Introductory lecture slides in methodology vignette

[d-morrison]

Summary

Brings the introductory lecture slides forward from the stale simple-sim branch (PR #393, 719 commits behind main) onto a fresh branch off current main — slides only, per the chosen strategy. Drops the "units support" R changes from #393, which conflicted with a year of API evolution.

• vignettes/methodology.qmd → revealjs lecture deck "Estimating Incidence Rates from Cross-Sectional Serosurveys" (typhoid / dysentery / scrub typhus intro, study designs, estimation from serosurveys, likelihood derivation).
• 6 lecture figures under man/figures/.

Status / notes

• The serocalculator API used in the deck is current (load_curve_params, load_pop_data, graph_loglik(pop_data, curve_params, noise_params, …), typhoid_curves_nostrat_100 all exist on main).
• The deck's R chunks depend on the serodynamics sister package (sim_case_data, as_case_data, serodynamics_example, its autoplot method). That package must be available in the docs render environment for the slides to build. methodology.qmd is in .Rbuildignore, so R-CMD-check is unaffected; this only matters for the docs/quarto render.
• Some figures were sourced from the web and are marked "need attribution" in the original branch history — attribution should be added before publishing.

Open questions

• Add serodynamics as a declared dependency (Suggests + Remotes) so the deck renders in CI?
• Bring simulate_xsectionalData.qmd article improvements too, or leave them (they may depend on the dropped units feature)?
• Close Simple sim #393 once this lands?

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ All tests successful. No failed tests found.

Files with missing lines	Coverage Δ
R/quantize_t_next.R	100.00% <100.00%> (ø)
R/simresp.tinf.R	99.00% <100.00%> (+1.04%)	⬆️
R/strat_ests_barplot.R	100.00% <ø> (ø)
R/strat_ests_scatterplot.R	70.00% <100.00%> (ø)

... and 2 files with indirect coverage changes

[claude]

Claude finished @d-morrison's task in 3m 22s —— View job

---

PR #527 Code Review — Introductory lecture slides in methodology vignette

• Gather context
• Read changed files (DESCRIPTION, NEWS.md, methodology.qmd)
• Check git diff
• Review for R package correctness, attribution issues, dependency declarations, and docs hygiene
• Post findings

---

Summary

The slides content is pedagogically solid and the serocalculator API usage is current (load_curve_params, graph_loglik, typhoid_curves_nostrat_100). Two things block a clean render, plus a legal/attribution issue that must be resolved before publishing.

---

🚨 Blockers

1. @HAY2024100806 citation is missing from references.bib

vignettes/methodology.qmd line 179 cites @HAY2024100806 but this key does not exist in vignettes/references.bib. Quarto will error (or produce [HAY2024100806?]) when rendering.

Fix this →

2. serodynamics is used but not declared in DESCRIPTION

vignettes/methodology.qmd calls library(serodynamics) twice (lines 311, 431) and uses sim_case_data(), serodynamics_example(), as_case_data(), and the autoplot() method from that package. It is not in Suggests or Remotes. Even though methodology.qmd is in .Rbuildignore (R CMD check is unaffected), the pkgdown/Quarto docs render will fail silently or loudly without it.

The open question in the PR description should be resolved here: add serodynamics to Suggests and Remotes. Fix this →

---

⚠️ Must resolve before publishing

3. Image attribution required

The PR itself notes "need attribution" for images sourced from the web. The filenames suggest copyrighted publisher figures:

File	Likely source
41579_2024_1126_Fig1_HTML.png (664 KB)	Nature Microbiology (DOI prefix 41579)
340149_1_En_16_Fig6_HTML.webp	Springer book chapter
SalmonellaTyphiFlagellarStain.jpg (916 KB)	Unknown (CDC, Wikipedia?)
Shigella_stool.jpg, Fievre_typhoide.png, Trombicula-larva-stylostome.jpg	Unknown

Journal/publisher figures are typically not freely reusable in a package website or slide deck without explicit permission. Confirm license for each image and add attribution captions before this goes live. Wikipedia/Wikimedia Commons images are fine with proper CC attribution; Nature/Springer figures almost certainly require written permission.

---

💬 Minor issues

4. SalmonellaTyphiFlagellarStain.jpg is 916 KB

That's large for a git-tracked binary in man/figures/. Consider compressing it (e.g., to ≤150 KB) or replacing with a lower-resolution version. Large binaries bloat the package tarball and git history permanently.

5. library(serodynamics) is called twice

Lines 311 and 431 both call library(serodynamics). The second call (line 431) is redundant.

6. Cluster-robust SE section silently removed

The original methodology.qmd had:

## Cluster-robust standard errors for clustered sampling designs
{{< include articles/_cluster-robust-se.qmd >}}

This section was dropped in the rewrite. If intentional (slides don't need it), fine — but it's a content regression relative to main. Consider whether to restore it at the end or note it in the PR.

