Writing a response to reviewer comments

Part of the process of publishing a manuscript is revising the manuscript in response to reviewer comments. Assuming you are resubmitting to the same journal*, you include a cover letter and a detailed response to reviewers. With these, the key message you want to send is: my coauthors and I take your feedback seriously, and we have thought carefully about the suggestions made by reviewers. A few general points: Making snarky comments in response to a reviewer is ill-advised. 😉 As Stephen Heard says in that post, you should keep in mind that the reviewers are likely to read your replies. They’ve devoted their time to reading and commenting on your manuscript; you should be gracious. As a reviewer, I try hard to be thorough, reasonable, and timely. So when the response to reviewers seems combative, that’s frustrating. A combative tone in a response to reviewers shouldn’t affect the recommendation or decision, but it sure doesn’t make the reviewer feel his/her efforts are appreciated. Okay, now on to more specifics. Things that I generally include in the cover letter are:

  • a brief discussion of any major comments that came up;
  • a statement thanking the reviewers for their feedback (usually saying that the manuscript has been improved by incorporating that feedback, because this is almost always true);
  • a note saying that detailed responses are in the “Response to Reviewers” section;
  • a statement thanking the editor for considering the revised version.

If the revisions were pretty straightforward, the cover letter is short. However, if it seems, based on the initial decision letter, that the manuscript really needed to change in order to clear the bar for publication, the cover letter is longer, and should include a paragraph laying out the major changes that were made in response to reviewers. I work on the “Response to Reviewer” document at the same time as I edit the manuscript. I find it helpful to have a pdf of the original submission open at the same time, to figure out what lines the reviewer is referring to (since those will shift around in the revision). This can make it tricky to work on this on my laptop! In the Response to Reviewer document, you should paste all the comments from the reviewers, and then put your responses immediately below each one.** Sometimes the responses will be short (even just one word, such as “Changed” or “Done”, when in response to a suggested wording change). Sometimes the responses will be longer. One type of longer response is explaining how the manuscript was changed in response to a reviewer’s comment or question. For example, if a reviewer asked for clarification regarding a point, it’s good to give a brief clarification in the response to reviewer document, and then to explain how the manuscript was changed in response to the reviewer comment. As an example, if the reviewer’s comment was “Line 193: More information is needed on how birth rates were calculated. Did you use the Paloheimo method?”, in the response, you could write “Yes, birth rates were calculated according to Paloheimo. The manuscript has been edited to make this more clear. (Note that this section is now on lines 200-205.)” As another example, a reviewer might have suggested reframing part of the introduction. In the response to reviewers, you would then explain how you had done that. Another type of response – and one that I argue should be used sparingly – is one where you say that you did not do something a reviewer suggested and explain why. Yes, some reviews are really bad. Fortunately, though, they are rare in my experience. If you have the misfortune of receiving such a review, hopefully the editor handling the paper gives you a guide about what parts of the review to focus on. Assuming the review is one that is reasonable overall, but where you disagree with a particular suggestion: when saying that you did not make the suggested change, you obviously should explain why you are not making that change.*** (I wonder how often Brian’s post on statistical machismo gets cited in response to a reviewer’s request to add in some fancy stats.) As a few examples of where I’ve done this:

  • a reviewer suggested I remove an experiment that I thought was a key part of the story;
  • a reviewer suggested adding in a different kind of analysis, but we lacked the sample size to pull off the analysis reasonably;
  • a reviewer suggested adding in discussion related to topic X, but that felt too far afield and speculative.

