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I am preparing a manuscript for submission to nature communications. Their formatting instructions are found here:

https://www.nature.com/ncomms/submit/how-to-submit

In particular, in the sections references they ask:

"References should be numbered sequentially first throughout the text, then in tables, followed by figures and, finally, boxes; that is, references that only appear in tables, figures or boxes should be last in the reference list."

I have a very large number of citations in the captions for my figures (it's a review plot). I was wondering if there was an easy way to specify this citation behavior or a way of doing it manually. I am not using bibtex, just the built in \cite{}.

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  • Welcome to TeX.SE. Are you saying that you create the bibliography by hand? That's what I would infer from "I am not using bibtex"; however, I may not have interpreted this correctly. Please advise.
    – Mico
    May 26, 2020 at 17:48
  • Hi Mico! I am using the cite package. I created the .bib file by hand (copying the bibtex references and appending them to the .bib file). May 26, 2020 at 17:53
  • Maybe I misunderstood your question. I generate the bibliography by using \bibliography{file.bib} where file.bib is the bib file I made by hand. May 26, 2020 at 17:54
  • The cite package helps to create numeric-style citation call-outs. It does not create the formatted entries in the bibliography, and it does not determine how the bib items are sorted. If you have a \bibliography statement in your document, that would very much suggest that you do, in fact, use BibTeX to create the bibliography. Does your document contain a \bibliographystyle instruction?
    – Mico
    May 26, 2020 at 18:06
  • Yes. I have a .bst file I have been using which I reference using \bibliographystyle. I made this .bst file by taking another nature journals .bst and making minor modifications to have it meet some of the formatting requirements of nature comms. Is there something I can do in the .bst to make my ordering happen? May 26, 2020 at 18:10

1 Answer 1

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All relevant instructions for you to heed are actually furnished in the link you provide. However, these instructions may not be easy to grasp if one is not at least somewhat familiar with basic publishing work flow.

Here are the most pertinent instructions:

All textual content should be provided in a single file.

To submit a TeX/LaTeX file, please use any of the standard class files such as article.cls, revtex.cls or amsart.cls. All textual material should be provided as a single file in default Computer Modern fonts. Please avoid non-standard fonts and packages and remove all personal macros before submitting. For graphics, we recommend graphicx.sty [and that package's \includegraphics macro].

The manuscript text file should include the following parts, in order: a title page with author affiliations and contact information (the corresponding author should be identified with an asterisk); the sections ... then References, Acknowledgements (optional), Author Contributions (Articles only), Competing Interests statement, [and figure and table environments].

Please use numerical references only for citations, and include the references within the manuscript file itself. If you wish to use BibTeX, please copy the reference list from the .bbl file, paste it into the main manuscript .tex file, and delete the associated \bibliography and \bibliographystyle commands. [emphasis added. See also below]

Before submission, please ensure that the complete .tex file compiles successfully on your own system with no errors or warnings.

There is no need to spend time visually formatting the manuscript: our style will be imposed automatically when the paper is prepared for publication.

So what does all this mean for you?

  1. Make sure you've finished writing your paper. In particular, have you \cited all pieces you wish to cite? Perform a full recompile cycle: LaTeX, BibTeX, and LaTeX twice more. Mare sure that there are no unresolved syntax errors, unresolved cross-references, or citation call-outs. Eliminate all typos and other mistakes of content.

  2. Move all figure environments to the very end of the main tex file.

  3. Move all table environments (if any) to after the figure environments, i.e., to the very end of the main tex file.

  4. Perform a full recompile cycle: LateX, BibTeX, and LaTeX twice more. Be sure to check that there are no unresolved references or citation call-outs. And, crucially, do verify that the numeric-style citation call-outs that pertain to \cite instructions that occur in the figure environments occur after all others, numerically speaking. If the ordering isn't right, you probably didn't run BibTeX properly. Make sure you BibTeX do run it properly.

  5. Delete (or comment out) the \bibliography and \bibliographystyle instructions in the main tex file, as per the instructions reproduced above. Do not delete the instruction that loads the cite package (likely: \usepackage{cite}).

  6. Find the file \jobname.bbl, where \jobname is the name of your main tex file. Open this file and copy and paste the entire contents of this file into the main tex file, right where the \bibliography statement used to be. (The contents of the bbl file will likely start with \begin{thebibliography} and end with \end{thebibliography}.)

  7. Save the main tex file and perform two more LaTeX runs (no BibTeX runs, though, as there should be no more \bibliography or \bibliographystyle instructions). Look closely at the pdf file to make sure that all citation call-outs continue to be correct and that they occur in the required order.

  8. Finally, assuming you have 5 external graphics files, you should be uploading (a) the main tex file and (b) the 5 external graphics files, using the publisher's software.

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  • I'm sorry to respond again when I thought this was done. Is there a way I can move the figure environments to the end of the paper so that they generate the citations in the correct order, but have the figures be generated in the correct order in the paper? The journal allows for figures to be in the correct place in the document when submitted, and I would like that to be the case if possible. May 26, 2020 at 22:06
  • @user8133910 - I don’t know the answers to your questions. The final sentence in your comment would appear to be in direct opposition to the requirements I excerpted. All I can suggest is that you look into whether the endfloats package does the job for you.
    – Mico
    May 27, 2020 at 2:13

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