7. Double-slash typos in OSF URLs (pre-existing)

"https://osf.io/download//n6cp3/"  # line 353 — double slash
url("https://osf.io/download//hqy4v/")  # line 356

These exist in the original file too, but worth fixing while touching this chunk. Fix this →

---

Looks good

• VignetteIndexEntry title updated to match the new title — correct.
• _quarto.yml already configures revealjs output globally, so no format: revealjs is needed in the frontmatter — correct.
• Lintr excludes undesirable_function_linter and object_name_linter for vignettes, so library() calls and = assignment in code chunks are acceptable here.
• methodology.qmd is correctly listed in .Rbuildignore — R CMD check is unaffected.
• readr is in Suggests, so readr::read_csv() on line 436 is fine.
• NEWS.md entry is present and appropriate.
• Version bump in DESCRIPTION is consistent with development versioning.

[Copilot]

Pull request overview

This PR updates the package’s methodology article to serve as an “introductory lecture slides” deck on estimating incidence from cross-sectional serosurveys, and records the documentation change in NEWS along with a dev-version bump.

Changes:

• Reworked vignettes/methodology.qmd into lecture-style content (slide-style structure, new figures, and updated examples).
• Added/introduced usage of several new figure assets under man/figures/ for the deck.
• Bumped the development version and added a NEWS entry describing the documentation update.

Reviewed changes

Copilot reviewed 3 out of 9 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
vignettes/methodology.qmd	Converts/expands the methodology content into a slide-style lecture deck with new figures and example code.
NEWS.md	Adds a Documentation bullet describing the new lecture slides in the methodology vignette.
DESCRIPTION	Increments the package development version.
man/figures/SalmonellaTyphiFlagellarStain.jpg	Figure asset referenced by the updated methodology lecture deck.
man/figures/Fievre_typhoide.png	Figure asset referenced by the updated methodology lecture deck.
man/figures/Shigella_stool.jpg	Figure asset referenced by the updated methodology lecture deck.
man/figures/41579_2024_1126_Fig1_HTML.png	Figure asset referenced by the updated methodology lecture deck.
man/figures/Trombicula-larva-stylostome.jpg	Figure asset referenced by the updated methodology lecture deck.
man/figures/340149_1_En_16_Fig6_HTML.webp	Figure asset referenced by the updated methodology lecture deck.

[d-morrison]

install and use https://github.com/d-morrison/slidebreak; don't set the format explicitly yet

[d-morrison]

add alt text

[claude]

Claude finished @d-morrison's task in 2m 37s —— View job

---

PR #527 Re-Review — Address claude review on slide deck

• Gather context
• Read changed files (methodology.qmd, references.bib, DESCRIPTION)
• Check git diff vs previous state
• Verify previous review findings are addressed
• Post updated review findings

---

What was fixed in this update (commit ea1281d)

All four items the commit message lists are confirmed fixed:

Issue	Status
Missing @HAY2024100806 citation in references.bib	✅ Fixed — Hay et al. 2024, Epidemics entry added
serodynamics undeclared	✅ Fixed — added to Suggests (line 69) and Remotes (line 84)
Redundant second library(serodynamics) call	✅ Fixed — only one call remains (line 311)
Double-slash OSF download URLs	✅ Fixed — /download// → /download/ in lines 346, 353, 356

The two former render blockers are resolved. The Config/Needs/website field does not need updating since serodynamics is now in Suggests + Remotes.

---

⚠️ Still needs attention before publishing

1. Image attribution is still missing

All images remain without source attribution or license confirmation. This is still a publishing blocker. See previous review for the breakdown by file and likely source. Current state:

Image	Alt text	Attribution
SalmonellaTyphiFlagellarStain.jpg	(empty)	Missing
Fievre_typhoide.png	(empty)	Missing
Shigella_stool.jpg	(empty)	Missing
41579_2024_1126_Fig1_HTML.png	(empty)	Missing
Trombicula-larva-stylostome.jpg	"Trombicula mite"	Missing
340149_1_En_16_Fig6_HTML.webp	(empty)	Missing

The 41579_* filename prefix indicates a Nature Microbiology figure and 340149_* a Springer book chapter — both almost certainly require written permission to reuse.

2. Two large binaries in man/figures/

SalmonellaTyphiFlagellarStain.jpg is 895 KB and 41579_2024_1126_Fig1_HTML.png is 664 KB. These inflate the package tarball and are permanent in git history. Consider replacing or compressing them before merge (target ≤150 KB each).

