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I am currently writting my first manuscript and there is no specifications about tables format in the author guidelines of the journal. If I follow the text format (double spaced, Times New Roman 12 pts) some of my tables which are very extensive will look awfull.

Should I modify their structure so they look better (but only in the manuscript) or should I keep my own format?

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First, make sure that you have read the author guideline between the lines in order not to miss any table preparation guidance that might have been stated somewhere in the middle of the author guideline. If nothing is said of table preparation, you could ask a colleague who has experience of publishing in the journal to which you are planning to submit your manuscript. If no colleague to consult, in some journals, it is possible to address queries to the editor or editorial assistant of the journal about manuscript preparation via the "contact us" address of the journal. If none of the preceding options seems to work, I think, you can apply (as you said) the formatting of the text to your tables as well (though the tables may seem a bit "awful", the tables, as well as the entire manuscript, undergo formatting during the production process and the published version of the tables would be compact).

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If you can't wait for a reply from the editor which is probably the best solution, then check out some of the articles that journal has already published and see how the tables were formatted.

You will recognise single spaced, double spaced etc...

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  • Sure but it does not mean this is the format I should use for the manuscript, because published articles and manuscript format are very different for this journal. – Circus pygargus Aug 24 '18 at 13:00
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If there is truly no guideline, lay out the table as you want, and the copy editor will make it match the journal style sheet before publication, and you will see it in the galley.

In fact, this is exactly how it would happen if you formatted the table exactly to their specification.

You are best off formatting the table for legibility instead of style, so the copy editor can accurately read it during the above process.

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