Fix broken cross-references and brace-protect bib title capitalization#877
Conversation
Wrap letters that must stay capitalized in sentence-case titles so
sentence-case citation styles don't lowercase them:
- acronyms: {EM}, {SAS}, {SPSS}, {WinBUGS}
- software/proper nouns: {R} (mid-title), {BuCy2}, {Fisher}, {Bayesian}
- named studies: {Nurses' Health Study},
{Heart and Estrogen/progestin Replacement Study},
{Western Collaborative Group Study}, {Gaspe Peninsula}
(The hepatitis {C} fix in tsui2009hcv is on the count-regression PR branch,
where that entry lives.)
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
From a whole-book crossref audit:
- @sec-linreg-inference -> @sec-infer-LMs (the anchor was never defined;
sec-infer-LMs is the LM-inference section).
- Add the named anchors the links expect: {#sec-intro-MLEs} on the
intro-MLEs H1 and {#sec-CI} on the "Confidence intervals" heading, so
intro-MLEs.qmd#sec-intro-MLEs (x2) and inference.qmd#sec-CI resolve.
- intro-bayes.qmd#sec-bayes -> bare intro-bayes.qmd (no such anchor; the
link points at the chapter).
- count-regression.qmd#sec-count-reg -> bare count-regression.qmd (no such
anchor).
- OR-RR.qmd (orphan, never rendered) -> logistic-regression.qmd#sec-OR-RR.
The count-regression poisson.qmd#def-offset link is handled on the
count-regression PR branch.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
|
Claude finished @d-morrison's task in 2m 30s —— View job Code Review
Cross-Reference Fixes ✅All six cross-reference fixes are correct and verified:
Bibliography Capitalization — One Issue Found
|
|
@claude please review — this fixes broken cross-references found in a whole-book audit and brace-protects capitalization in bib titles. Note cross-chapter crossref/link resolution is best confirmed against the rendered preview. |
|
👀 Picked up by workflow run #26910001527. R/Quarto/renv setup runs first (~3-5 min); Claude itself responds after that. |
|
I've reviewed all the changes. Here's my assessment: Cross-references — all verified ✓
Bibliography capitalization — correct throughout All braced terms are legitimate sentence-case hazards: acronyms ( One minor gap to consider (non-blocking): In title={SAS and {R}: Data management...}In BibTeX sentence-case rendering, only the first character of the first word is preserved — so Changes look correct. Ready to merge. — posted by @claude post-step from workflow run |
|
@claude review |
|
👀 Picked up by workflow run #26915836969. R/Quarto/renv setup runs first (~3-5 min); Claude itself responds after that. |
|
Claude Code CLI (local session) is working on this — paws off until I'm done. |
Only the first character of a title is auto-protected in BibTeX sentence-case conversion, so AS would be lowercased to 'as'. Wrap SAS in braces to preserve the acronym. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
|
Addressed the one finding from the latest review: in |
|
Claude finished @d-morrison's task in 2m 7s —— View job Code Review — PR #877
Cross-Reference Fixes ✅All six cross-reference fixes are correct and verified against the current branch:
Bibliography Capitalization ✅All brace-protections are correct, including the
All changes are verified correct. Ready to merge. |
A `(@ref)` at the start of a (wrapped) line inside a bullet-list item is parsed by Pandoc as an example-list marker `(@Label)`, not a cross-reference: the label is consumed and the following text becomes an `<ol class="example">` item, so the crossref silently vanishes in the rendered output. Move the `(@ref)` to the end of the preceding line so it parses inline: - _sec_linear_algebra.qmd: @sec-vector-calculus, @sec-infer-LMs (the "quadratic forms" list — both were rendering blank). - _calc_integrals_ftc.qmd: @eq-ftc-deriv-of-integral, @eq-ftc-part2 (the FTC Part 1 / Part 2 list). (Six other `(@…)`-at-line-start spots exist but sit in plain paragraphs, not list items, so Pandoc renders them correctly; left unchanged.) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
|
Claude finished @d-morrison's task in 2m 15s —— View job Code Review — PR #877
Latest Commit (8fdc87c) — Pandoc example-list fix ✅This is a real and subtle Pandoc parsing issue: The fix (move
The commit message notes 6 other Cross-Reference Fixes (431db10) ✅All six fixes verified:
Bibliography Capitalization (97aaec3 + 320b507) ✅All brace-protections correct, including the
All changes verified correct. Ready to merge. |
2026-06-05 00:20 UTC |
1 participant
Global cleanup split off from the count-regression work (per request to keep these separate from the per-chapter PRs).
Broken cross-references (from a whole-book audit)
@sec-linreg-inference@sec-infer-LMssec-infer-LMsis the LM-inference sectionintro-MLEs.qmd#sec-intro-MLEs(×2){#sec-intro-MLEs}to the intro-MLEs H1inference.qmd#sec-CI{#sec-CI}to "Confidence intervals"intro-bayes.qmd#sec-bayesintro-bayes.qmdcount-regression.qmd#sec-count-regcount-regression.qmdOR-RR.qmdlogistic-regression.qmd#sec-OR-RROR-RR.qmdis an orphan, never renderedBibliography capitalization
Brace-protected letters that must stay capitalized in sentence-case titles so sentence-case citation styles don't lowercase them: acronyms (
{EM},{SAS},{SPSS},{WinBUGS}), software/proper nouns ({R},{BuCy2},{Fisher},{Bayesian}), and named studies ({Nurses' Health Study},{Heart and Estrogen/progestin Replacement Study},{Western Collaborative Group Study},{Gaspe Peninsula}).Not in this PR (handled on their own branches)
poisson.qmd#def-offsetlink and thetsui2009hcv"hepatitis {C}" fix live on the count-regression PR (revise count regression chapter #860), where those entries exist.🤖 Generated with Claude Code