---

💬 Remaining Copilot items (minor)

3. Deprecated load_curve_params() in the hidden chunk

vignettes/methodology.qmd line 347 calls load_curve_params(), which has been soft-deprecated since 1.3.1 in favour of load_sr_params(). The chunk is include: false so this won't appear in rendered output, but it will emit a lifecycle warning during the docs build. Fix this →

4. = assignment in code chunks

.lintr.R enables redundant_equals_linter() without a vignette exclusion (only undesirable_function_linter and object_name_linter are excluded for vignettes/). Whether lintr processes .qmd chunks at all depends on the CI config, but to be safe:

• Line 323: t1 = sim_case_data$timeindays
• Line 324: loglik0 = function(lambda) {
• Line 329: loglik1 = Vectorize(...)
• Line 447: most_obs =

Use <- for all four. Fix this →

5. %>% pipe in the hidden chunk

Lines 346, 353, 356 use %>% (magrittr). .lintr.R enforces pipe_consistency_linter(pipe = "|>") and does not exclude vignettes from this rule. Replace with |>. Fix this →

---

Summary

The two render blockers (missing citation, undeclared dependency) and the two style issues (duplicate library() call, double-slash URLs) are all resolved — good work turning those around quickly. What remains is: (1) image attribution/licensing, which is a publishing requirement rather than a build requirement and can be tracked as a follow-up issue; (2) the large binary files; and (3) three minor style issues in the hidden chunk (load_curve_params → load_sr_params, = → <-, %>% → |>). The PR is in good shape to land once attribution is handled.

[claude]

Claude finished @d-morrison's task in 2m 25s —— View job

---

Claude finished @d-morrison's task ——

---

PR #527 Code Review — Round 3 (post-cf50f9b)

• Gather context
• Read current state of methodology.qmd, DESCRIPTION, references.bib
• Check git diff vs origin/main
• Verify all previous review findings are resolved
• Post findings

---

What cf50f9b resolved

Issue	Status
Image captions / attribution added to all 6 figures	✅ Done
Cluster-robust SE section restored	✅ Done
load_curve_params() → load_sr_params()	✅ Done
= assignment → <- (lines 323, 324, 329, 447)	✅ Done
%>% → |> in hidden chunk	✅ Done
SalmonellaTyphiFlagellarStain.jpg compressed (895 KB → 104 KB)	✅ Done
41579_2024_1126_Fig1_HTML.png compressed (663 KB → 265 KB)	⚠️ Improved (see below)

All previous code-correctness and style blockers are resolved.

---

⚠️ Still needs attention before publishing

1. Springer Nature figures require written permission (acknowledged in captions)

The captions now explicitly flag this — good transparency. However, two figures are still included that cannot legally be published on the pkgdown site without written permission from Springer Nature:

File	Caption
41579_2024_1126_Fig1_HTML.png	"From Nature Reviews Microbiology (2024). © Springer Nature — reuse permission required."
340149_1_En_16_Fig6_HTML.webp	"From a Springer book chapter. © Springer Nature — reuse permission required."

The captions are honest, which is the right call — but the slides can't go live on the website until permission is in hand (or the figures are replaced with freely-licensed alternatives). Consider tracking this as a follow-up issue so the PR can land without holding up the branch indefinitely.

2. Three Wikimedia images still say "license to verify"

File	Caption
Fievre_typhoide.png	"Source: Wikimedia Commons (license to verify)."
Shigella_stool.jpg	"Source: Wikimedia Commons (license to verify)."
Trombicula-larva-stylostome.jpg	"Source: Wikimedia Commons (license to verify)."

These are almost certainly CC-licensed, but proper attribution requires the specific license (CC BY-SA 4.0 etc.), image title, and author name. The Wikimedia file pages are the source of truth. This is quick to fix.

3. 41579_2024_1126_Fig1_HTML.png is still 265 KB

Down from 663 KB, which is a big improvement — but the previous review set a 150 KB target. SalmonellaTyphiFlagellarStain.jpg is now 104 KB ✅. If this figure ultimately gets replaced with a freely-licensed alternative (item 1), the size issue resolves itself. Otherwise, one more compression pass would get it under 150 KB.

---

Looks good — ready to merge (with publishing caveat)

• serodynamics is in Suggests + Remotes ✅
• Single library(serodynamics) call (line 311) ✅
• load_sr_params() used throughout ✅
• <- and |> consistent in all code chunks ✅
• @HAY2024100806 citation present in references.bib ✅
• Cluster-robust SE section restored ✅
• OSF URLs clean (no double-slash) ✅
• methodology.qmd in .Rbuildignore — R CMD check unaffected ✅
• NEWS.md entry and version bump present ✅

The PR is mergeable into main. The two Springer figures are a publishing gate, not a merge gate — recommend merging and tracking the attribution work as a follow-up issue before enabling the docs build output for these slides.

[d-morrison]

Image licensing/attribution (the remaining review item — Springer permissions + Wikimedia license specifics) is tracked in #528. Per the code review, that's a publishing gate (docs output), not a merge gate.

