![]() ![]() References are managed with Mendeley and an appropriate CSL. The final version will eventually be converted into PDF. qmd (this will be very annoying, but googledocs and trackdown is sadly not an option). Drafts will be send to my adviser and I will use msword track changes function to manually pour them into the. I have a draft template and will create a final version template for final proofreading and publication purposes. I plan on creating all my figures and tables with ggplot and kableExtra, and embedding them inline with the text. I created a RStudio project, a global _quarto.yml config file, and a. I'm currently using quarto/RMarkdown for writing my thesis. In conclusion, it is not a streamlined process. CSL file (in github citation-style-language/styles or zotero styles) for your journal and set it in your YAML (see in 'R for Data Science' online book the 'YAML Header' section). bib format (make sure you assign a Citation Key to each reference) and cite in your manuscript as you write. For citations, I recommend you use Mendeley/Zotero (or whichever reference manager you like) and export you citations in. Again, final formatting will be done by the journal. As I said, if you're lucky, the journal you want to publish with will have a Tex template, otherwise create a standard msword template that's easy to collaborate with (double spaced, numbered lines, etc.). What can be standardized is citation style, font type/size, and page format. Most of these you will type, so read the guidelines and try to keep them in mind when writing. Journal guidelines mostly focus on how to process figures and tables, how to cite, word count, symbols and abbreviations, etc. Other than that, journals will do their own formatting, so I fail to find a reason to try and do it myself. ![]() Regarding Tex/PDF, if you are lucky and your journal accepts tex files, they usually have their own template. Journal guidelines usually only require minimum page and typography formatting so you can easily create your own templates if you can't find any online. ![]() Regarding rendering, I only render into msword, using a template docx file. I haven't tested it, but maybe it's worth looking into. You could try Jupiter notebooks, but I find that the tex formatting is less appealing that markdown (specially if you are collaborating with non-tech savvy people).Įdit: Googling stuff for this post I ran into Manuscript. I do not know if there are programs/platforms that let you achieve this in a seamless way. It requires working on google docs files, though. It is far from ideal, and it requires everyone to agree on some workflow ground-rules, but it tackles one of the most difficult issues on collaboration (i.e: Tracking changes to manuscripts). The best approximation I could find is the Trackdown package by Emily Kothe et al. ![]() There is no simple way to approach collaboration if people aren't willing to migrate to a markdown format. It defeats most of the purpose of reproducible documents. I'm really looking to use Quarto for manuscript drafting, but too often I've had to resort to rendering a Word document and then making manual changes to conform to submission guidelines. How do you deal with the annoying and specific submission guidelines for each journal? Do you tweak your Quarto/R Markdown for each journal you submit to? What is everyones strategy for creating publication-ready tables for PDF or Word documents? I still just create my tables manually in a separate Word document. How? Seriously, this has got to be the most annoying aspect of scientific manuscripts via Quarto/RMarkdown. My co-authors (and some journals) require Word documents to provide feedback, but this is by far the most annoying format to work with and getting appearance-parity with PDF is generally a nightmare. Which formats do you render to? I prefer to render to TeX/PDF to get a nicely formatted manuscript. Spinning up a PDF or Word format manuscript and submitting it to a journal. I am genuinely curious if anyone is using RMarkdown or Quarto to prepare scientific manuscripts for submission to peer-reviewed journals? Not using a pre-defined TeX template or one of the Quarto journal formats. ![]()
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