In the first, case, we explained why we thought it was important to include, but explained to the editor that we could remove it if he agreed with the reviewer that it should be removed. In the last case, we gave our speculation in the Response to Reviewers, explained that we felt adding it in would not be appropriate, and said that, if the editor disagreed, we could add it in. In all cases, in the response to reviewers, we explained why we were not making the suggested change. It’s okay to respectfully disagree. But if you find yourself fighting every suggestion the reviewer made, it’s worth considering whether you are not being sufficiently open to (hopefully constructive) criticism. Another situation that often comes up when writing these responses is what to do when reviewers disagree. Sometimes, the reviewers are both suggested that something needs to be changed, but have different suggestions for what to change. This is a pretty clear indication that something isn’t working with that part of the manuscript. In these cases, I choose which one I think makes the most sense and explain why in the response to reviewers. When responding to the reviewer whose suggestions I did not take, I explain that the reviewers suggested different changes and that I changed this section in accordance with the other reviewers’ suggestion and give a brief explanation for why. In other cases, one reviewer disliked something and another reviewer liked it. (This is why it can be helpful to include a section noting strengths of the paper at the beginning of a review!) Assuming you agree with the reviewer who liked it, you can explain that in the response when saying that you did not make the suggested change. Finally, a few very specific things that I think are important:

  1. Format your response so that it’s easy to read. (This is sometimes only possible if you can upload a pdf, since many online submission systems will remove formatting if you just paste it into a text box.) One thing that works well is to italicize all the reviewer’s comments and then not italicize your responses (or vice versa).
  2. Update the line numbers. Generally, reviewers use line numbers to refer to a section of text. Don’t change the line numbers they used, but, in your response, tell the reviewer and editor what the updated line numbers are. (I included this in one of the examples I gave above.) They should read the whole thing anyway, but it’s nice to be able to spot check a few things quickly, and line numbers help with that. And, yes, this is a major pain as you prepare the letter, since the line numbers change as you edit it. Making sure the new line numbers are all correct is generally the last thing I do before submitting the revised version.
  3. If it’s a substantive change (that is, not the sort of thing that can be addressed with a “done” or “changed” sort of response), you might want to paste the revised text into the cover letter, especially if it’s an important point. But this obviously makes even more for the editor and reviewers to read through, so there are arguments for doing this and for not doing it. But, as an associate editor, I find this helpful.

Coming back to what I said at the beginning: the key message you want to send is “my coauthors and I take your feedback seriously, and we have thought carefully about the suggestions made by reviewers.” The associate editor and reviewers are volunteering their time, and are trying to help strengthen the paper before it is published. Work with them. * If you aren’t resubmitting to the same journal, you should still address the reviewer’s comments, but wouldn’t write detailed responses when submitting it to a new journal. ** Sometimes reviewers start out with a summary of the manuscript and/or a section with praise related to the manuscript. You can leave those sections out, leave them in but not have a response to them, or leave them in and just have a brief statement along the lines of “We are glad that the reviewer appreciated the study” or even just “Thank you”. The twitter consensus seemed to be for the last of those options. *** “I didn’t feel like it.” is not a recommended reason to give. 😉

Update: It turns out Andrew Hendry and I had posts on responding to reviewers that appeared on the same day! Also check out an older (and very funny) post by Tim Vines on the same topic.

46 thoughts on “Writing a response to reviewer comments

  1. I’ve taken to submitting as supporting material a track changes version so that the editor can clearly see where changes were made, in addition to all the above – anything to make their job easier, I reckon.

  2. I use LaTeX to write my papers and the response letters.

    Here’s the response letter to the second round of reviews of my recent paper: https://github.com/EDiLD/usetheglm/blob/master/manuscript/revision2/response/reponse.pdf

    Using git, LaTeX and latexdiff it is easy to produce a version with highlighted changes: https://github.com/EDiLD/usetheglm/blob/master/manuscript/revision2/diff/diff.pdf

    You can find the source to reproduce this also in the github repo (I tried to make everything open and reproducible): https://github.com/EDiLD/usetheglm

    I am quite happy with this workflow – it is reproducible and makes fun. What do you think about my response letter? Does it reduce the work of the reviewers? Is it readable? How can it be improved?

    • Another great advantage for LaTex: line numbering! You could use the package ‘xr’ in the response letter to get the exact line number from the manuscript itself. It requires another round of compilation, but what comfort! You can never be wrong with line numbers!