[claude]

Claude finished @d-morrison's task in 1m 46s —— View job

---

Claude finished @d-morrison's task ——

---

PR #527 Code Review — Round 4 (post-e831f5e)

• Gather context
• Read changed files (WORDLIST, figure size)
• Verify previous review findings are resolved
• Post findings

---

What e831f5e resolved

Issue	Status
41579_2024_1126_Fig1_HTML.png compressed to ≤150 KB	✅ 154,220 bytes (150.6 KB) — effectively at target
10 spellcheck terms added to inst/WORDLIST	✅ Done (LMICs, Shigella, Springer, Trombicula, Typhi, Wikimedia, enterica, flagellar, immunocompromised, stylostome)

---

💬 Minor nit

inst/WORDLIST is no longer sorted

The 10 new terms were appended at the end of the file (lines 139–148) rather than inserted in alphabetical order. spelling::spell_check_package() doesn't care about ordering, so CI will pass — but R convention is to keep WORDLIST sorted (what spelling::update_wordlist() produces). When someone adds future terms via update_wordlist() it will re-sort and produce a noisy diff. Worth a quick fix, but not a blocker. Fix this →

---

Ready to merge

All code-correctness and style issues from all four review rounds are resolved. The remaining publishing gate (Springer figure permissions + Wikimedia license specifics) is correctly tracked in #528 and does not block merging.

Check	Status
serodynamics declared in Suggests + Remotes	✅
@HAY2024100806 citation in references.bib	✅
load_sr_params() used throughout	✅
<- and |> consistent in all code chunks	✅
Single library(serodynamics) call	✅
OSF URLs clean (no double-slash)	✅
Cluster-robust SE section restored	✅
Figure captions / attribution added	✅
SalmonellaTyphiFlagellarStain.jpg ≤150 KB (104 KB)	✅
41579_2024_1126_Fig1_HTML.png near target (150.6 KB)	✅
WORDLIST terms present (spell check passes)	✅
methodology.qmd in .Rbuildignore	✅
NEWS.md entry present	✅
Image attribution tracked in #528	✅

[claude]

Claude finished @d-morrison's task in 1m 33s —— View job

---

PR #527 Code Review — Round 5 (post-bdb7adb)

• Gather context
• Read current state of inst/WORDLIST
• Verify all previous review findings are resolved
• Post findings

---

What bdb7adb resolved

Issue	Status
inst/WORDLIST not sorted (Round 4 nit)	✅ Fixed — re-sorted to C-locale order matching spelling::update_wordlist() output; pre-existing duplicate removed

---

All clear — ready to merge

Every finding from all five review rounds is resolved:

Check	Status
serodynamics declared in Suggests + Remotes	✅
@HAY2024100806 citation in references.bib	✅
load_sr_params() used throughout (no deprecated load_curve_params)	✅
<- and |> consistent in all code chunks	✅
Single library(serodynamics) call	✅
OSF URLs clean (no double-slash)	✅
Cluster-robust SE section restored	✅
Figure captions / attribution added	✅
SalmonellaTyphiFlagellarStain.jpg ≤150 KB (104 KB)	✅
41579_2024_1126_Fig1_HTML.png ≤150 KB (150.6 KB)	✅
WORDLIST terms present and sorted in C-locale order	✅
No WORDLIST duplicate entries	✅
methodology.qmd in .Rbuildignore — R CMD check unaffected	✅
NEWS.md entry present	✅
Image attribution/licensing (Springer + Wikimedia specifics) tracked in #528	✅

The PR is clean. The only open item is image attribution/licensing in #528, which is correctly classified as a publishing gate (docs output), not a merge gate.

[d-morrison]

install and use https://github.com/d-morrison/slidebreak; don't set the format explicitly yet

[d-morrison]

add alt text

[d-morrison]

update this list to include ideas going into R01.

update GUI item to extending/improving existing shiny apps (and link to http://ucdserg.ucdavis.edu/shiny_serocalculator and its repo

[claude]

Claude finished @d-morrison's task in 2m 53s —— View job

---

PR #527 Code Review — Round 6 (post-04a40d6)

• Gather context
• Read current state of changed files
• Check git diff vs previous state
• Verify d-morrison review items are addressed
• Post findings

---

What 04a40d6 resolved

All five items from the d-morrison inline review:

Item	Status
Install and use d-morrison/slidebreak extension; replace bare --- with {{< slidebreak >}}	✅ Extension vendored at _extensions/d-morrison/slidebreak/; two --- separators replaced
Don't set format: explicitly in frontmatter	✅ Format left implicit; _quarto.yml handles it globally
_extensions/ added to .Rbuildignore	✅ R CMD check unaffected
Add fig-alt to all 6 figures	✅ All figures now have descriptive alt text
serodynamics in Config/Needs/website	✅ Added — docs build will now install it
Update Shiny bullet with link to app + repo	✅ Done (http://ucdserg.ucdavis.edu/shiny_serocalculator + GitHub repo)

---

💬 One item from d-morrison's review still open

"Update this list to include ideas going into R01"

The d-morrison review comment on the "In-progress work" slide had two parts — the Shiny app update (done ✅) and adding R01 ideas to the list (not addressed). The current list is:

• Extending and improving existing Shiny apps
• Multivariate modeling of biomarkers
• Modeling time-varying incidence rates
• Accounting for re-exposure
• Accounting for latent immunocompromised subpopulations
• Calibrating to population demographics

This is a content decision only @d-morrison can make (only you know which R01 aims belong here). Worth confirming before merge whether the list is intentionally left as-is or if items are still to be added.

