LaTeX Research
Article Guide

Apply the Guide to an Existing Article

1. Open the existing Overleaf project in a file-capable AI assistant. Give the agent access to the complete project, including the main file, preamble, sections, appendix, bibliography, figures, tables, and journal instructions.
2. Copy the application instructions. Click the primary button above and paste the copied text into the agent working on the manuscript.
3. Let the agent inspect before editing. The instructions require it to preserve substantive content and working project infrastructure, identify conflicts, and apply only compatible improvements.
4. Review the compiled result. Require a clean build, visual PDF inspection, a precise file-change summary, and an explanation of any guide rule that was not applied.

Most users should apply the guide to their existing project. Download the complete template only when starting a new article or when a project needs a clean replacement scaffold.

Use the Complete Template When Appropriate

The repository also provides a working reference implementation. Use it as a new-project scaffold, a source of compatible LaTeX infrastructure, or a concrete example when adapting an existing manuscript. The sections below document that implementation.

Project Structure

latex-research-article-template/
├── main.tex
├── preamble.tex
├── titlepage.tex
├── sections/
├── appendix/
├── figures/
├── bibfiles/
└── latexmkrc

The main file assembles the article. Global packages and formatting live in preamble.tex; author information and the abstract live in titlepage.tex; main-text sections, supplementary sections, figures, and bibliography files stay in their own directories.

Compile the Article

The project is configured for latexmk, which handles the repeated LaTeX and BibTeX passes required for citations, references, and the supplementary-materials contents.

latexmk main.tex

To remove generated auxiliary files while preserving the source files, run:

latexmk -c main.tex

On Overleaf, set main.tex as the main document and select pdfLaTeX under Menu → Settings → Compiler. The supplied latexmkrc attaches automatic TeXcount generation to its $pdflatex rule.

Automatic Word Count

Before each local PDF build, latexmkrc runs TeXcount and writes the result to wordcount.tex. The title page displays that value automatically.

Compiler requirement: With the supplied latexmkrc unchanged, automatic word-count regeneration requires pdfLaTeX. If Overleaf is set to LuaLaTeX or XeLaTeX, wordcount.tex will not update because the TeXcount command is attached only to the pdfLaTeX rule.

The reported count excludes:

• the title page and abstract metadata;
• the main bibliography; and
• all supplementary materials, including the appendix bibliography.

The exclusion boundaries are already marked in main.tex, so no manual recount is required after ordinary edits.

If an existing manuscript must use LuaLaTeX or XeLaTeX, preserve that compiler and add the equivalent TeXcount hook to its latexmkrc rule. Then confirm that an ordinary build regenerates wordcount.tex. Do not change compilers merely to obtain the word count when the manuscript depends on engine-specific fonts or packages.

Figures and Tables

Keep every figure or table in its own .tex wrapper. A figure PDF and its wrapper use the same filename stem and stay together in figures/.

figures/sample_flowchart.pdf
figures/sample_flowchart.tex

Reference each float before inserting it, and keep the reference and \input{} together so the prose continues as one paragraph.

The design proceeds in four stages (see Figure~\ref{fig:sampleflowchart}).\input{figures/sample_flowchart.tex} The next sentence continues the paragraph.

Figure captions appear below graphics; table captions appear above tables. Extended definitions, coding details, and uncertainty information belong in notes rather than in the plotted graphic.

Supplementary Materials

The appendix begins with a centered supplementary-materials title and a native appendix-only table of contents. Appendix sections are lettered A, B, and so forth; subsections appear as A.1, A.2, and so forth.

Supplementary materials are single-spaced, including footnotes. Their pages use A-prefixed labels, and tables and figures are numbered within appendix sections. Appendix-only citations use the separate bibliography commands already configured in the template.

Blind Review

Set the switch near the top of preamble.tex:

\newcommand{\blind}{1}

Use 1 for the blind version and 0 for the author-identifying version. In blind mode, the title page omits author information and displays the automatic word count.

Adapt Without Rebuilding the Infrastructure

• Replace the sample metadata in titlepage.tex.
• Replace the sample prose in the numbered files under sections/.
• Add or remove section inputs in main.tex as needed.
• Add bibliography records to bibfiles/main.bib and cite them with natbib commands.
• Add supplementary sections through appendix/appendix.tex.
• Preserve the citation, bibliography, word-count, and appendix setup unless the target journal requires a change.

Always follow the target journal's current submission requirements when they differ from the template defaults.

Related Guides

• BibTeX Cleaning Agent Guide for source-backed bibliography cleanup.
• QSF Audit Agent Guide for pre-fielding audits of Qualtrics survey files.
• AI-Assisted Research Project Management and Replication Guide for organizing a research workspace and preparing a replication package.
• Guide to Recording AI Use for maintaining a durable record of substantive AI-assisted work.