UBC School of Population and Public Health · Term 1, 2026W
Student preview — 2026W. This repository is available now so you can see the course structure, materials, and submission formats. Minor wording and Canvas configuration updates may still be made before this version is declared final.
All course materials live here. Canvas carries submissions and grading, and the things the syllabus points there for: the rubric grids, the worked AI-use example, Zoom links, and anything posted in the weekly Modules.
Prefer a guided view? Use the SPPH 604 student guide for a week-by-week map, assignment overview, repository map, and searchable file catalogue. This README remains the compact overview of the repository itself.
You pick one recent, open-data paper in Week 3 and carry it all term:
Orient → Lock → Build → Replicate → Review → Improve & Defend → Reanalyse
You form a group, lock one feasible paper, build the analysis through P1–P5, assemble the first complete argument at M1, review another group’s work at M2, improve and defend your own analysis at M3, and carry the best-defended version into the final M4 reanalysis.
| What | Weight | |
|---|---|---|
| M0 | Feasibility memo — lock your paper | pass/fail |
| L1–L6 | Weekly labs on fixed teaching data | 10% |
| P1–P5 | Weekly increments on your paper — optional, ungraded, no deadline, nothing to submit | — |
| M1 | Your five increments compiled + which threat most endangers the paper (deck + repository zip) | 30% |
| M2 | A live critique of another group’s M1 | 15% |
| M3 | Individual oral defense: improve and defend the analysis; changes may be reviewer-prompted or self-initiated | 15% |
| M4 | Reanalysis letter + reproducible repository | 30% |
The full rules are in the syllabus.
| Folder | What’s in it |
|---|---|
syllabus/ |
The syllabus. Authoritative on deadlines, weights and policy. |
labs/ |
L0 setup (self-study) and the L1–L6 handouts. Labs run Thursdays 10–12, SPPH 143, Weeks 2–7. |
practice/ |
P1–P5 handouts — the same methods applied to your own paper. |
milestones/ |
M0–M4 assignment briefs — what each milestone asks for. |
examples/ |
Worked model answers for P1–P5 and M0–M4, on the demonstration paper. |
reproduction/ |
The full R pipeline behind the demonstration paper. |
lectures/ |
Week 1–7 plans and slide decks. |
paper/ |
Two papers under different licences — the demonstration paper (CC BY-NC) and a second NHANES paper (CC BY) read alongside P4 — and their attribution. |
index.md |
Index of every document in the repository. |
practice/README.md
— it explains how P1–P5 build into M1.examples/P1_analytic_cohort/,
to see the standard.labs/L0_setup.md before
the first class — R, RStudio, the PDF toolchain, a GitHub
account, and a test knit.If you already know the filename you need, open index.md or use the complete
file catalogue.
Everything in examples/ and reproduction/
is built on:
Kueh MTW et al. Body weight categories and fat distribution in relation to all-cause mortality among adults with MASLD. BMJ Open 2026;16:e113719. NHANES 2007–2018 with NCHS linked mortality. doi:10.1136/bmjopen-2025-113719
It reproduces: N = 6,371 against the paper’s ~6,300, groups 391 / 4,585 / 787 / 608, 586 deaths, and a Group IV hazard ratio of 15.14 unadjusted → 2.91 adjusted (published: 15.13 → 2.89).
These are answer keys, not templates to copy. You will do this on your paper. What transfers is the sequence of moves, not the numbers.
The article is included in paper/
and is redistributed under CC BY-NC (© Author(s) 2026,
published by BMJ Group; no commercial re-use). See paper/README.md for the full
attribution. Its peer-review history file carries no stated licence and
is not redistributed here.
# from the reproduction/ folder
source("R/run_all.R")Needs R with haven, dplyr,
survival, survminer, rms,
survey, mice, tableone,
ggplot2, nhanesA.
The NHANES microdata is not in this repository — it
is ~211 MB and freely available from CDC. R/01_download.R
fetches it into reproduction/data/. The URL pattern is:
https://wwwn.cdc.gov/Nchs/Data/Nhanes/Public/<year>/DataFiles/<FILE>.xptPermitted, with disclosure, and specified per assessment in the syllabus. Two things are never permitted: AI assistance during the live M3 defense, and putting any part of another group’s unpublished work into an AI tool. Preparing for M3 with an AI is permitted and needs no disclosure, because M3 has no submission. While running a reviewed group’s code you may ask an AI about your own machine and public documentation: paste what is yours or public, describe what is theirs. Supports approved through UBC’s Centre for Accessibility are the exception to the live-defense rule; they are arranged in advance through the syllabus section Academic Accommodation Letter.
You remain responsible for the integrity and accuracy of everything you submit. The oral defense is where the course checks that the reasoning is yours.
Dr. M. Ehsan Karim — ehsan.karim@ubc.ca ·
ehsank.com Put
SPPH 604 in the subject line. Replies within 48 hours on
weekdays. Ask the TA in lab or in TA office hours, not by email.
Course materials are CC BY 4.0 — reuse and adapt
freely with attribution, with named carve-outs rather than one
exception: material distributed only through Canvas and not published
here — if it is not in this repository, do not post it — plus
third-party material, the exercise datasets, session recordings, student
work, and the papers in paper/, which carry their own
publisher licences (the demonstration paper is CC BY-NC). See LICENSE.md.
UBC’s Point Grey Campus is located on the traditional, ancestral, and unceded territory of the xʷməθkʷəy̓əm (Musqueam) people.