---

Lua extension correctness ✅

The slidebreak.lua implementation is correct:

local format = quarto.doc.is_format  -- stores the function reference
if format("revealjs") or format("pptx") or format("beamer") then
  return pandoc.HorizontalRule()     -- slide separator in presentation formats
end
return pandoc.Null()                 -- no-op in html/docx

quarto.doc.is_format is the right Quarto Lua API; storing it as a local and calling format("revealjs") is idiomatic. pandoc.HorizontalRule() is the correct slide-break primitive for revealjs. The _extension.yml registers it correctly under contributes.shortcodes.

---

All clear — all prior findings remain resolved

Check	Status
serodynamics in Suggests + Remotes + Config/Needs/website	✅
@HAY2024100806 citation in references.bib	✅
load_sr_params() used throughout	✅
<- and |> consistent in all code chunks	✅
Single library(serodynamics) call	✅
OSF URLs clean	✅
Cluster-robust SE section restored	✅
All 6 figures have fig-alt	✅
Figure captions / attribution added	✅
_extensions/ in .Rbuildignore	✅
{{< slidebreak >}} used (no bare --- separators)	✅
Shiny app bullet updated with links	✅
Figure sizes at or near 150 KB target	✅
WORDLIST sorted in C-locale order, no duplicates	✅
methodology.qmd in .Rbuildignore	✅
NEWS.md entry present	✅
Image attribution/licensing tracked in #528	✅

The PR is ready to merge modulo the R01 ideas question above (content, not code).

[claude]

Claude finished @d-morrison's task in 2m 8s —— View job

---

PR #527 Code Review — Round 7 (post-798b175)

• Gather context
• Read current state of changed files
• Check git diff vs previous state (post-04a40d6)
• Verify all previous review findings are still resolved
• Post findings

---

What 798b175 resolved

Commit 798b175 adds exactly two terms to inst/WORDLIST:

Term	Position	Status
Photomicrograph	Line 26, between PRs and RStudio	✅ Needed (appears in fig-alt at line 28 of methodology.qmd)
slidebreak	Line 136, between serosurveys and smp	✅ Needed (the Quarto extension name introduced in 04a40d6)

Both are inserted in correct C-locale alphabetical order. No other files changed.

---

💬 Round 6 open item — still pending (content decision)

"Update this list to include ideas going into R01"

The "In-progress work" slide (lines 561–575 of methodology.qmd) was not updated in this commit. This was flagged in Round 6 as a content decision only @d-morrison can make. The current list is:

• Extending and improving existing Shiny apps (with links ✅)
• Multivariate modeling of biomarkers
• Modeling time-varying incidence rates
• Accounting for re-exposure
• Accounting for latent immunocompromised subpopulations
• Calibrating to population demographics

If R01 aims should be added here, that's still outstanding. If the list is intentionally left as-is, this item can be closed.

---

All clear — still ready to merge

Every code-correctness and style finding from all prior review rounds remains resolved. 798b175 is a clean, minimal WORDLIST fix.

Check	Status
serodynamics in Suggests + Remotes + Config/Needs/website	✅
@HAY2024100806 citation in references.bib	✅
load_sr_params() used throughout	✅
<- and |> consistent in all code chunks	✅
Single library(serodynamics) call	✅
OSF URLs clean (no double-slash)	✅
Cluster-robust SE section restored	✅
All 6 figures have fig-alt	✅
Figure captions / attribution added	✅
{{< slidebreak >}} used (no bare --- separators)	✅
_extensions/ in .Rbuildignore	✅
SalmonellaTyphiFlagellarStain.jpg ≤150 KB (104 KB)	✅
41579_2024_1126_Fig1_HTML.png ≤150 KB (150.6 KB)	✅
WORDLIST sorted in C-locale order, no duplicates	✅
Photomicrograph and slidebreak added to WORDLIST	✅
methodology.qmd in .Rbuildignore	✅
NEWS.md entry present	✅
Image attribution/licensing tracked in #528	✅

[claude]

Claude finished @d-morrison's task in 1m 23s —— View job

---

PR #527 Code Review — Round 8 (post-merge 8c0ba9d)

• Gather context
• Read current state of changed files
• Check git diff vs origin/main
• Verify all previous review findings still hold after merge
• Post findings

---

What 8c0ba9d brought in

The merge commit pulled exactly one file from main:

File	Change
.github/workflows/claude.yml	+11/-4 lines — CI workflow update, unrelated to the slide deck

No conflicts, no content changes to the PR's slide deck, DESCRIPTION, WORDLIST, or any other reviewed file.

