fixed dois, and changed create_pup_listing.r function to render dates…

[kaiemjoy]

… in quotations. this fixed the issue where some dates were being rendered as "January 1970"

[github-actions]

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[dem-extra1]

@claude review

[dem-extra1]

/review

[dem-extra1]

Self-review as fallback for unreachable Claude.

[dem-extra1]

@agy review

[dem-extra1]

Closing in favor of #117 to re-trigger CI

[github-actions]

Claude finished review — View run

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Review: PR #107 — "fixed dois, and changed create_pub_listing.r function to render dates … in quotations"

Summary of changes

• R/create_pub_listing.R: adds a stringr::str_replace() step that wraps the issued: field in double quotes when it's a bare year or YYYY-MM(-DD) value, so YAML/Quarto doesn't parse it as a number (root cause of the reported "January 1970" bug).
• papers/DOIs.csv: swaps 2 stale preprint DOIs for their published versions, adds 6 new preprint entries, and prefixes nearly all nicknames with YYYY Author.
• publications.bib / publications.yml: regenerated from the updated DOI list; issued/date fields are now quoted strings.
• people/kaiemjoy/.gitignore: new, ignores .httr-oauth (sensible — avoids committing an OAuth token cache).

No CLAUDE.md files exist anywhere in this repo (root or any touched directory), so there's nothing to check for CLAUDE.md compliance on this axis. I evaluated the R change against the SERG lab manual coding style instead — the fix uses the native pipe, namespaced stringr::str_replace(), and a single justified comment explaining the non-obvious YAML-numeric-coercion reason; no violations found there.

Verified finding: the fix silently drops the month for 8 publications (regression, not cosmetic)

I reproduced the actual create_pub_listing.R pipeline (installed pandoc 3.1.3 and ran it against extracted bib entries) rather than just reading the diff, because the regenerated publications.yml contained a suspicious pattern: several pre-existing entries that had date: YYYY-MM in the base branch now only have date: "YYYY" after this PR, e.g.:

• publications.yml (Kamau_2025): base had issued: 2025 / date: 2025-07; this PR produces issued: "2025" / date: "2025" — the month is gone.
• Same pattern for Teunis_2023, Garrett_2022, Aiemjoy_2020, Morrison_2018 (all pre-existing entries, publications.bib source unchanged for these — confirmed via git show against the merge-base), plus it will also affect the new entries Lai_2025, Shrestha_2026, Tedijanto_2023.

Root cause: data-raw/papers.R fetches BibTeX from Crossref via rcrossref::cr_cn(..., format = "bibtex"), and for some entries Crossref exports the month as a full/nonstandard word (month=July, month=June, month=Sept) instead of the standard 3-letter BibTeX macro (jul, jun, sep). I verified directly with pandoc that this is exactly where it breaks:

$ echo '@article{T,title={T},author={A,B},year=2025,month=Jul}'  | pandoc --from=bibtex --to=markdown   # → issued: 2025-07  (correct)
$ echo '@article{T,title={T},author={A,B},year=2025,month=July}' | pandoc --from=bibtex --to=markdown   # → issued: 2025      (month silently dropped)

grep -oE "month=[A-Za-z]+" publications.bib shows exactly the affected macros: July (4), June (2), Sept (2) — all non-standard. Because create_pub_listing.R's date: field is derived directly from pandoc's issued: line (grep(" issued:", ...) |> str_replace(" issued: ", " date: ")), pandoc's silent parsing failure propagates straight into publications.yml.

This matters because publications.qmd uses date-format: 'MMMM,<br>YYYY' and sorts by issued desc — i.e., the very rendering path this PR is trying to fix. A bare "2025" (no month) being fed into a month/year date-format is likely to render with a wrong or default month (commonly January), which is functionally the same class of bug this PR sets out to resolve, just for a different subset of entries (and now newly introduced for 3 of the entries this PR adds). I could not run an actual Quarto render to confirm the exact rendered output (no R/Quarto toolchain available in this sandbox), but the underlying data loss is directly reproduced and unambiguous — these entries have measurably less date precision after this PR than before it, despite their source .bib year/month fields being unchanged.

Suggested fix: normalize non-standard month names in data-raw/papers.R (or the CSL-fetch step) to the 12 standard 3-letter BibTeX macros before writing publications.bib — e.g. a small case_when/lookup mapping full month names → 3-letter abbreviations — so pandoc's BibTeX date parser can pick up the month for every entry, not just Crossref's "well-behaved" ones.

Other checks performed (no issues found)

• All new/changed DOIs (10.12688/verixiv.3487.2, the four 10.64898/... openRxiv preprints, 10.1016/j.lanmic.2026.101450, 10.3201/eid3208.250753, 10.3201/eid3203.250469, 10.1038/s41467-023-38940-5) resolve via doi.org/Crossref content negotiation and their titles match the corresponding publications.bib entries — no hallucinated citations.
• Entry counts are consistent across papers/DOIs.csv (27 rows), publications.bib, and publications.yml (27 - author: blocks, up from 20).
• The regex in create_pub_listing.R is correctly anchored (^...$) and scoped to the issued: field only — it can't accidentally match issue:, and doesn't affect other numeric CSL fields (volume, page, etc.) that are supposed to stay unquoted.
• Aiemjoy_2022 appears twice as a bibtex citation key — pre-existing in the base branch, not introduced by this PR, so not flagged as a new issue.
• .gitignore addition is a reasonable, low-risk credential-hygiene fix.

Verdict

Needs more work — the issued:/date: quoting fix in R/create_pub_listing.R is correct and does resolve the numeric-YAML-coercion bug for entries with well-formed months, but the PR as a whole regresses date precision for 8 publications (5 pre-existing, 3 newly added) because Crossref's BibTeX export uses non-standard month spellings (July, June, Sept) that pandoc's citeproc parser silently fails to parse, dropping straight to year-only. Since this is the exact rendering path (publications.qmd, date-format: 'MMMM,<br>YYYY') the PR is meant to fix, I'd recommend normalizing month abbreviations in data-raw/papers.R before merging, or at minimum spot-checking the rendered /publications page for Kamau, Teunis, Garrett, Aiemjoy 2020, and Morrison 2018 to confirm the displayed dates are still correct.

Reviewed commit: ffc4c5a

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💰 Cost: $2.7469 (review) — run