PUBH 523/623 Syllabus

Modified

October 2, 2026

Key Course Info

  • Late work, closed Brightspace assignment, or need an extension? Just email me (addresses on the instructor page).
  • Practice: turn in any time before the course ends (on-time work gets feedback).
  • Labs: one “no questions asked” 3-day extension; after that, 1 point off per day late.
  • Used AI on an assignment? Add an AI Use Statement at the top (see the Generative AI Policy).
  • No attendance policy: your grade isn’t tied to watching videos, but you’re responsible for their content.
  • Class ends December 07, 2026. All coursework MUST be completed by December 13, 2026.
  • Questions or concerns anytime? Use the Ongoing Course Feedback form.

Description

Welcome to PUBH 523/623! This course introduces programming in R for public health, medicine, and related fields. We’ll focus on reproducible workflows, data manipulation, visualization, and reporting: working in project-based folders, transforming and summarizing data, making plots, generating dynamic reports, and building summary tables. No prior statistics or coding experience is expected. By the end, you’ll be comfortable starting a data exploration project in R and ready to use these skills in future analysis courses.

Course Learning Objectives

By the end of this course, you should be able to…

  1. Set up and manage project-based folders to build reproducible workflows.
  2. Clean, filter, restructure, and summarize datasets using standard R toolkits.
  3. Create clear, publication-quality data visualizations that represent trends and summaries.
  4. Launch a data exploration project on a new dataset, preparing it for advanced statistical analysis.

Instructors & Meeting Times

This class is asynchronous, so there are no set class times, but we’ll have recurring office hours. Office hours and contact info are on the instructor page.

Materials

Textbooks

You don’t need to read along with each lesson. These are here for when you want another explanation, more examples, or extra practice.

R and RStudio

We’ll use R and RStudio (both free). Please install them before our second lesson, and email me if you get stuck. Here’s some helpful installation documentation.

  1. R: https://www.r-project.org/
  2. RStudio: https://posit.co/download/rstudio-desktop/

Where things live

  • This website: all course materials (lessons, practice, data, recordings).
  • Brightspace: where you submit assignments (“Assignments” tab) and see your grades (“Grades”).
  • Slack: our main way to communicate! Post questions about practice, labs, or anything else. Here’s the invitation link to our Slack workspace! Slack is not behind the OHSU firewall, so for accommodations or sensitive topics you may prefer email. You’re welcome to message me about sensitive things on Slack, but I won’t start those conversations there.
  • Webex/Zoom: for virtual office hours. Please stay muted until you want to talk, drop your question (or “I have a question”) in the chat so we can go in order, and turn your video on if you’re comfortable, since it helps me get to know you and how you learn.

Course Structure

Component Frequency Description
Video lessons Weekly Pre-recorded lessons with explanations, interactive examples, and demos.
Practice Weekly 9 assignments to practice coding and engage with key concepts. Working in groups is encouraged, but everyone submits their own work.
Project (Labs + Poster) 4 labs, 1 final poster Labs guide you step-by-step through the coding for a data project, which comes together in a final poster (information sheet) at the end of the quarter.
Office hours Weekly Live time to ask questions, work on assignments, and meet classmates.

All components are online.

Grading & Requirements

This class uses two types of assessments:

  • Formative: work meant to help you learn and practice. Feedback helps both of us see gaps and celebrate progress.
  • Summative: work meant to show how well you’ve met the learning objectives and can use your skills outside the classroom.
Course activity Type Due PUBH 523 PUBH 623
Practice Formative Every 1-2 weeks 40% 40%
Office hours visit — Once during the quarter 2% 2%
Slack post — Once during the quarter 1% 1%
Project Labs Formative/Summative Every 2-3 weeks 40% 40%
Project Poster Summative 12/09 17% 17%

Letter grades: A (≥93%), A- (90-92%), B+ (88-89%), B (83-87%), B- (80-82%), C+ (78-79%), C (73-77%), C- (70-72%), D (60-69%), F (<60%).

Points are posted to the Brightspace Gradebook (“Grades” in the left navigation).