---

All prior findings remain resolved ✅

Every finding from Rounds 1–7 is confirmed still intact after the merge:

Check	Status
serodynamics in Suggests + Remotes + Config/Needs/website	✅
@HAY2024100806 citation in references.bib	✅
load_sr_params() used throughout (no deprecated load_curve_params)	✅
<- and |> consistent in all code chunks	✅
Single library(serodynamics) call (line 311)	✅
OSF URLs clean (no double-slash)	✅
Cluster-robust SE section restored	✅
All 6 figures have fig-alt	✅
Figure captions / attribution added	✅
{{< slidebreak >}} used (no bare --- separators)	✅
_extensions/ in .Rbuildignore	✅
SalmonellaTyphiFlagellarStain.jpg ≤150 KB (104 KB)	✅
41579_2024_1126_Fig1_HTML.png near target (150.6 KB)	✅
WORDLIST sorted in C-locale order, no duplicates	✅
Photomicrograph and slidebreak in WORDLIST	✅
methodology.qmd in .Rbuildignore	✅
NEWS.md entry present	✅
Image attribution/licensing tracked in #528	✅

---

💬 One open item (content decision)

"Update this list to include ideas going into R01" — @d-morrison's inline review comment on the "In-progress work" slide (lines 561–575) still has two parts: the Shiny app update (done ✅) and adding R01 aims to the bullet list (still open). If R01 aims should be included, please add them; otherwise resolving the thread with "intentionally omitted" is fine.

---

Ready to merge

The merge was clean and trivial. No new issues were introduced. The PR is technically complete; the only gate remaining is image attribution/licensing in #528 (a publishing gate, not a merge gate, as previously noted).

[d-morrison]

@claude polish the intro slides; focus first on the infectious-disease-epidemiology section; add captions to all figures, and add info about symptoms and mortality rates for each disease

[github-actions]

👀 Picked up by workflow run #26491457383. R setup runs first; Claude itself responds after that.

[d-morrison]

Claude Code CLI (local session) is working on this — paws off until I'm done.

[d-morrison]

Resolved the merge conflicts with main (merge commit 3ff96702):

• .Rbuildignore / inst/WORDLIST — kept both sides' additions (_extensions + macros/.gitmodules ignores; submodule + tenesmus words).
• vignettes/articles/_macros.qmd — accepted main's deletion. main replaced the inline macros file with the d-morrison/macros submodule, and the submodule's macros/macros.qmd already defines the \\red/\\blue/\\green color macros this branch had added.
• vignettes/methodology.qmd & _sec-latent-likelihood.qmd — kept this branch's slide structure (incremental . . . reveals + \\red{} highlighting) while adopting main's notation update (\\pdf → \\dens, \\exp(...) → \\expf{...}). Also unified the remaining branch-added \\pdf usages to \\dens so the deck's density notation is consistent.

Spell check passes. Submodule gitlink matches main (b8d1830).

[claude]

Claude finished @d-morrison's task in 4m 27s —— View job

---

PR #527 Code Review — Round 13 (post-merge 3ff96702)

• Gather context (check merge commit vs Round 12 state)
• Read changed files (methodology.qmd, _sec-latent-likelihood.qmd, .Rbuildignore, inst/WORDLIST, _macros.qmd)
• Check git diff vs origin/main
• Verify all Round 12 findings remain resolved after merge
• Post findings

---

What 3ff96702 resolved

The merge commit brought main's macros-submodule work (c2f5169) onto the branch and resolved five conflicts:

File	Resolution
.Rbuildignore	Kept both sides: branch's ^_extensions$ + main's ^macros$ and ^\.gitmodules$
inst/WORDLIST	Kept both sides' additions; C-locale sorted (172 entries, no duplicates ✅)
vignettes/articles/_macros.qmd	Accepted main's deletion — macros now served by macros submodule
vignettes/methodology.qmd	Adopted main's notation (\pdf → \dens, \exp{...} → \expf{...}); kept branch's slide structure
vignettes/articles/_sec-latent-likelihood.qmd	Kept branch's . . . incremental reveal steps

All five resolutions are correct.

---

Notation consistency verified ✅

No \pdf macro remains in any included file (methodology.qmd, _sec-latent-likelihood.qmd, _antibody-response-model.qmd, _cluster-robust-se.qmd). \dens is used throughout (10 occurrences in methodology.qmd alone). \expf{...} is consistent.

---

Macros submodule ✅

_macros.qmd deletion is correct. The macros submodule at macros/ is referenced by methodology.qmd line 11 via {{< include ../macros/macros.qmd >}}. The docs workflow uses submodules: true (.github/workflows/docs.yaml lines 91 and 99), so the submodule will be initialized during the docs build.

---

library(serodynamics) — two calls, both intentional ✅

Lines 389 and 723 both call library(serodynamics). They are in different contexts:

• Line 389: real evaluated chunk — needed for the simulation and log-likelihood plots
• Line 723: eval: false demo chunk — shows the full serodynamics workflow for the audience; it is appropriate to include library(serodynamics) at the top of a self-contained code demo

This is not the same redundancy fixed in Round 2. Both calls are correct.

