  • You have to type a message and hit Commit a second time

Git to GitHub

git push (green up arrow button) to move files to GitHub

Resulting commit now visible on GitHub

Automatically updates website as well

File no longer listed in Git pane - no new changes

  • If I make more changes, file will reappear as M

GitHub

For us, GitHub is just a “dumping ground”

  • Only send data to GitHub from a single computer
  • Much more complex workflow if moving changes up and down

Warning: Do not make any edits using the GitHub website. This will cause tons of pain. All changes should be made from one computer and pushed upwards only.

GitHub Pages

GitHub provides GitHub Pages

  • Free hosting for static web pages
  • Static means no login or server-side interactivity
    • Limited client-side activity via JavaScript

We will use GitHub pages for all work submission in this class

  • Public visibility (portfolio)
  • Uploading qmd files allows automatic checks
  • Peer evaluation
  • Follow instructions carefully & I can automate

GitHub Instructions

By default, URLs look like:

https://YOUR_GITHUB_ID.github.io/YOUR_REPO_NAME

If you create a repo called YOUR_GITHUB_ID.github.io, URL simplifies:

https://YOUR_GITHUB_ID.github.io/

If you own a domain, you can map to arbitrary base URL:

https://DOMAIN_NAME/YOUR_REPO_NAME

E.g., https://michael-weylandt.com/STA9750 from michaelweylandt/STA9750 on GitHub

Names in Instructions

Throughout course instructions, you will see things like YOUR_GITHUB_NAME; substitute your GitHub account name for the whole string

For me, if instructions say

STA 9750 YOUR_GITHUB_ID Mini Project #00

I will type

STA 9750 michaelweylandt Mini Project #00

(no brackets)

How to Ask for Help

How to Ask for Help

Professional programming is at least half looking things up; at beginning stages, the fraction is even higher.

So it’s important to know how to see help the smart way:

  1. Official documentation. Free software almost never becomes famous without great documentation: R and its packages are no exception. Everything we will use in this class has solid documentation.

How to Ask for Help

  1. Search Engine.

Most programming challenges have been faced by somebody before, so Google it!

Tips:

  • Include R or rstats in your search query
  • It’s better to search what you want to do rather than how you think you should do it.
  • Search programming Q&A sites like StackOverflow for specific code questions; blogs and course materials are better for “big picture” questions

How to Ask for Help

  1. Ask on a Forum with a Reproducible Example

Programming fora, like StackOverflow, are full of great resources. Most of what you need is already there. But if you need to ask a new question, make sure to create a minimal reproducible example

Make it easy for your helper to help you.

  • Minimal: narrow down to as few lines of code as possible
  • Reproducible: self-contained without dependencies on libraries (if can be avoided); load all packages needed; use standard data

Pro-Tip: You’ll solve over 50% of your problems in trying to create an MRE.

How to Ask for Help

Tips:

  • Show the code, even if it doesn’t work
  • Send code as text, not screenshot (so your helper can run it)
  • Smaller examples help narrow down problems
  • Avoid IO (file input and output) unless specifically relevant to problem
  • Remove everything you can

The reprex R package helps with this: see this talk.

For this class, rely on Piazza!

Wrap-Up

Markdown, Quarto, GitHub

  • Use Markdown to write web-native documents
  • Render to HTML using Quarto
  • Share via GitHub
  • Host via GitHub Pages

Looking Ahead

Course Project:

  • Start looking for teammates and topics

Life Tip of the Week

Recommendations from Professors

In the near future, you may want recommendations from your professors. Some advice on getting good recommendations:

  1. Understand professional vs academic recommendations
  2. Seek out strong recommendations
  3. Confidential recommendations highly preferrable

Professional vs Academic

  • Professional: For a job. Typically a brief survey or quick reference check.

  • Academic: For awards, fellowships, research positions, graduate admissions. A personalized letter from me.

I can usually do professional recommendations quickly (4-5 business days). Academic recommendations require a minimum of two weeks.

Strong Recommendations

A strong recommendation is one that supplements what is already in your application.

  • Say things that aren’t on your transcript
  • Attest to character and quality of work

The better I know you, the stronger a letter I can write.

You can ask if a professor can write you a strong recommendation. If they say they can write, but it may not be strong, consider asking elsewhere.

Strong Recommendations

Ugly:

Student N took my class and received an A.

Bad:

Student N took my XYZ class and received an A. My XYZ class covers ABC at an advanced level and provides N a strong foundation for your program.

Good:

I first met student N in my XYZ class. She was an active participant in class, regularly attended my office hours, and regularly asked for additional advanced material. She had a remarkable final project in which she ABC. It is clear that her drive and passion for XYZ make her an excellent candidate for your fellowship.

Confidentiality

Under some parts of US law, you have the right to see what letters for you I write unless you specifically waive that right.

Waive the right


Readers will assume you have read a non-confidential letter and discount whatever I say.

My Policy

I will write a letter for any student who has passed one of my classes (C or higher) or is on track to do so.

No guarantee it is strong unless you ask. I understand that sometimes you are just trying to make sure you have enough.

Give me at least 3 weeks, ideally more. A rushed letter is a short and generic letter.

My Policy

Send me:

  • Description of who I’m writing to
  • Your CV / Resume
  • Your latest transcript
  • Presentations/project materials from my class

Once a letter is written, it’s easy for me to update and re-use.

Help me help you.



Musical Treat