Add chapters 19–23 (Part III) and standardize LaTeX macros across all chapters#69
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Add chapters 19–23 (Part III) and standardize LaTeX macros across all chapters#69Copilot wants to merge 9 commits into
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Chapter 19: Time-varying treatments
- Treatment history notation, counterfactuals under strategies
- Static vs. dynamic treatment strategies
- Sequentially randomized experiments
- Sequential exchangeability and positivity
- Time-varying confounding and feedback
Chapter 20: Treatment-confounder feedback
- Elements of feedback: L_k affected by A_{k-1} and confounds A_k
- Why standard regression (stratification, multivariable) fails
- Structural nature of the bias — not fixable by model flexibility
- Adjusting for past treatment produces controlled direct effects
Chapter 21: G-methods for time-varying treatments
- G-formula for time-varying treatments (big g-formula)
- IP weighting with stabilized weights SW^A and SW^C
- Doubly robust AIPW estimator
- G-estimation of structural nested mean models (SNMMs)
- Censoring as a time-varying treatment
Chapter 22: Target trial emulation
- ITT vs. per-protocol effects
- Specifying the target trial components
- Immortal time bias and new user/active comparator design
- Sequential trials design for time zero alignment
- Unified framework for observational causal inference
Chapter 23: Causal mediation
- Limitations of classical Baron-Kenny mediation analysis
- Natural direct and indirect effects (NDE, NIE)
- Controlled direct effect (CDE)
- Interventionist/stochastic mediation approach
- Time-varying mediators as a special case of g-methods
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Agent-Logs-Url: https://github.com/ucdavis/win/sessions/a538ac1b-2966-4beb-8ded-682aaf0e2482 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
Agent-Logs-Url: https://github.com/ucdavis/win/sessions/a538ac1b-2966-4beb-8ded-682aaf0e2482 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
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changed the title
[WIP] Transcribe lecture notes to match textbook content
Add chapters 19–23 (Part III) and standardize LaTeX macros across all chapters
May 4, 2026
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@copilot fix spellcheck |
Agent-Logs-Url: https://github.com/ucdavis/win/sessions/649063ba-d668-42f8-8808-dc446b1d6867 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
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Pull request overview
Adds Part III content (Chapters 19–23) to the Quarto lecture notes and standardizes common LaTeX operator notation across the existing chapters using the shared latex-macros submodule.
Changes:
- Added new Quarto chapters 19–23 (time-varying treatments through mediation), each rendering to HTML/RevealJS/PDF (and DOCX, consistent with existing chapters).
- Standardized expectation and independence notation across chapters (e.g.,
E[...]→\E{...},\perp\!\!\!\perp→\ind). - Updated
_quarto-website.ymlnavigation and expandedinst/WORDLISTfor new technical terms.
Reviewed changes
Copilot reviewed 23 out of 23 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| inst/WORDLIST | Added causal-inference terms for spellcheck; removed duplicate entry. |
| _quarto-website.yml | Added sidebar navigation entries for new Chapters 19–23. |
| chapters/01-introduction.qmd | Macro standardization updates in math notation. |
| chapters/02-randomized-experiments.qmd | Macro standardization updates in math notation. |
| chapters/03-observational-studies.qmd | Macro standardization updates in math notation. |
| chapters/04-effect-modification.qmd | Macro standardization updates in math notation. |
| chapters/05-interaction.qmd | Macro standardization updates in math notation. |
| chapters/06-graphical-representation.qmd | Macro standardization updates in math notation. |
| chapters/07-confounding.qmd | Macro standardization updates in math notation. |
| chapters/09-measurement-bias.qmd | Macro standardization updates in math notation. |
| chapters/10-random-variability.qmd | Macro standardization updates in math notation. |
| chapters/11-why-model.qmd | Macro standardization updates in math notation. |
| chapters/12-ip-weighting-marginal-structural-models.qmd | Macro standardization updates in math notation. |
| chapters/13-standardization-parametric-g-formula.qmd | Macro standardization updates in math notation. |