      It will look like this: first in the response letter,

      %%% In the preamble %%%

      %%% In the text
      Blabla (l.\ref{ms-mod1})

      then in the manuscript itself:

      Blabla \linelabel{mod1}

      That simple! Once you start using it, there’s no coming back 🙂

  3. I’ll just add that there’s no informal length limit on a response to reviewers. Don’t be needlessly wordy. But be thorough, and if that takes a lot of space, so be it. I just met someone who once wrote a response to reviewers that was longer than the ms! That’s very unusual, but it does happen.

      • @Jeremy: I like this as an AE, but Andrew’s piece yesterday said not to. So, clearly this is a point where it varies! But I find it helps as I’m reading through the cover letter. I still verify the changes and read the whole manuscript thoroughly, but it helps me go through and do an initial check.

    • Maybe not that unusual… I’ve had that already in my rather short career, and I’ve seen it too with close colleagues. Basically, my approach on this (it’s actually the way I was taught) is that the response letter should be enough in and of itself, it has to be self-sufficient to evaluate the modified version. In other words, a reviewer should not have to go back to the ms itself to judge whether his comments were taken into account or not.

      In the end, I cite every difference in the response letter, with line numbers, so that my responses are usually along these lines:

      “We agree [or not!] with the reviewer. [explain why we agree, then what we changed step by step]. This now reads (l.XXX–XXX): ‘[modified text]’…”

      As a reviewer myself, I find it very good practice, which allows to quickly check how specific things were actually modified, without going through the whole ms (how many times did I see authors acknowledging a point, but actually do very little in their ms?). I’m not saying a reviewer should not read the modified ms though, which is still necessary to have a good overview of the text as a whole…

      That can make a response letter quite thick indeed…

      • Hmm…I think it’s a little unusual to quote the revised ms. As a reviewer or editor, I wouldn’t find that helpful. On the one hand, if the revisions are minor, I don’t need to see them quoted. Just give me the line numbers for the revised passages and if I feel it necessary, I’ll glance at the ms. Don’t make me wade through a bunch of unnecessary quotes. But if the revisions are major, you can’t quote sufficiently lengthy passages in your response letter to satisfy me. I’m going to need to read the whole ms, or at least large chunks of it. In which case, lengthy quotes in your response letter are redundant.

        Not that it’s a huge deal. I have seen authors do it, though it’s rare in my experience. But personally, I’d rather the response letter just summarize the revisions rather than quoting them. But I imagine referees and editors may vary on this.

      • Two things:
        1. I messed up the threading on my first reply, so look up!
        2. Something I was reminded of this morning as I worked on a Response to Reviewers: having the text quoted in the RtR makes it easier for me to do a search in the main body of the manuscript to make sure the line numbers match up at the end. That’s handy (but, on its own, not sufficient reason to quote the changes in the letter).

      • @Jeremy: I think I see your point, and I need to agree on at least one: it has to make sense to include the quote, so very minor ones (typos, cosmetic changes, plain agreement with a reviewer’s suggestion, etc.) don’t need that for the biggest part. But I’m not sure I agree on redundancy: that’s precisely my point! I usually have lots of quotes from the ms, this is almost my track change at this point.

        As a reviewer, when I read a response letter, I don’t want to go back and forth from the letter to the ms. I’d rather read the whole letter first, see if and how my comments were taken into account, one by one. At this stage, I really focus on each comment individually. Then I go through the whole ms and see if it makes sense altogether, but that only comes in a second stage.

        And IANAAE (I am not an associate editor!) yet, so I’m not sure how this applies 😉
        (but to quote Andrew Hendry from the post linked below: “You need to convince the reviewers not the editor”)

  4. I read a blog post somewhere a while back (I thought it was from Jacquelyn Gill but now I can’t find it) that suggested if you have a LOT of suggested revisions with line numbers from multiple reviewers, paste them all into an excel spreadsheet in such a way that you can sort by line number, then re-sort later by comment to put them back in the original order when you’re ready to send back. I did this recently with an overwhelming set of reviews and it was more work at the outset but ultimately made the process much less painful.

