Prompt de estrutura de artigo: BJPsych

Esta é a versão especializada para o Brazilian Journal of Psychiatry (BJPsych) do prompt do capítulo anterior. A diferença em relação ao genérico: aqui o agente já recebe a URL confirmada do estilo CSL no Zotero, a URL confirmada das Instructions for Authors da revista, e a estrutura de pastas com nomes em inglês (a revista publica em inglês). Use este capítulo se você vai submeter para BJPsych. Se for para outro periódico, copie este prompt e troque os dois URLs e o nome da pasta — a moldura segue válida.

O prompt está em inglês porque o agente trabalha melhor em inglês para tarefas de execução (mkdir, curl, R), e porque os nomes de arquivos e seções do manuscrito ficam em inglês. As decisões de design e o comportamento “plan-first → entrevistar antes de criar” são os mesmos do 02.

O prompt

You are an expert in academic publishing and Quarto.

Create the complete folder and file structure for a scientific article to be submitted to the Brazilian Journal of Psychiatry (BJPsych).

This project will be used by a researcher who is not familiar with Quarto or Positron. Keep all technical complexity hidden inside _quarto.yml. The .qmd files the researcher edits should look as clean and simple as possible.

Your job is to build the structure only — do not write the article content, do not simulate data, and do not run any analysis. The project must be complete and ready for the researcher to open, write, and render.

──────────────────────────────────────────── HARD RULES (apply to the entire task) ────────────────────────────────────────────

DO NOT access the internet at any point. Do not run curl, wget, WebFetch, WebSearch, or any tool that touches the network. Do not download files (CSL, DOCX, PDFs, fonts, anything). Do not look up journal guidelines online or from memory of online sources. DO NOT infer or invent journal-specific rules (running-title length, abstract structure, allowed languages, citation style specifics). Use sensible, generic defaults and label them as “verify before submission”. DO NOT create the CSL file or the Word reference template. The folders references/csl/ and templates/ must exist but stay empty. The CSL is addressed in Step 7. The Word template is non-blocking: the reference-doc: line in _quarto.yml stays commented out so that quarto render works immediately with Pandoc defaults until the researcher adds the journal’s template. All file generation must be local and offline. ──────────────────────────────────────────── STEP 1 — CREATE FOLDER STRUCTURE AND ROOT SCAFFOLDING ────────────────────────────────────────────

1a) Create folders (safe even if some already exist):

mkdir -p sections analysis data/raw data/processed \
         output/tables output/figures \
         references/csl templates submission \
         instructions-for-authors

Target project structure:

bjpsych-article/
├── _quarto.yml                ← all technical settings (researcher does not edit)
├── manuscript.qmd             ← MAIN file (clean YAML, includes sections)
├── README.md                  ← project description + how to render
├── .gitignore                 ← ready for when Git is initialized later
├── sections/                  ← IMRaD sections, included by manuscript.qmd
│   ├── 00-abstract.qmd
│   ├── 01-introduction.qmd
│   ├── 02-methods.qmd
│   ├── 03-results.qmd
│   ├── 04-discussion.qmd
│   └── 05-conclusion.qmd
├── analysis/                  ← scripts that generate tables and figures
│   ├── 01-cleaning.R
│   ├── 02-analysis.R
│   └── 03-figures.R
├── data/
│   ├── raw/                   ← read-only, gitignored
│   └── processed/             ← derived, gitignored
├── output/
│   ├── tables/                ← generated tables (.csv, .html)
│   └── figures/               ← generated figures (.png, .pdf)
├── references/
│   ├── references.bib         ← single bibliography file
│   └── csl/                   ← EMPTY — CSL will be added later (Step 7)
├── templates/                 ← EMPTY — Word template optional, added when available
├── instructions-for-authors/  ← EMPTY — PDF may be added later (Step 7)
└── submission/                ← rendered files for submission (gitignored)

1b) Create .gitignore at the project root:

# Data — never version raw or derived data
data/raw/
data/processed/

# Generated output — regenerable from analysis/
output/
submission/

# Quarto cache and freeze
_freeze/
.quarto/

# R environment library (lockfile is versioned, library is not)
renv/library/
renv/local/
renv/cellar/
renv/staging/

# OS junk
.DS_Store
Thumbs.db

1c) Create README.md at the project root with:

