How to respond to reviewer comments
Most reviewer objections are about a methodological decision that was never explained. The response that works says what changed, where, and why — including where nothing changed.
A revision is a technical document with a persuasive job. The editor has to see, quickly, that every point was taken seriously and that the manuscript is now better.
Structure
Reproduce each comment verbatim, numbered, followed by your response and the revised text with its new location. Editors read hundreds of these; anything that makes them search costs you goodwill.
Three things belong in every response: what you changed, where it now appears, and why the change addresses the concern. The third is the one most often left out, and it is the one that shows you understood the objection rather than merely complied with it.
Read the comment behind the comment
"The statistical analysis is unclear" is rarely a request for more detail about the software. It usually means a reader could not follow why that analysis answers that question.
Adding a sentence naming the version of R will not address it. Explaining why the model was specified as it was will.
Deciding which analyses to run
Not every requested analysis is appropriate. Some strengthen the paper, some require caution, and some should be politely declined.
Run it when it tests the robustness of your conclusion or answers a real ambiguity. Decline it when it would be a post-hoc subgroup analysis the study was not powered for, when it would require assumptions the data do not support, or when it would answer a different question. Say which of those applies.
An analysis run only because a reviewer asked, presented without comment on its limitations, is exactly the exploratory result that later fails to replicate.
Disagreeing well
You are allowed to disagree. Do it by giving the reasoning and, where possible, a citation — not by restating the original text more firmly.
Offer something: an acknowledgement in the limitations, a sensitivity analysis, a clarification of scope. A reviewer whose concern is visibly recorded in the paper is usually satisfied even when the analysis did not change.
After a rejection
Reviewer comments from a rejection are free peer review for the next submission. Address them before resubmitting elsewhere, because the same reviewer may see it again — the pool is small, and an unchanged manuscript arriving at a second journal is a recognisable thing.
Frequently asked questions
How do you structure a response to reviewer comments?
Reproduce each comment verbatim and numbered, then give your response, the revised text, and its new location. Every response should say what changed, where it appears, and why the change addresses the concern.
Do you have to run every analysis a reviewer requests?
No. Run analyses that test the robustness of the conclusion or resolve a genuine ambiguity. Decline, with reasons, those that would be underpowered post-hoc subgroups, require unsupported assumptions, or answer a different question.
Can you disagree with a reviewer?
Yes, if you give the reasoning and, where possible, a citation. Offering something — a limitation, a sensitivity analysis, a clarification of scope — usually satisfies a reviewer even when the analysis does not change.