How each activity is graded

Practice (40%)

Everyone has a different amount of time for coursework, and practice is for learning, so grading is simple: you get a check if you complete at least 75% of the question parts, whether your answers are right or wrong. Each of the 9 practice assignments counts equally.

  • On time: you get the check and feedback on one or more problems.
  • Late: no grade penalty. You still get the check if submitted before the course ends, just no feedback (unless you email me to ask). Compare your work to the solutions or bring it to office hours.

Practice is the most helpful work in this class, so I encourage you to keep up with it and put in what effort you can!

Office hours visit (2%)

Come to office hours at least once during the quarter for full credit. You don’t need a question! Stopping by to say hi, working quietly on practice, or listening to others’ questions all count. If none of the office hour times work for you, email me and we’ll find another time to meet.

Slack post (1%)

Post in our Slack page at least once during the quarter for full credit. You may respond to someone else’s question or ask for help. As long as you show some engagement within the Slack page!

Project Labs (40%)

There are 4 labs, each worth an equal share of the 40%. Labs walk you through the coding and deliverables that build toward your poster. Each lab is graded with a rubric that focuses on completing the required code and deliverables and clear, reproducible work (e.g., code that runs and outputs that match what’s asked). You’ll get feedback on each lab, and I encourage you to use it in your next lab and your poster.

Labs follow the late policy below: one no-questions-asked 3-day extension, then 1 point off per day late.

Project Poster (18%)

The poster (an information sheet) is your chance to bring together what you built in the labs and decide what’s most important to share about your data. It is graded with a rubric that looks at accurate, reproducible analysis, clear and well-designed visualizations and tables, and communicating your findings to a public health audience. Because it’s due at the end of the quarter, feedback will be lighter, but feel free to email me with questions about your grade. And you can add this project to your resume!

Course Policies

Late Work Policy

I encourage you to submit work on time, but I know life happens. Here are some examples of extenuating circumstances (not a complete list, so please reach out with questions).

  • Practice: submit any time before the course ends for full credit. For feedback, submit on time or email me.
  • Labs: you get ONE no-questions-asked, 3-day extension. Just email me: “I am using my no-questions-asked extension for Lab __.” After that, email me to explain and ask for an extension; otherwise, 1 point is deducted per day late.
  • Final poster: email me to explain your circumstances. You may ask for an extension, but I won’t necessarily grant one.
  • All coursework must be completed by December 13, 2026. If extenuating circumstances mean you need more time, or may affect your work for several weeks, contact me and we’ll make a plan together (including any registrar logistics).

If you have an emergency

Whether it involves yourself, family, a pet, a friend, or anyone/anything important to you, please don’t worry about contacting me right away. We’ll work it out afterward. If I reach out during an emergency, it’s only because I’m worried, and you do NOT need to respond until you’re able.

Regrade Policy

If you think something was graded incorrectly, first compare your answer to the solutions. If you still think a regrade is warranted, email me the question and a short explanation within one week of the assignment being returned.

Generative AI Policy

This policy is adapted from the OHSU-PSU SPH Biostatistics program’s AI policy, which classifies PUBH 523/623 as a foundational course. Everything you need for this class is below.

Using AI is not required in this class. If you choose to use it, please follow these guidelines. AI tools (like ChatGPT, Claude, Copilot, Gemini, or an AI assistant built into RStudio) are becoming an essential skill for public health data work, so the goal is to use them responsibly, not avoid them.

The toolbox analogy

Think of this class as assembling a toolbox. A new handyperson might need help finding their tools or remembering which one does what, but eventually using them becomes second nature.

For now, generative AI can help us find and use our tools, but we’re working toward using them as second nature!

Four guiding principles

  1. Learning comes first. Ask yourself: Is AI helping me learn this skill, or doing the skill for me? If it’s doing the skill the assignment is meant to teach, don’t use it that way.
  2. Understanding is the priority. You should be able to explain and reproduce (without AI) any code or conclusion you turn in. Following along with an AI answer is not the same as understanding it!
  3. Build the foundation first. In this course, writing and debugging R code from a blank script is the skill we’re practicing. That’s why some AI uses are limited here, not because AI is untrustworthy.
  4. Be honest about AI use. Tell me when and how you used AI (see the AI Use Statement below).