    • Interesting! I’ve never heard of this. I can see how it would help when there are lots of revisions to do.

    • “Tell your cat that the reviewers are misguided fools, then sit back down and write a charming and polite response letter.” I love it! Thanks for sharing!

  5. Question to readers, especially those who’ve written at least one response to reviewers in the past: was any of Meg’s advice new to you, or did any of it contradict advice you’ve received elsewhere?

    I ask because many of our advice posts, including this one, offer advice that I at least would’ve thought would be familiar to most readers. But then I see how often our advice posts are read and shared (many of them are among our most popular posts), and I wonder if perhaps the advice isn’t nearly as familiar to nearly as many readers as I’d have thought. Alternatively, perhaps the amount of traffic and social media sharing a post gets is a poor index of how useful people found the post themselves. Maybe it’s all people reading and sharing advice that’s already familiar to them?

    • This is basically what I was taught, except ideas from the comments weren’t common then–submit track changes, latexdiff, and Rmarkdown. I’m sure I’ll be using these in the future.

    • From my perspective, it’s mostly familiar – accumulated experience much of which has been learnt the hard way.

      But this doesn’t change the fact that it’s extremely valuable, supportive advice! One reason these posts may be so popular is exactly because many readers recognise some/many features and feel “Thank gawd I’m not the only one who has to deal with this!”

    • I don’t think anyone ever taught me how to reply to reviewers. I’m glad to see that I mostly do things the way Meg suggests. I found the post very helpful, as I feel like I’ve just been mostly guessing at how I’m supposed to go through the publication process.

      • You are so right. Few grad students and postdocs are taught to finesse these letters, which are so critical. Hope this changes; very tough to be a brand new young investigator trying to learn how to 1) write a paper all by your lonesome and 2) get funding.

    • Nothing really new here, that’s more or less what I’ve been taught. But:

      * This post is a great resource for new students! Of course, “live” advice from the supervisor is great, but I can certainly see myself using this post for my own students when they will have to write a response letter. My way to say “Thanks” to Meghan I guess 🙂

      * From my experience as reviewer though, does not seem to be so widespread! I’ve had several revised manuscripts with very little in the response letter, the worse being a simple paragraph for the editor saying that they took all comments into account (which they clearly did not! The manuscript was hardly modified at all) and that the ms was now suitable for publication (yep, they know better than the editor). Not always that bad (fortunately!), but very often slightly frustrating from my point of view… And frustrating reviewers is definitely not a good advice for people who wants to get published.


      • “From my experience as reviewer though, does not seem to be so widespread! ”

        That’s surprising to hear. My own experience as a reviewer and editor is that doing what Meg advises is universal. I can’t recall the last time I encountered someone deviating substantially from her advice, and I do a fair bit of reviewing.

      • @Jeremy: I definitely see people varying from this (which is why I wrote the post). And the post by Tim Vines (link above) suggests Molecular Ecology sees a fair amount of variation, too!

      • @Jeremy: well, at least that comforts me! I’m glad to see another, more positive, opinion about authors’ care for a detailed response letter. I will just blame bad luck on this one, hoping for better experience in the future! 🙂
        (I can at least say that the last few were much more positive!)

  6. Steering this towards Open Science and perhaps how things will change in the future, check out publons.com if you haven’t already. Here you can get credit for your peer reviews by sending the confirmation letters from the editors to verify the review or even by submitting the review itself. I have two thoughts about this and I’m curious what others think.

    1. If we start publishing our peer reviews, this will probably cut way down on the snarkiness. People have reputations to maintain. Also, it should cut down on unfair requests, self promotion (you should cite my paper), and rubber stamps.

    2. Who decides whether a review is published or not? The reviewer could post a review without the permission of the authors or vice versa. Reviewers could publish reviews from, say 5 years ago when there was no prospect they would ever see the light of day, and authors may be embarrased by snarky remarks, etc. Do journals currently have guidelines for what we can do with our reviews? If so, I’m not aware. I can’t find a link online, but I got an email today from publons with various metrics they record. Not surprisingly, the median value across site members for the “openness” index was 0.

