README

This repo is a file store and version control for a manuscript on the bias within total opioid burden metrics.

Submission status

This paper is currently being drafted and has not been submitted

How to run

1. Clone the repo
2. Install key packages
3. Render with one of the two Quarto profiles:

Command	Output
quarto render	Full book (website profile, the default): HTML with hyperlinked cross-references, plus PDF and DOCX downloads, in _book/
quarto render --profile submission	supplement.docx, manuscript.docx and cover-letter.docx in _submission/submission/

How it is set up

• _quarto.yml holds shared settings only. Do not add lists (chapters, render, filters) here: profile lists are appended, not replaced.
• _quarto-website.yml holds the book configuration and a copy of the author block.
• _quarto-submission.yml renders the wrappers in submission/. Each wrapper uses {{< include >}}, so chapter files must not have their own YAML front matter.
• The supplement renders first because it writes data/shared_objects_*.rds, which communication.qmd reads.
• Authors for the Word documents live in _authors.yml. Keep it in sync with _quarto-website.yml.
• Chunk labels and top-level R object names must be unique across the files included in one wrapper.

Cross-references in the Word documents

References that point to the other document are replaced with fixed text by xref-hardcode.lua. The text is set under xref-hardcode: in submission/manuscript.qmd and submission/supplement.qmd. If supplement sections or equations are added or reordered, update those numbers and check them against supplement.docx.

Title page

title-page.lua builds the BJA title page for any submission document that sets title-page: true (currently only manuscript.qmd). All author, affiliation, ORCID and corresponding-author details come from _authors.yml, so correct them in the plume source sheet and re-run pre_render.R. Affiliations are numbered in order of first appearance. Keywords are set under keywords: in submission/manuscript.qmd and are sorted alphabetically by the filter.

Word styling

submission/reference.docx is the Word template. It defines an Address style, right-aligned, which the cover letter's address block uses. Add journal formatting (fonts, spacing) to this file.

Bibliography

bibliography points at an absolute OneDrive path, so it only works on this machine. A Better BibTeX auto-export into the project folder would make the project portable.