One-paragraph placeholder description (researcher fills in) “How to render” section with: quarto render manuscript.qmd “How to reproduce” note pointing to renv::restore() after cloning A “Pending artefacts before submission” section listing: • CSL file at references/csl/ — required for citations to render with the journal’s style. Until present, the csl: line in _quarto.yml will cause render to fail; comment it out for a preview-quality render, or place the file and leave the line as is. • BJPsych Word reference template at templates/bjpsych-template.docx — NOT required for render to work. The reference-doc: line in _quarto.yml is commented out by default, so DOCX renders use Pandoc’s generic styling. Once the journal’s template is in place, uncomment that line in _quarto.yml. Do not submit a manuscript rendered with Pandoc defaults — the formatting will not meet journal requirements. ──────────────────────────────────────────── STEP 2 — PROJECT CONFIGURATION (_quarto.yml) ──────────────────────────────────────────── Create _quarto.yml with ALL technical settings:

project:
  type: default
  output-dir: submission

# NOTE: The file referenced by csl: is NOT created during setup.
# The researcher must add it before rendering with citations,
# or comment out this line for a preview render.
bibliography: references/references.bib
csl: references/csl/brazilian-journal-of-psychiatry.csl

execute:
  echo: false
  warning: false
  message: false

format:
  docx:
    # Word reference template for BJPsych formatting.
    # The line below is commented out so that quarto render
    # works immediately using Pandoc's default styling.
    # AFTER placing the journal's template at
    # templates/bjpsych-template.docx, uncomment the line.
    # Submitting a manuscript rendered without the journal's
    # template is NOT acceptable for final submission.
    # reference-doc: templates/bjpsych-template.docx
    fig-dpi: 300
    tbl-cap-location: top
    fig-cap-location: bottom
    number-sections: false
    lang: en  # generic default; researcher to verify
  pdf:
    documentclass: article
    papersize: a4
    fontsize: 11pt
    linestretch: 1.5
    geometry:
      - margin=2.5cm
    number-sections: false
    fig-pos: "H"
    keep-tex: false

DOCX is the primary output for review and submission. PDF is included for sharing polished versions. Both render from the same manuscript.qmd.

──────────────────────────────────────────── STEP 3 — MANUSCRIPT FILE AND SECTION FILES ────────────────────────────────────────────

3a) Create manuscript.qmd. The YAML contains only the fields the researcher needs to fill in; everything else lives in _quarto.yml.

---
title: "Article Title"
author:
  - name: "Author Name"
    orcid: "0000-0000-0000-0000"
    affiliation: "Institution, City, Country"
    email: "email@institution.edu"
    corresponding: true
  - name: "Co-author Name"
    orcid: "0000-0000-0000-0000"
    affiliation: "Institution, City, Country"
running-title: "Short title — verify length limit before submission"
date: today
---

{{< include sections/00-abstract.qmd >}}
{{< include sections/01-introduction.qmd >}}
{{< include sections/02-methods.qmd >}}
{{< include sections/03-results.qmd >}}
{{< include sections/04-discussion.qmd >}}
{{< include sections/05-conclusion.qmd >}}

## Acknowledgments {.unnumbered}

[Funding sources, collaborators.]

## Conflicts of Interest {.unnumbered}

[Declare any conflicts, or state: The authors declare no conflicts of interest.]

## Funding {.unnumbered}

[Funding sources and grant numbers.]

# References {.unnumbered}

::: {#refs}
:::

3b) Create each file in sections/ with a top-level heading and a short placeholder line. Section files have NO YAML of their own — they are includes and inherit context from manuscript.qmd. Use a generic IMRaD structure with a structured abstract; do NOT try to enforce specific journal rules.

sections/00-abstract.qmd:

  ## Abstract {.unnumbered}

  **Objective:** [State the study objective.]
  **Methods:** [Describe study design, participants, main analyses.]
  **Results:** [Summarise principal findings.]
  **Conclusions:** [State the main conclusion.]

  **Keywords:** keyword1; keyword2; keyword3.

sections/01-introduction.qmd:

  ## Introduction

  [Background, rationale, and objective of the study.]

sections/02-methods.qmd:

  ## Methods

  ### Study Design and Participants

  [Describe study design, setting, inclusion/exclusion criteria.]

  ### Measures

  [Describe instruments and outcome variables.]

  ### Statistical Analysis

  [Describe statistical methods, software, significance threshold.]

sections/03-results.qmd:

  ## Results

  [Present findings. Reference tables as @tbl-label and figures as
  @fig-label.]

sections/04-discussion.qmd:

  ## Discussion

  [Interpret results, compare with literature, discuss limitations.]

sections/05-conclusion.qmd:

  ## Conclusion

  [Main conclusion and clinical or scientific implication.]

