# Week 1 Lecture Plan — Course Introduction & Procedures

Duration: 2 h (Thu Sept 10, 10 am–12 pm, by Zoom — the one-off opening session; **no lab** this week, the in-person labs L1–L6 begin Thu Sept 17)

> Week 1 is orientation, not content. It explains **how the course works** and
> **mentions** the demonstration paper on a single teaser slide. The paper itself is
> unpacked one piece at a time in Weeks 2–7, exactly when each method needs it
> ("just-in-time"). Do **not** teach MASLD / the Fatty Liver Index today.

## Learning objectives
- Understand the course's aim (applied capstone) and the term-long project.
- Know the **Replicate → Interrogate → Improve → Defend** spine and the Tue-lecture → Thu-lab → increment rhythm.
- Know the milestone map (M0–M4) and **how grading works** (3-band; M1/M2/M3/M4 carry weight; P1–P5 are optional and ungraded; labs are Complete/Incomplete)
- Know the ground rules: AI co-pilot + individual defense; reproducibility (zip submission).
- Know how to **choose an eligible project** (the M0 feasibility gate).
- Leave able to set up R/Quarto/GitHub and start scanning candidate papers.

## Continuity
- **First week** — no prior lab to recap.
- **Today** sets up everything: the project arc and the machinery used all term.
- **Sets up:** environment setup + the M0 paper hunt (locked Week 3) + next week's first method.

## Slide blueprint

1. **Welcome to SPPH 604** (8 min) — capstone/applied; theory → reproducible practice; "just-in-time" teaching.
2. **The big idea: one paper, all term** (7 min) — the Replicate → Interrogate → Improve → Defend spine.
3. **The weekly rhythm** (6 min) — Tue lecture → Thu lab (L1–L6) → increment (P1–P5); P1–P5 optional and ungraded, with no separate deadline and nothing to submit, compiled into M1.
4. **The milestone map** (6 min) — M0 (Wk3) → M1 (Wk8) → **M2, a live critique of another group's M1** (Wk9) → M3 (Wk11) → M4 (Dec). There is no separate peer-review milestone; the critique *is* M2.
5. **What each milestone asks** (7 min) — M0 gate; M1 replication + dominant threat; M2 critique of another group's M1; M3 present your own improved analysis + defend *whether it's justified*; M4 dense letter.
6. **How you're graded** (6 min) — 3-band Weak/Adequate/Exceptional; weights **M1 30, M2 15, M3 15, M4 30, Labs 10 (Complete/Incomplete), M0 pass/fail**, bonus +2.
7. **Choosing your project (M0 feasibility gate)** (7 min) — the six criteria; start scanning now.
8. **BREAK** (10 min).
9. **AI is a co-pilot — you are accountable** (6 min) — allowed/encouraged; "the AI did it" is no defense; individual M3 is the backstop; disclose use in every cover note (M0, M1, M2, M4). M3 preparation needs no disclosure — there is no M3 submission; at M2, paste what is yours or public and describe what is theirs.
10. **Reproducibility is the standard** (5 min) — runs on a fresh machine; submit a **zip of your repo** (no repo access).
11. **Logistics** (6 min) — meeting times and modality (Tue class by Zoom; Thu lab in person, SPPH 143); OER textbooks; communication; groups vs individual defense; accommodation letters.
12. **Our demonstration paper — the ONLY paper slide** (5 min) — Kueh et al. 2026 (MASLD/NHANES); four body-shape groups; the paper's headline: the **non-obese, high-waist** group dies most; we rebuild + interrogate it. **MASLD hook (the whole mention):** that's the *what/why*; the *how* starts next week, distributed across the term.
13. **This week: get set up** (5 min) — R/RStudio/Quarto + Git/GitHub; verify render + first commit; form groups; scan candidate papers.
14. **Bridge to next week (Week 2 → L1)** (4 min) — NHANES + reading Methods critically; L1 data wrangling; begin shortlisting for M0; come with a working toolchain and 1–2 candidate papers.

The rebuilt deck (`slides/Week1_intro_slides.qmd`, 17 slides) runs ~113 min including the break, which is what fits the 2-hour opening session; the blueprint above is still the older 3-hour, 14-slide plan and needs retiming to match. Deck: `slides/Week1_intro_slides.qmd`.