Respond To Referee

These principles, distilled from journal editor guidelines and published advice (Noble 2017, PLOS Comp Bio; Review of Finance "Tips for Authors"), govern all referee responses.

Tone

• Grateful but not obsequious: "We thank the referee for this suggestion" (good) vs. "We are deeply grateful for this invaluable insight" (too much)
• Accept blame for misunderstandings: If the referee misread something, it is our exposition failure. "We realize our original text was ambiguous and have revised it as follows..."
• Never dismissive: No bare "we respectfully disagree." Every disagreement must be backed by evidence, data, or a reference.
• Direct answers first: Start each response with what you did ("We have added...", "We agree and now show..."), then explain why.
• Remember the audience: You are writing to the editor, not (only) the referee.

Structure

• Respond to every point: No exceptions, including minor ones.
• Self-contained responses: Quote or paraphrase the revised manuscript text directly in the letter.
• Reference by section name: Not page numbers (which shift between drafts).
• Group related points: When two comments address the same underlying issue, respond jointly.

Substance

• Do what the referee asks, even if you disagree: Run the requested analysis, report results in the letter, then explain why you believe the main text should differ.
• Don't over-revise: Restrict changes to what is requested.
• Address general criticisms globally: If the referee cites two examples, fix the problem paper-wide.

Common Mistakes to Avoid

Mode 1: Single-Point Workflow

Step 1: Load Context

1. Read the referee report file
2. Read the project's CLAUDE.md for paper state and claims
3. Read .claude/rules/academic-writing.md for style rules
4. Identify the specific referee point

Step 2: Map to Affected Sections

1. Identify which section(s) in the .tex file are affected
2. Read the affected passage(s)
3. Check if the point has already been partially addressed

Step 3: Draft Response Letter Paragraph

\item[\textbf{Referee:}] \textit{``[abbreviated quote of referee comment]''}

\item[Reply:] [We thank the referee for... / We agree that...]
[1-2 sentences explaining what we did and where]
[If helpful: quote the revised text in a \begin{quote} block]
[1-2 sentences explaining the rationale]

Step 4: Draft LaTeX Edits

1. Write proposed edits using the paper's terminology
2. Follow all rules from academic-writing.md
3. Show old text -> new text for each edit

Step 5: Consistency Check

Verify proposed edits do not:

• Contradict claims in other sections
• Change quantitative results that appear elsewhere
• Introduce terminology violations
• Break cross-references

Step 6: Output

REFEREE RESPONSE: Point [N] -- [topic]
======================================

REFEREE SAID:
[brief summary]

RESPONSE LETTER TEXT:
[draft LaTeX paragraph]

PROPOSED EDITS:
  File: [filename]
  Location: Section [key], ~line [N]
  OLD: [existing text]
  NEW: [proposed replacement]

CONSISTENCY NOTES:
- [any cross-section impacts]

STATUS: [Ready / Needs human review on X]

Mode 2: Full-Reply Workflow

Step 1: Load Context

1. Read the referee report file (all points)
2. Read the project's CLAUDE.md and academic-writing.md

Step 2: Plan the Reply

1. Enumerate all referee points (substantive + minor)
2. Check which have already been addressed
3. Group related points
4. Flag any points where paper edits are still needed vs. reply-only

Step 3: Create Reply Document

1. Create _replies/reply_referee{N}.tex using the LaTeX template below
2. Point-by-point responses with \item[\textbf{Referee:}] / \item[Reply:]
3. Opening and closing paragraphs

Step 4: Compile and Verify

1. Run pdflatex + bibtex + pdflatex + pdflatex (paths from canonical local state reported by tools/bootstrap.py audit, or a repo-root compatibility shim if present)
2. Check for undefined citations or references
3. Read through for tone, completeness, accuracy

Step 5: Output

Report the compiled PDF location, page count, and any issues.

LaTeX Template (for full replies)

\documentclass[12pt,letterpaper]{article}
\usepackage[top=1.0in, bottom=1.0in, left=0.90in, right=0.90in]{geometry}
\usepackage{amsfonts,amsmath,amssymb}
\usepackage{setspace,titlesec,xcolor,booktabs,enumerate}
\usepackage{natbib}
\usepackage{hyperref}

\renewcommand{\baselinestretch}{1.10}
\titleformat{\section}{\centering\large\bfseries}{\thesection.}{1em}{}
\renewcommand{\thesection}{\Roman{section}}

\begin{document}

\noindent \textbf{{\large Reply to Referee [N] for ``{Paper Title}''}}
\medskip

\noindent Manuscript [ID]

\bigskip

\noindent [Opening paragraph: thank referee, brief overview of revision scope]

\section{Response to the Referee's comments}

\noindent
\begin{enumerate}

\item[\textbf{Referee:}] \textit{``[quoted comment]''}

\item[Reply:] [response]

% ... repeat for each point ...

\end{enumerate}

\bigskip
\noindent [Closing paragraph]

{\footnotesize
\singlespacing
\setlength{\bibsep}{6pt}
\bibliographystyle{jf}
\bibliography{../latex/references}
}

\end{document}