| chapters/14-g-estimation-structural-nested-models.qmd | Macro standardization updates in math notation. |
| chapters/15-outcome-regression-propensity-scores.qmd | Macro standardization updates in math notation. |
| chapters/16-instrumental-variable-estimation.qmd | Macro standardization updates in math notation. |
| chapters/18-variable-selection-causal-inference.qmd | Macro standardization updates in math notation. |
| chapters/19-time-varying-treatments.qmd | New Chapter 19 content (Part III). |
| chapters/20-treatment-confounder-feedback.qmd | New Chapter 20 content (Part III). |
| chapters/21-g-methods-time-varying.qmd | New Chapter 21 content (Part III). |
| chapters/22-target-trial-emulation.qmd | New Chapter 22 content (Part III). |
| chapters/23-causal-mediation.qmd | New Chapter 23 content (Part III). |
Collaborator
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@copilot apply changes based on the comments in this thread |
…ize nested E[] macros in ch02 and ch11 Agent-Logs-Url: https://github.com/ucdavis/win/sessions/29247ca6-572c-4454-bb3b-38fc70b077c5 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
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Author
Applied all three reviewer changes in 42c47e0:
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@claude review |
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Claude finished @d-morrison's task in 4m 0s —— View job PR Review
SummaryThis PR adds Part III chapters (19–23) covering time-varying treatments through causal mediation, and standardizes LaTeX macro notation across all chapters. The content is substantively strong and the previously-flagged reviewer issues have been addressed. One outstanding issue remains. Outstanding Issue:
|
| Issue | Status |
|---|---|
immunosuppression removed from WORDLIST (ch08 still uses it) |
Fixed in 42c47e0 — word is present at line 48 |
Raw E[\hat{\theta}] inside \E{...} in chapters/11-why-model.qmd:215 |
Fixed — now reads \E{(\hat{\theta} - \E{\hat{\theta}})^2} |
Nested raw E[Y^a|L] / E[Y|A=a,L] in chapters/02-randomized-experiments.qmd |
Fixed — all four lines now use \E{\E{... \mid ...}} |
New Chapters 19–23 — General Assessment
All five chapters follow the established patterns correctly:
- Format headers match existing chapters exactly (html + revealjs + pdf + docx with correct output-file names)
- Macro include
{{< include ../latex-macros/macros.qmd >}}is present in every chapter - No raw
E[...]or\perp\!\!\!\perpfound — all expectations use\E{...}and all independence statements use\ind - Textbook citations follow the
@hernan2020causal [Chapter N, pp. X–Y]convention
One minor inconsistency: the new chapters use \Pr[...] (the LaTeX operator command, which renders Pr in roman) while most existing chapters use plain Pr[...] (renders italic in math mode). The new approach is technically more correct, but it creates a cross-chapter inconsistency. This is a low-priority cosmetic issue.
Navigation (_quarto-website.yml)
Clean addition — chapters 19–23 are appended in correct numeric order after chapter 18, with filenames and display text consistent with the established Chapter N: Title pattern.
WORDLIST New Terms
The 16 new terms (adherence, blip, blipped, CDE, collider, emulation, estimand, estimands, immortal, ITT, NDE, NIE, PP, pseudo-population, qmd, semiparametric, SNMM) are all legitimate technical terms or acronyms used in the new chapters. The removal of the duplicate ggdag entry is correct.
Bottom line: The PR is ready to merge once the WORDLIST alphabetical order is corrected. All substantive reviewer comments have been addressed.
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chapters/19-time-varying-treatments.qmd(pp. 255-265)chapters/20-treatment-confounder-feedback.qmd(pp. 267-275)chapters/21-g-methods-time-varying.qmd(pp. 277-302)chapters/22-target-trial-emulation.qmd(pp. 305-320)chapters/23-causal-mediation.qmd(pp. 323-330)_quarto-website.ymlnavigation to include chapters 19-23\indmacro (replaces\perp\!\!\!\perp) across all chapters\E{...}macro (replacesE[...]) across all chaptersinst/WORDLIST; remove duplicateggdagentryqmdtoinst/WORDLISTto fix spell check CI failureimmunosuppressiontoinst/WORDLIST(was accidentally removed)E[\hat{\theta}]→\E{\hat{\theta}}inchapters/11-why-model.qmdE[Y^a|L]/E[Y|A=a,L]→\E{\E{...}}with\midinchapters/02-randomized-experiments.qmdspelling::spell_check_package()locally — no errors