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I am about to resubmit a manuscript to a journal, having now addressed the reviewers' feedback.

The instructions say to submit my final manuscript along with a "marked-up manuscript", which is "the final version showing all changes from the former version".

Since my manuscript is in LaTeX, what is the standard way of highlighting the changes I made? Had it been a Microsoft Word document, I would have used the "track changes" feature. More so than technical methods, I am wondering what format the reviewers typically expect. Are they asking for a marked-up, compiled PDF? Or a marked-up TeX source code? Or a side-by-side comparison of the source code?

closed as off-topic by jakebeal, Enthusiastic Engineer, Peter Jansson, David Richerby, Fomite Mar 29 '15 at 0:08

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    I think you can receive good answers to this question on TeX.sx. It is at least slightly off topic here since it is mostly a software issue. – Peter Jansson Mar 28 '15 at 15:53
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    There is a duplicate of your question on TeX.SX; “Track changes” in LaTeX – Enthusiastic Engineer Mar 28 '15 at 15:59
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    More so than technical methods, I am asking what format the reviewers are possibly expecting. Are they asking for a marked-up compiled PDF? Or a marked-up TeX source code? Our a two-column comparison of the source code? – Doubt Mar 28 '15 at 16:11
  • @Doubt Besides you may update your question to clarify your question regarding your comment; I believe that your question is primarily opinion-based, because every journal may have different taste on receiving updated manuscripts (for updates to be tracked) and there is no standard way on it. You'd better to contact the journal you are submitting to. – Enthusiastic Engineer Mar 28 '15 at 16:18
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    I'm voting to close this question as a duplicate of this question of TeX.SE – jakebeal Mar 28 '15 at 18:21
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When submitting to IEEE journals which require to highlight the changes, I simply colour them in red (no one complained so far...).

\usepackage{xcolor}   
\newcommand{\rev}[1]{{\color{red} #1}} 
%
%...
%
\rev{Hey, I'm a change}

For purpose of reviewing, they just need a compiled PDF. For the final submission, you can simply redefine the \rev command to do nothing.

  • I often use this solution when sending new versions of a manuscript to collaborators. I have used it at least once that I remember for a revised submission to JAP and that seemed to be fine too. – Miguel Mar 28 '15 at 21:25
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At least on one occasion, I used Latexdiff’s output with the default settings for this purpose and nobody complained. In some cases, you might want to manually tweak this, e.g., if you moved larger pieces of text. If I recall correctly, I reviewed some manuscript, for which the editorial system automatically applied Latexdiff (or something that generates a very similar output) to the manuscript.

Speaking more generally, the point of this requirement is quite obviously that the reviewers and the editor can easily see, which aspects of the manuscript were changed and how. More precisely, it should be easily visible where you added something to the manuscript, and (what is sometimes done badly) where you removed something. Latexdiff’s output fulfils these criteria in most circumstances, but there are other ways to do this.

I would not know why anybody would want to see your source code at this point, as it is more difficult to read and it also contains changes that do not affect the compiled manuscript. Also, depending on your field, some reviewers may not know LaTeX.

Finally, I think that whoever wrote marked-up manuscript actually wanted to say marked manuscript (or mark up is actually also used in this meaning and I managed to be ignorant of this).

  • +1 for latexdiff -- fantastic tool for exactly this purpose. – Wolfgang Bangerth Mar 28 '15 at 20:40

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