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
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
.rtf, including support for comments, revision control, equations, or Zotero references.
In contrast and in spite of some theoretical claims, Microsoft's
.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||?|
|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|
|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|
- 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
- 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.
.odtis almost never accepted. I guess that it is because it is assumed that
.rtfis 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?