What’s allowed

Can I use AI to… Practice Labs & Poster
Coding
Explain an error message Yes Yes
Explain what a function does Yes Yes
Help debug my code Yes Yes
Give me extra practice problems Yes Yes
Style or tidy my code Yes Yes
Check an answer I already got on my own Yes Yes
Draft code for repetitive data management (e.g., categorizing a numeric variable) No Yes
Draft code for a whole analysis or explore approaches beyond what we’ve learned No No
Take an assignment question and write the code for me No No
Data and statistics
Explain a concept or method in general terms Yes Yes
Check reasoning I’ve already written about which summary or plot to use Yes Yes
Pick the summary/plot for me or interpret my output for me No No
Writing
Give grammar or clarity feedback on my own draft Yes Yes
Brainstorm structure or an outline Yes Yes
Critique an interpretation I wrote myself Yes Yes
Help find background sources (that I then read and verify) Yes Yes
Draft my background or interpretation of results No No
Paste in AI-written text without substantial editing No No

There may be exceptions. For example, if a question asks you to explain what a function does, you can’t paste in AI’s explanation. When in doubt, just ask me!

Never allowed

  • Copying and pasting AI-generated answers into your assignment
  • Pasting all or part of an assignment into AI and asking for the solution
  • Presenting AI output as your own reasoning
  • Uploading confidential or restricted data (including any data with protected health information) into an AI tool, unless it’s a university-approved platform under a data use agreement
  • Using AI-generated datasets or output as if they came from the assigned data and methods
  • Using AI-generated references, results, or facts without verifying them yourself
  • Submitting AI-assisted work without an AI Use Statement

Even for allowed uses, always inspect AI-generated code and its output, whether it’s a whole chunk or a single comma. You’re responsible for making sure it does what it’s supposed to.

Practice is graded on completion, so I’d much rather see a half-written answer that shows your thinking than a polished answer from AI. And if AI helped you understand something, tell me! I’d love to incorporate it into future classes.

AI Use Statement

If you used AI on an assignment, add a brief statement at the top that includes which tool(s) you used, what for (a sentence or two), and where it contributed to any written interpretations. For example:

AI Use Statement: Claude was used to explain an error message in Q3 and to give grammar feedback on my poster summary. All code review, reasoning, and conclusions are my own.

You don’t need to share a link or transcript of your conversation.

If the guidelines aren’t followed

If I notice AI was used outside these guidelines, I’ll reach out to let you know which assignment and which guideline, and you can choose to:

  1. Take a 0 on the assignment as submitted,
  2. Redo the assignment without AI for a new score, or
  3. Explain to me (by email or in a meeting) exactly how you used AI and show that you can do the work on your own. If that works out, you keep your original grade; if not, the question(s) where AI was used get 0 points.

First-time, good-faith mistakes (like forgetting an AI Use Statement) will generally be treated as a learning moment, not an integrity issue. Undisclosed AI use, or turning in work you can’t explain, may lead to consequences under this policy and university academic conduct policies.

Academic Integrity

As a PSU/OHSU student, you’re expected to act with professionalism and integrity. Academic misconduct (plagiarism, cheating, fabricating data, falsifying records, or helping others do so) will be taken seriously. Your submitted work should reflect your own effort, and any resources you use should be cited.

How to Succeed in This Course

Every instructor uses resources and assignments a little differently, so here’s how to get the most out of each in this class.

Resources

Resource How to use it
Lesson videos Watch all of them, following the schedule. Follow the slides, take notes on details mentioned out loud, and work through examples with me.
Office hours Ask questions about assignments or lessons, work on your assignments with help nearby, or meet classmates to collaborate with.
Slack Ask questions anytime. Chances are a classmate has the same question!
Textbooks Not required reading. Use them when you’re stuck on a topic, want another example, or want more practice.
Website Home for all course materials. Explore the tabs to get a sense of how it’s organized.