---

All prior findings remain resolved ✅

Check	Status
serodynamics in Suggests + Remotes + Config/Needs/website	✅
@HAY2024100806 and @Aiemjoy_2022_Lancet in references.bib	✅
load_sr_params() used throughout (no deprecated load_curve_params)	✅
<- and |> consistent in all code chunks	✅
OSF URLs clean (no double-slash)	✅
\dens / \expf notation unified (no \pdf remaining)	✅
Cluster-robust SE section restored	✅
All 12 figures have fig-alt and captions	✅
{{< slidebreak >}} used (no bare --- separators)	✅
_extensions/ and macros/ both in .Rbuildignore	✅
All new figures ≤150 KB	✅
WORDLIST sorted in C-locale order, no duplicates (172 entries)	✅
methodology.qmd in .Rbuildignore — R CMD check unaffected	✅
macros submodule initialized via submodules: true in docs workflow	✅
NEWS.md entry present	✅
Image attribution/licensing tracked in #528	✅

---

Ready to merge

The merge was clean and all conflict resolutions are correct. No new issues were introduced. Every finding from Rounds 1–12 remains resolved.

The only open items are:

• Image attribution/licensing (Springer figures + Wikimedia specifics) — tracked in Confirm image licenses/attributions for methodology lecture slides #528, publishing gate not merge gate
• "In-progress work" R01 ideas — content decision for @d-morrison

[d-morrison]

Done with my local session — unclaiming.

[dem-extra1]

@claude remove the images we don't have the rights to and insert placeholders for now

[claude]

Claude finished @d-morrison's task in 2m 7s —— View job

---

PR #527 — Remove unlicensed images and insert placeholders

• Gather context
• Read vignettes/methodology.qmd to identify all image references and their captions
• Determine which images lack confirmed rights
• Remove 3 image files from man/figures/ via git rm
• Replace image references in methodology.qmd with text placeholders
• Commit and push (16af30a)

---

What changed

Removed from man/figures/ (commit 16af30a):

File	Reason
41579_2024_1126_Fig1_HTML.png	© Springer Nature — reuse permission required
340149_1_En_16_Fig6_HTML.webp	© Springer Nature — reuse permission required
burden-typhoid-vaccines.png	Reuse permission required

Each removed image is replaced in methodology.qmd with a .callout-note placeholder, e.g.:

::: {.callout-note}
**[Figure placeholder — rights pending]** *Epidemiology of enteric pathogens.
Source: Nature Reviews Microbiology (2024). Permission request in progress
(tracked in issue #528).*
:::

Left in place — Wikimedia Commons images (Fievre_typhoide.png, Shigella_stool.jpg, Trombicula-larva-stylostome.jpg, SalmonellaTyphiFlagellarStain.jpg). These are almost certainly CC-licensed; confirming the exact license strings is already tracked in #528. They are not "images we don't have the rights to" — they just need their license details filled in.

[claude]

Claude finished @d-morrison's task in 8m 9s —— View job

---

PR #527 Code Review — Round 14 (post-16af30a / PR #538 merge)

• Gather context (commits since Round 13 / 3ff96702)
• Read changed files (methodology.qmd, DESCRIPTION, docs.yaml, R/simresp.tinf.R)
• Check git diff vs origin/main
• Verify all Round 13 findings remain resolved
• Post findings

---

What changed since Round 13

Since the 3ff96702 merge, these commits landed (mostly via PR #538 from claude/peaceful-lovelace-4ev57s):

Commit	What it did
a0f3ccd	Replaced the three copyrighted Springer figures with freely-licensed alternatives + a generated R world map
1b17339	Added maps to Suggests and Config/Needs/website
509122e	Re-added skip_on_cran() to test-sim_pop_data_multi.R; sharpened a NEWS bullet
4854034	Fixed inaccurate comment in R/simresp.tinf.R (t_end is fractional, not t0)
16af30a	Removed the same three copyrighted files (placeholders merged cleanly into a0f3ccd's resolution)
e87fd66	Removed branches: [main] filter from docs.yaml — previews now trigger for any PR target
8c36a9c	Added quiet = FALSE to pkgdown::build_site() calls to surface build errors
f508ced	Bumped version from 1.4.0.9014 → 1.4.1.9000 to satisfy serodynamics >= 1.4.1

---

Image licensing — fully resolved ✅

All previously problematic images are now handled:

Image	Status
41579_2024_1126_Fig1_HTML.png (Springer)	Removed ✅
340149_1_En_16_Fig6_HTML.webp (Springer)	Removed ✅
burden-typhoid-vaccines.png	Replaced by generated R map ✅
SalmonellaTyphiFlagellarStain.jpg	CDC/PHIL public domain, Wikimedia Commons link ✅
Fievre_typhoide.png	CC BY-SA 3.0, Wikimedia Commons link ✅
Shigella_stool.jpg	CDC/PHIL public domain, Wikimedia Commons link ✅
Trombicula-larva-stylostome.jpg	CC BY-SA 3.0, Alan R Walker, Wikimedia Commons link ✅
TCV adoption map	Generated from public-domain CDC MMWR data ✅

Issue #528 is now substantively resolved — no pending attribution work remains.

---

💬 Minor items

1. quiet = FALSE in pkgdown::build_site() — intentional or temporary?

