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.