Do ecological journals accept LaTeX and open document formats?

By | May 18, 2015

Last week I started to draft a manuscript that is heavy on the computation side and it uses large data. This requires everything to be well documented and organized, otherwise I get lost in my own code. The real challenge is then to confront my analyses with the co-authors and, ultimately, journal referees -- a little request ("oh, it would be nice to add this or that" or "you've forgot to log-transform this") can easily force me to re-analyze everything.

One way to minimize the hassle and to prevent errors is to make everything transparent, open and reproducible, and to link the the manuscript with the figures and tables produced directly by the code. An open framework that enables all of this is LaTeX with its .tex extension.

Another 100% open format is OpenDocument (with the .odt extension). It lacks the LaTeX's ability to link stuff and to deal with math, but it is the default format of the most popular free office suite, and so it is accessible to anyone with limited budget. Plus, it has all of the functionality of .doc, .docx and .rtf, including support for comments, revision control, equations, or Zotero references.

In contrast and in spite of some theoretical claims, Microsoft's .doc and .docx are not open -- a painful experience of anyone who tried to use LibreOffice to open an MS Word document containing equations, comments or reference fields.

But back to my manuscript; because of its computational nature I'd prefer to write it in LaTeX; now I need to choose the suitable journal, which I've found to be Global Change Biology. However, when I check the author guidelines I realize that it doesn't take LaTeX. So I turn to Global Ecology and Biogeography, then to Ecography, only to realize that none of them takes LaTeX.

So I've made a quick research, checking the acceptable manuscript formats in major ecological journals, plus Nature, Science, PLOS and PNAS. Here is what I've found:

Journal Accepted formats Accepts LaTeX?
Diversity and Distributions ? ?
Journal of Ecology Word processor ?
Trends in Ecology and Evolution Word no
Frontiers in Ecology and the Environment .doc, .docx no
Ecography .doc, .docx, .pdf no
Oecologia Word, .rtf, .pdf ?
Conservation Biology Word no
Functional ecology Word, .rtf no
Global Change Biology Word, .wpd, .rtf, .ps no
Journal of Biogeography .doc, .docx, .rtf no
Oikos Word, .rtf, .ps no
American Naturalist Word, .rtf, .tex yes
Ann. Rev. of Ecol., Evol. and Systematics .doc, .rtf, .tex yes
Biological Conservation Word, .pdf, .tex yes
Global Ecology and Biogeography Word, .tex yes
Journal of Animal Ecology Word, .tex yes
Journal of Applied Ecology Word, .tex yes
Journal of Evolutionary Biology .doc, .docx, .rtf, .tex yes
Molecular Ecology Word, .pdf, .tex yes
Science .docx, .pdf yes
Evolution Word, .rtf, .tex yes
Methods in Ecology and Evolution Word, .tex yes
PNAS Word, .rtf, .tex yes
Proceedings B Word, .pdf, .tex yes
PLOS BIOLOGY .doc, .docx, .rtf, .pdf, .tex yes
PLOS ONE .doc, .docx, .rtf, .pdf, .tex yes
Ecological Monographs .doc, .docx, .wpd, rtf., .tex yes
Ecological Applications .doc, .docx, .wpd, rtf., .tex yes
Ecology .doc, .docx, .wpd, rtf., .tex yes
Ecology Letters .doc, .rtf., .pdf, .tex yes
Nature Word, .wpd, .eps, .ps, .rtf, .tex yes

Some highlights

  • Diversity and Distributions gives almost no information on what it accepts. So I assume that it accepts everything, but I'd still prefer the journal to state it explicitly.
  • Ecography and Frontiers in Ecology and the Environment are the strictest supporters of Microsoft's proprietary formats by not even allowing .rtf, let alone .tex.
  • Journal of Ecology, TREE, Frontiers , Conservation Biology, Oecologia, Functional Ecology, Global Change Biology, Journal of Biogeography and Oikos seem not to take LaTeX (if they do, I missed it). I was especially surprised by Oikos which used to be known for publishing papers in theoretical population ecology, something that looks especially crisp in LaTeX.
  • There is an explicit statement in Methods in Ecology and Evolution guidelines that they cannot take OpenDocument. I wonder why is that.
  • Surprisingly, .odt is almost never accepted. I guess that it is because it is assumed that .rtf is open enough, but maybe there is another reason; I'd be curious to hear that.
  • There are journals that seem to make an effort to accommodate LaTeX -- and they are the majority, which is great! It is the group at the lower part of the table starting with American Naturalist. Especially welcoming is the attitude of all ESA journals (Ecology, Ecological Monographs, Ecological Applications), Royal Society journals, Ecology Letters, PLOS, PNAS and Nature. If these guys can take it, why can't the others?

9 thoughts on “Do ecological journals accept LaTeX and open document formats?

  1. Mathieu

    Hi, great list! Thanks for this summary.

    One quick comment to add: from my experience, many of them will accept PDF for a submission, even if not stated as such (from your list, I successfully tried with Am Nat, Oikos, J Ani Eco, J Appl Eco, Ecology, PNAS). It will usually go through their document converter, which will convert it from PDF to... PDF! Just check the outcome before finalizing!

    That's enough for a submission, and if everything goes well and comes the time of publishing, well, that's probably worth the pain and accommodating with the format of their choice (although I agree that in some cases, e.g. multiple complex equations, it can be fairly annoying).

    That's been my approach so far. Let's worry about LaTeX only after all rounds of revision are past, and use it until then just because it's the best tool for authoring!

    Mathieu.

    Reply
      1. Petr Keil Post author

        Thanks Mathieu and Florian! I guess that you have a nice pragmatic approach -- submit whatever works and if there is a problem, try to negotiate, or accept their terms.

        However, I still think that converting between formats is a hassle that could be avoided by a little bit more openness and clarity on the journals' side. Plus, MS Word really is a pain -- not as much for MS Word users, but for those who try to live without it.

        Reply
  2. Adriana De Palma

    Note that even if a journal says that they accept latex documents at submission, they may still require a word document later if the paper gets accepted (e.g. Journal of Applied Ecology).

    Reply
  3. Fran├žois

    Very nice post Petr !

    I do concur with you that trying to live without MS (Word, and even Windows) is very painful in our world. If you work with linux, it makes your life so hard because most of your colleagues will call you a fanatic if you ask them to accept handling open formats (e.g. odt), not talking about latex (then they will call you a crazy annoying geek, a crazy annoying geek they will call as soon as they need some analytical advice ...).

    All this as to do, in my opinion, with education (people are trained with MS products as soon as in primary school, and this is because MS as huge programs to "collaborate" with schools), but also with the inherent people's propensity to avoid any change (asking them to download LibreOffice and to learn the slightly different ergonomic of the program seems like asking them to walk on their hands). It's a shame for academics and scientists, who should embrace evolution and be able to change their mind by thinking about issues and accept constructive debates.

    All this being said, it's a shame that journals do not accept open format, as if MS was paying them for this. By so doing, they do not consider the financial situation of people living in developing or least developed countries, and this is clear discrimination that should be avoided.

    Reply
  4. Marco

    Hi,

    I wonder if one day, journal will accept RMarkdown format. That would mean we have to share the dataset and the primary code to make our analysis. Would it be problematic?

    Reply
    1. Aaron

      I might be a bit late responding, but I believe this is extremely important especially with the science reproducibility issues!

      Reply
  5. daniele

    great post!
    the only reason I can find is that they are paid by MS and this is to be condemned. we as scientists should do something against this and try to make pressure over them or at least to shout it around.

    Reply

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