──────────────────────────────────────────── STEP 4 — PLACEHOLDER BIBLIOGRAPHY (references/references.bib) ──────────────────────────────────────────── Create references/references.bib with a single placeholder entry so the file is not empty and Quarto does not error on render.

% This file is managed by Zotero + Better BibTeX.
% To add references: export your Zotero collection in Better BibTeX
% format with the "Keep updated" option pointing to this file
% (references/references.bib).
% Cite in text using [@placeholder2024] or @placeholder2024.

@article{placeholder2024,
  author  = {Author, Name},
  title   = {Article title},
  journal = {Journal Name},
  year    = {2024},
  volume  = {1},
  number  = {1},
  pages   = {1--10},
  doi     = {10.0000/placeholder}
}

──────────────────────────────────────────── STEP 5 — DO NOT CREATE CSL OR DOCX TEMPLATE ──────────────────────────────────────────── Skip creation of:

references/csl/brazilian-journal-of-psychiatry.csl templates/bjpsych-template.docx Both folders exist but stay empty. The CSL is addressed in Step 7.

The DOCX template is non-blocking: the reference-doc: line in _quarto.yml is commented out (see Step 2), so quarto render works immediately with Pandoc’s default styling. The researcher uncomments that line after placing the journal’s template at templates/bjpsych-template.docx.

──────────────────────────────────────────── STEP 6 — VERIFICATION (LOCAL ONLY, NO RENDER) ────────────────────────────────────────────

Show the complete folder tree. Confirm these files EXIST and are non-empty: _quarto.yml manuscript.qmd README.md .gitignore references/references.bib sections/00-abstract.qmd sections/01-introduction.qmd sections/02-methods.qmd sections/03-results.qmd sections/04-discussion.qmd sections/05-conclusion.qmd Confirm these files are intentionally ABSENT (folders exist, files do not): references/csl/brazilian-journal-of-psychiatry.csl templates/bjpsych-template.docx Confirm in _quarto.yml that the reference-doc: line under format: docx: is present BUT commented out, with the explanatory block above it. This is what allows render to work without the Word template. Validate manuscript.qmd YAML and code-fence balance statically. Display the first 30 lines of manuscript.qmd. Do NOT run quarto render. Render will work for DOCX as soon as the CSL question in Step 7 is resolved (either the file is provided or the csl: line is commented out). The Word template is optional for an initial preview render. State the render command for the researcher: quarto render manuscript.qmd List explicitly any external assumption you had to make (default language, default running-title placeholder, default abstract structure, etc.) — flag each as “verify before submission”. ──────────────────────────────────────────── STEP 7 — FINAL QUESTIONS TO THE RESEARCHER ────────────────────────────────────────────

After completing Steps 1–6, ASK the researcher the following two questions and WAIT for their reply before doing anything else. Do not act on either step on your own initiative.

QUESTION 1 — CSL (citation style file) “The Brazilian Journal of Psychiatry CSL file was intentionally not created. The folder references/csl/ is empty. Would you like to: (a) place the CSL there yourself, or (b) have me download it for you from the official source? Please reply (a) or (b).”

QUESTION 2 — Instructions for Authors “The journal Instructions for Authors PDF is not yet present in instructions-for-authors/. Would you like to: (a) place the PDF there yourself, or (b) skip this step for now? Please reply (a) or (b).”

If the researcher replies (a), do nothing further on that point. If they reply (b) to QUESTION 1, then (and only then) you may fetch the CSL from a single trusted source. If they reply (b) to QUESTION 2, do nothing further — do not attempt to fetch the PDF.

Do not bundle these questions with other actions. Stop and wait.

──────────────────────────────────────────── NOTE ABOUT GIT ──────────────────────────────────────────── This prompt does not initialize Git. The researcher may not be familiar with version control yet, and will start versioning when ready.

The .gitignore file is already in place (Step 1b), so once Git is initialized it will immediately ignore data/, output/, submission/, _freeze/, and renv library folders.

When the researcher is ready to start versioning, they should run, from the project root:

git init
git add .
git commit -m "initial structure"

From that point on, every change to manuscript.qmd, sections/, analysis/, and configuration files can be tracked with Git.

O que vem a seguir

Estrutura BJPsych pronta. Volte ao fluxo normal do bloco: o próximo passo, igual ao do capítulo 02, é dar à IA o contrato persistente que ela vai consultar em toda conversa futura sobre este projeto — o AGENTS.md.

→ 03 · Prompt para AGENTS.md customizado