Assignments

Assignment Before you submit After it’s graded
Practice • Try each problem on your own first
• Talk it through with a peer
• Ask on Slack or come to office hours
• Show your thought process
• Search Stack Overflow for errors		 • Review the solutions and your mistakes
• For written answers, check with me or a TA if yours fits
• Bring questions to office hours
Labs and Poster • Start early!
• Check your coding with classmates
• Bring specific R questions to office hours
• For the poster, pull together your lab work and decide what matters most		 • Use lab feedback in future labs and your poster
• Email me with grade questions
• Keep your poster and add it to your resume!

Want another part of the course explained like this? Let me know through the Ongoing Course Feedback form.

Course Expectations

What you can expect from me

  • Commitment to your success. I believe everyone can succeed in this course, and I’ve designed it to support your learning. Reach out anytime about anything that’s unclear.
  • An inclusive, supportive community. I’ll work to build a space of generous listening, civility, humility, and patience, where you feel free to share your views and ask questions.
  • Openness to feedback. Tell me when something isn’t clear or isn’t meeting your needs, and especially if you notice bias or stereotyping in my materials. Tell me what you enjoy, too!
  • Responsiveness. I check email and Slack daily and aim to reply within 24 hours, Monday-Friday.
  • Clear guidelines and prompt feedback. Clear instructions and rubrics for assignments, helpful feedback, and prompt grade updates in Brightspace.

What I ask of you

  • Watch the lessons following the schedule.
  • Participate in discussions on Slack and in office hours, and be respectful of everyone’s contributions.
  • Reach out early. If you’re having trouble keeping up, let me know as soon as possible so we can find a solution together.
  • Submit assignments through Brightspace, following the late policy if you need more time.
  • Tell me about accommodations before or during the first week. Students seeking academic accommodations should register with the appropriate service (see the SPH/OHSU policies on Brightspace). If a religious holiday affects your schedule, let me know and we’ll plan around it.
  • Take care of yourself and seek help if you need it (see Student Wellness below).

Course Communications

  • Brightspace announcements: for important or urgent updates, sent to your OHSU email. I’ll copy non-sensitive ones to Slack.
  • Slack: for questions and general discussion.
  • Email: for private matters. Please use my OHSU address (wakim@ohsu.edu). Messages sent through Brightspace Inbox will not be answered.

Course Feedback

Ongoing Course Feedback

You can share anonymous feedback anytime through this Microsoft Form (leave your email only if you’d like a reply). I review it regularly. If I’ve done anything that made you uncomfortable, please tell me so I can change. Ultimately, this class is for you, and my social identity/behavior should not get in the way of your learning. Some examples:

  • Nicky talks a little fast in the videos. Could you slow down?
  • During office hours, Dr. Wakim made a face when I asked a question, and it made me feel self-conscious.
  • Dr. W asked about my experience in a way that made me feel like a monolith. Please don’t assume I can speak for my social identity groups.
  • The examples don’t make me more interested in the material.

Final Course Feedback

At the end of the course, you’ll be asked to complete a formal evaluation. Your feedback is critical for improving this course and matters for my career advancement. Since our class is on the smaller side, everyone’s participation is needed for the feedback to be released. Thank you!

Schedule

See the Schedule page. I may adjust it if we need more or less time on a topic.

Student Resources

Student Wellness

I care about your physical and emotional well-being. If a health issue is affecting your work, or you’d like help connecting with resources, please reach out.

Food Insecurity

Students with Children

PSU’s Resource Center for Students with Children offers family-friendly study spaces, baby starter packs, free kids’ clothing, and childcare financial resources.

Writing Support

  • SPH Writing Support: one-on-one help from Leslie Bienen, MFA, DVM, on papers, dissertations, applications, grants, and more. Email writingsupportsph@pdx.edu or book on Calendly.
  • Grammarly: SPH students get a free subscription. Sign up with your PSU login through this form.

SPH and OHSU Policies

See the Brightspace syllabus for additional SPH and OHSU policies and resources.