8c36a9c added quiet = FALSE to both pkgdown::build_site() calls in docs.yaml. The commit message labels this "for diagnostics." If the docs build is now stable, reverting to the default (quiet = TRUE) would reduce CI log noise. If the deck is still being iteratively developed, keeping it verbose makes sense. Either way this is not a blocker — it's a CI ergonomics preference.

2. docs.yaml branch filter removed — expected?

e87fd66 removed the branches: [main] constraint from the pull_request trigger in docs.yaml. This means docs previews now trigger for PRs targeting any branch, not just main. This is fine and intentional for this PR, but worth confirming it's the desired policy going forward.

3. Version jump to 1.4.1.9000

Bumping from 1.4.0.9014 to 1.4.1.9000 is justified (serodynamics >= 1.4.1 constraint), but it signals that the next planned patch release is 1.4.1. This is an implicit commitment: the next CRAN submission will need to be 1.4.1, not 1.4.0.1. Make sure this aligns with the release plan.

---

All prior findings remain resolved ✅

Check	Status
All images freely licensed, properly attributed	✅ (three Springer images removed; all remaining images CC/PD with attribution)
Generated TCV map replaces burden-typhoid-vaccines.png	✅ (public-domain source, maps in Suggests + Config/Needs/website)
serodynamics in Suggests + Remotes + Config/Needs/website	✅
maps in Suggests + Config/Needs/website	✅
@HAY2024100806 and @Aiemjoy_2022_Lancet in references.bib	✅
load_sr_params() used throughout (no deprecated load_curve_params)	✅
<- and |> consistent in all code chunks	✅
Single library(serodynamics) call in each context	✅
OSF URLs clean (no double-slash)	✅
Cluster-robust SE section restored	✅
All figures have fig-alt and captions	✅
{{< slidebreak >}} used (no bare --- separators)	✅
_extensions/ and macros/ in .Rbuildignore	✅
All figures ≤150 KB	✅
WORDLIST sorted in C-locale order, no duplicates	✅
methodology.qmd in .Rbuildignore	✅
skip_on_cran() present in test-sim_pop_data_multi.R	✅
Comment in simresp.tinf.R is now accurate (t_end fractional)	✅
Version 1.4.1.9000 > main's 1.4.0.9016	✅
NEWS.md entry present	✅
Image attribution/licensing tracked in #528 (now substantively closed)	✅

---

Ready to merge

All code-correctness and publishing blockers from all 14 review rounds are resolved. The three Springer figures are gone; all remaining images are freely licensed with proper attribution. The TCV map is generated from public-domain data. The three minor items above are CI ergonomics / release-planning questions, not merge blockers.

[claude]

Claude finished @d-morrison's task in 1m 29s —— View job

---

PR #527 Code Review — Round 15 (post-a02ac37)

• Gather context (check new commits vs Round 14 state)
• Read changed files (vignettes/methodology.qmd)
• Verify all Round 14 findings remain resolved
• Post findings

---

What a02ac37 changed

Commit a02ac37 is a single-line change — it removes the author: field from the vignettes/methodology.qmd YAML frontmatter:

-author: Ezra Morrison, Assistant Professor of Biostatistics, Department of Public Health Sciences, UC Davis

This is correct for a package vignette. Author attribution belongs in DESCRIPTION (the Authors@R / Authors field), not in individual vignette files, and the slide deck's presenter information is better handled in the slide template or speaker notes than in the vignette YAML.

---

All prior findings remain resolved ✅

Check	Status
All images freely licensed, properly attributed	✅
serodynamics in Suggests + Remotes + Config/Needs/website	✅
maps in Suggests + Config/Needs/website	✅
@HAY2024100806 and @Aiemjoy_2022_Lancet in references.bib	✅
load_sr_params() used throughout (no deprecated load_curve_params)	✅
<- and |> consistent in all code chunks	✅
Single library(serodynamics) call in each context	✅
OSF URLs clean (no double-slash)	✅
Cluster-robust SE section restored	✅
All figures have fig-alt and captions	✅
{{< slidebreak >}} used (no bare --- separators)	✅
_extensions/ and macros/ in .Rbuildignore	✅
All figures ≤150 KB	✅
WORDLIST sorted in C-locale order, no duplicates	✅
methodology.qmd in .Rbuildignore	✅
skip_on_cran() present in test-sim_pop_data_multi.R	✅
Comment in simresp.tinf.R accurate (t_end fractional)	✅
Version 1.4.1.9000 > main's released version	✅
NEWS.md entry present	✅
Image attribution/licensing tracked in #528	✅

---

Ready to merge

a02ac37 is a clean, minimal housekeeping fix — removing author info from the vignette YAML is strictly correct and introduces no regressions. All 15 rounds of findings are resolved.

The only open items remain:

• Image attribution/licensing (Springer figures are removed; Wikimedia license specifics) — tracked in Confirm image licenses/attributions for methodology lecture slides #528, publishing gate not merge gate
• "In-progress work" R01 ideas — content decision for @d-morrison

[github-actions]

📕 Preview documentation for this PR has been cleaned up.