Here I want to talk about R Markdown, which is quite close to \(\LaTeX\) in many respects and entirely different from Word, although you can still make your Word-demanding publishers happy with the help of packages like officedown ( Gohel and Ross 2021). In certain fields \(\LaTeX\) is also very popular. Thanks Stephan! I hope it makes things easier for MS-word submissions.Ĭomments are closed.As a researcher with (maybe quantitative) data, what do you use to write, and did you ever think of alternatives? A very common answer to the first question is MS Word, because it’s a popular program that comes with the very popular OS Windows, everyone knows how to use it (it is indeed quite user-friendly) and publishers will often ask you for Word files 1. I came across some other ways to deal with this that I did not like as much but they are simpler. csl file for Clinical Mass Spectrometry–’cause MSACL. json abbreviations database I have provided. The references in your documnent (and shown below) will have appropriate abbreviations based on the. Here is a great resource on the bookdown package and reproducible research and here are references where the journal title is longer. This Template also Takes Care of Reference Abbreviation.Īs usual, you can make a citation with the code where bibtexname is the articles’s abbreviated handle in your bibtex database. Here is a cross reference to table 1 using the code. Of course, tables can be cross referenced in the same manner as figures. Keywords: "CRAN, R, RMarkdown, RStudio, YAML"įigure 3: This is also great. citation-abbreviations=Extras/abbreviations.json csl=Extras/clinical-mass-spectrometry.csl **Conclusion**: Give me more grant money. **Methods**: My experiments are pure genius. **Introduction**: There's a big scientific problem out there. UofO: University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada UofT: University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT Canada Reference Abbreviations for MS-Word Output docx formatting, then put this word document in the same folder.ĭownload the contents of this folder from my github repo that has everything set up as I describe above.įor two authors, your YAML will need to look like this: If you want to avoid Pandoc’s goofy default.Put the two Lua scripts, the Bibtex database, the abbreviations database and the.Create a directory in it called “Extras”.This can be exported from various reference managers or built by hand. bibtex database which is just your list of references. I have made one for you from the Web of Science list and you can download it here. You will also need a journal abbreviations database. This will tell Pandoc how to format the references. Install the prebuilt binaries if you can.įinally, you need to use some scripts written in the Lua scripting language which means you will need the language itself: There are some extra installs required to help Pandoc do its job. Mac users can do this with Homebrew on the terminal command line: You will also need to install Pandoc which is the Swiss Army Knife of document conversion. Dependencies for MS-Word and the Associated YAML This allows you to avoid the horror of manually fixing your Word document after it generated from RMarkdown. In the mean time, here are the workarounds for getting the affiliations to display correctly along with all the other stuff we want, namely, cross referencing of figures and tables and correct reference formatting and abbreviation of journal names. Parenthetically, it is my hope that since AACC has indicated that they intend to make Data Science a strategic priority for Lab Medicine, they will soon accept submissons to Clinical Chemistry and Journal of Applied Laboratory Medicine written reproducibly in RMardown or LaTeX. As those of us in medical fields know, most journals (with some notable exceptions like the Clinical Mass Spectrometry Journal and other Elsevier journals like Clinical Biochemistry and Clinica Chimica Acta) require submission of a document in MS-Word format which goes against all that Data Science and Reprodicible Research stands for–he says, with hyperbole. The situation worsens if you want MS-Word output.
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