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I revised and resubmitted my manuscript (rejected with the chance of resubmission) to the same journal. I listed all my answers to the reviewers' comments at the beginning of the document. Later, the editor asked me to highlight the changes in the text to make it easier to track them. Since I almost rewrote the entire paper (I mention it in the resubmission letter), about 85-90% of the text would be colored.

I have two questions:

  1. Should I fulfill the editor's request even if almost the whole manuscript turns into let's say red? I'd prefer yes.
  2. Should I place color tags in the Latex source file, or should I highlight changes directly in the pdf file? Which of these or even other choices are the most appropriate?
  • I did not ask how to track changes in Latex. I would like to know if it is acceptable to highlight changes in PDF instead of Latex (the source files need to be uploaded as well). And if it is awkward to color almost the whole manuscript. – BalazsToth Apr 4 '18 at 10:36
  • Ah, yes, you're right: I've misread the question. I now retracted the close vote. – Massimo Ortolano Apr 4 '18 at 10:38
  • I wouldn't touch the latex source, there's a good chance you'll loose track of changes and end up with two versions. Speaking from experience here. Colour the pdf. – Karl Apr 4 '18 at 11:23
  • You might wish to color the old text only and tell the editor that the new text is in black. – Orion Apr 4 '18 at 11:47
  • Just to check, are you positive the editor meant to literally highlight the changes, or to emphasize the major changes by adding a thematic overview/summary of what you did? The latter is certainly what I thought when I first read that sentence. – cactus_pardner Apr 4 '18 at 20:11
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If the editor's already asked you to highlight the changes, then you should highlight the changes even if it's 85-90% of the text.

As for color tags, it's up to you. Both are equally good. I would highlight on the PDF since I find it easier to do, but if you prefer color tags that's just as good. Be sure to pick a color like red or blue - something that makes it easy to discern the changes from the rest of the text.

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    A text that is 90% coloured won't help the editor or reviewer. – Karl Apr 4 '18 at 11:15
  • I agree with @Karl. What about highlighting what did not change? – Matteo Apr 4 '18 at 11:19
  • No, but it's what the editor requested. I would consider it pretty impudent if I directly request an author do something and they don't do it (without a very good reason). – Allure Apr 4 '18 at 11:19
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    Let's try to move away from the letter of the request, and focus on the need behind the request: the editor wants to be able to distinguish between parts that changed and parts that didn't. Highlighting the parts that didn't change satisfies the need behind the request. Explaining to the editor why one did it this way should be sufficient to convince them. – Matteo Apr 4 '18 at 11:43
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    @Matteo I would make sure to highlight the explanation, then because, like all of us, editors are creatures of habit. – aeismail Apr 4 '18 at 13:19
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I recommend that you submit multiple files, which should fulfill the practical solution of submitting the more useful unmarked file for review while also explicitly fulfilling the editor's request. Specifically, I recommend that you submit:

  • The revised manuscript with no revision marks. This should be your official resubmission file.
  • The colour-highlighted PDF file in fulfilment of the editor's request: this should be an additional file for reviewers only. Since the editor requested it and you are submitting it as a supplementary file, there should be no problem even if it is 90% highlighted. Concerning your second question, I think highlighting the PDF is sufficient, if it is easy for you to do. However, if it is easier for you to highlight the Latex version (e.g. via diff), then you could do that instead.
  • The Latex source of your final version: You mentioned in a comment that you are required to upload this, so you should do so regardless. Concerning your second question, I don't see why you would need to highlight the Latex if you submit a highlighted PDF version.

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