Skip to main content
Week 2: Modern Workflows
Final Checklist
Health Data Science: AI and Knowledge Translation
The Project
About the Course
Course Overview
Week 0: Asynchronous Onboarding
Week 0: Asynchronous Onboarding
Week 1: Health Data, KT & Ethics
Health Data & Ethics
Activity: Data Intake Card
Week 2: Modern Workflows
Modern Workflows
The Analogy: Public Computer vs Cloud Drive
Tour of the Repository
Opening Your First Codespace
Reopening a Codespace
VS Code Orientation
Files vs Folders
The Magic Moment: Render Quarto
Commit Your Work
Troubleshooting: Rebuild Container
Stop Your Codespace
Final Checklist
Week 3: R with AI
Week 3: R with AI
The Setup (The Cockpit)
Packages (The Toolbox)
Basics: Boxes & Toasters
Control Flow
The Loading Dock (Data Import)
The Detective (Debugging)
AI Safety: The Audit Checklist
The Paper Trail (Comments)
Assignment 2: R With AI
Final Summary Checklist
Week 4: Git & Collaboration
Git & Collaboration
Git Basics
Time Travel
Repo Hygiene
Branching
Pull Requests
AI Auditing
Setting Up Your Group Repository
Knowledge Check
Practice Exercise: Full Workflow
Quick Reference
Week 5: Polyglot Awareness & R Deepening
Polyglot Awareness & R Deepening
R Deepening and Parity Check
Python vs. R
Python Environment
Packages and Reproducibility
Translation Traps
Load and Inspect Data
Python Tracebacks
One Step, One Cell
Mixing R and Python
Reusable Python Scripts
Git Progress
Proposal Readiness
Knowledge Check
Bilingual Translation
R To Python Cheatsheet
Week 6: Data Visualization
Week 6: Data Visualization
Why Visualize, and What For
Grammar of a ggplot, and Your First Plot
Worked Example: Descriptive BMI Visualization
How a Plot Can Mislead
AI Prompts You Can Defend
In-Class Studio: AI Visual Audit
Assignment 5 Walkthrough and Reference
Week 7: EDA, Table 1 & AI Auditing
Week 7: EDA, Table 1 & AI Auditing
EDA as Evidence Stewardship
Cohort and Missingness
Worked Example: EDA and Table 1
What Each Statistic Claims (and Does Not)
Four Audit Categories for AI-Drafted EDA
In-Class Studio: Planted-Error Audit
Assignment 6 Walkthrough and Reference
Week 8: Dashboard Prototypes for KT
Week 8: Dashboard Prototypes for KT
What a Dashboard Is, and Three Pathways
From One Finding to a Prototype: The 1-1-1-1-1 Rule
Starter Dashboard
Audience-Facing Text: What You Can and Cannot Change for A7
Testing, Privacy-Safe Publishing, and the Shiny Demo
In-Class Studio: Dashboard Adaptation
Assignment 7 Walkthrough and Reference
Week 9: Communication of Scientific Findings
Week 9: Communication of Scientific Findings
Why Communication Is KT
Claim, Evidence, Limitation
Revealjs Starter
Peer Feedback
Assignment 8 Walkthrough
Week 10: Writing & Publishing Reports
Week 10: Writing & Publishing Reports
Report Goals
Report Structure
Report Template: NHANES Equity Summary
Citations and Grounding
Private Preview
Assignment 9 and M3
Week 11: Portfolio Surgery
Week 11: Portfolio Surgery
Surgery Goals
Fresh Codespace Test
README and Repo Hygiene
Peer Review and M4
Optional Pathways
Portfolio Surgery and the Final Portfolio
Project Presentation (Online)
Project Presentation (Narrated Deck)
Assignments and Milestones
Assignment Schedule
Assignments
Assignment 1: Modern Workflows
Assignment 2: R With AI
Assignment 3: Git Collaboration
Assignment 4: Polyglot Parity
Assignment 5: Visualization Audit
Assignment 6: EDA and AI Audit
Assignment 7: Dashboard KT Prototype
Assignment 8: Scientific Communication
Assignment 9: Reproducible Report
Milestones
M0: Group Formation
M1: Project Proposal
M2: Preliminary Analysis
M3: Project Update
M4: Peer Review
Presentation (Final Portfolio Component)
Final Portfolio
Final Portfolio Checklist
Repository Sharing Guidance
Worked Example (NHANES)
Worked Example (NHANES)
Example: M0 — Group Formation
Example: M1 — Project Proposal
Example: M2 — Preliminary Analysis
Example: M3 — Project Update
Example: M4 — Peer Review
Example: Presentation — Narrated Deck
Example: Final Portfolio
Reference: Data Sources
NHIS
NHANES
BRFSS
CCS
CADS
CTNS
CSADS
PHAC Health Infobase
CCDSS
GHO
Open Portal
BC Data Catalogue
Table of contents
Reflection
Edit this page
Report an issue
Week 2: Modern Workflows
Final Checklist
Final Checklist
I understand repository vs Codespace
I created or located my forked course repository
I rendered a
.qmd
file
I committed changes
I know how to rebuild container
I know how to stop Codespace
Reflection
Write 2–3 sentences:
What was easiest?
What was confusing?
What questions do you still have?
Stop Your Codespace
Week 3: R with AI