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. Then make your YAML header look like this: -Īffiliation: University of Tuktoyaktuk, CXVG+62 Tuktoyaktuk, Inuvik, Unorganized, NT CanadaĪffiliation: University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, CanadaĪnd as you can see in figure 3 you get a correctly list of authors.įigure 3: This is also great. Open it up in a text editor and find the section that reads: $if(author)$ If that seems difficult, you can also download it here. Move the file to the “Extras” folder discussed above. To get your current working copy of the Pandoc LaTeX template open up a terminal (Mac/Linux) and type: pandoc -D latex > mytemplate.tex So what you need to do is modify the Pandoc LaTeX template. tex template that Pandoc uses for generating LaTeX files does not support author affiliations as descibed in the Pandoc documentation. You don’t need the lua scripts for LaTeX although you can use them. Do a full install with all the glorious bloat of all LaTeX packages. For Linux, just install from the command line with your package manager. LaTeX markup language is available here: Mac, Windows. It goes without saying that you need to install LaTeX. Keywords: 'CRAN, R, RMarkdown, RStudio, YAML'Įt voila! Figure 2 shows that we have something reasonable.įigure 2: This is so great Dependencies for LaTeX and the Associated YAML reference-doc=Extras/Reference_Document.docx citation-abbreviations=Extras/abbreviations.json **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: title: | 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: brew install pandoc 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.

Rmarkdown to pdf