    • Re: publishing reviews, Terry McGlynn and Britt Koskella have old posts on this. Briefly, some journals do have policies forbidding reviewers from publishing the reviews they write, and even for those that don’t, publishing the reviews you write would be a clear violation of confidentiality. So no, as a reviewer, you can’t ever publish the reviews you write, unless the journal for which you’re writing them explicitly gives you permission. But most journal policies are ambiguous or silent on whether authors can publish reviews they’ve received. Terry’s and Britt’s posts and the associated comments have good discussion of the pros and cons of authors publishing the reviews they’ve received.

      In order to obtain the benefits of open peer review that you cite in your first point, reviewers can’t be anonymous. Removing anonymity has costs. For instance, many reviewers will refuse to review if their names are to be published, and often for good reasons (e.g., the possibility that a powerful author might retaliate against a junior reviewer). Here’s a review of the comparative and experimental literature on anonymity and openness in peer review: blogs.plos.org/absolutely-maybe/weighing-up-anonymity-and-openness-in-publication-peer-review/.

  7. This sounds exactly the way I write my responses to reviewers. Also, if there are a lot comments/questions (I get that quite often), I start with the easiest/shortest ones. Then you get a better idea how to answer the more complicated comments. And updating the line numbers is the last thing I do for the responses. At the same time I also accept all the changes in the manuscript.

    • Huh, I do the opposite. I attack the hardest and longest changes first, because maybe in the process of doing so, some of the easy/short changes will disappear (through revising a whole section, e.g.).

      • I agree. Answer the tough ones first. Or better yet, answer them in the order the reviewer presented them, which is 99% of the time the most challenging first.

      • If there has been 3+ months break when I’ve last seen the text, then I think it’s helpful to start with the small corrections. Also, those I can usually do myself. But if there are several authors then we need to discuss the larger questions/comments together. I don’t want to do everything by myself and then find out that my coauthors see the situation differently. 😉

      • I do the easy ones first. It helps me to feel like I’m ticking some things off the to do list. Sometimes I need to warm up to the big edits. But I can see how there might be times where those minor edits get obliterated by a big edit.

  8. Great post! In terms of when and how to respond to reviewer comments even if submitting to a new journal, I would add a word of caution. I’ve seen (and been part of) really nice coherent manuscripts that become a jumbled mess due to too much rewriting in response to reviewers with different ideas of what should or shouldn’t be said. I would suggest taking reviewers comments into account, but not being too prescriptive about addressing each suggestion. After all, the next set of reviewers will almost certainly have different ideas and suggestions and may even ask for the exact opposite change!

    • This gets back to Meg’s comments on what to do when reviewers disagree. In such cases, as an author you definitely don’t want to try to please everyone, for exactly the reason you note. In such cases, you should go with whichever reviewer you agree with. And don’t be afraid to come right out in the cover letter and point out that the reviewers disagree on if/how the ms should be revised. Let the editor know that you took the comments seriously and made a good faith effort to address them, but that it was impossible to please everyone because some of the comments were contradictory.

      EDIT: Wanted to add that, when referees disagree, a good editor will recognize this and will give you guidance in the decision letter as to how to address it.

  9. I am a scientific editor also and love this discussion. These rebuttal letters can be harder to write than the paper itself sometime. Going to share these ideas with clients.

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  12. As a former editor of an entomological journal, this was good advice. It’s important to remember that reviewers can vary greatly in the quality of their reviews. Some are more nit-picky over technique and writing than they are of the actual science. Others, the opposite. Reviewers often have a lot in their plates, as well, so patience is a good thing. However, as an editor, I definitely didn’t like reviewers that took way too long to review a manuscript, and then rushed through it at the last moment. My advice to newer authors is to have people in your department give the manuscript a look-over before submitting it. It will often be improved by that simple act, and a more-polished manuscript is always appreciated.

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