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. Once created, templates are easily accessed within RStudio, and will appear within the “New R Markdown” window as shown in Figure 17.1.The situation worsens if you want MS-Word output. For example, you can add a department field to be included within your title page. Updating the default YAML settings to include standard fields for title, author, date, or default output options.Ĭustomizing the layout of the output document by adding additional fields to the YAML metadata. Some additional examples of where a template could be used include:Ĭreating a company branded R Markdown template that includes a logo and branding colors. The rticles package in Chapter 13 is a good example of custom templates for a range of journals. In fact, you can create custom document templates by yourself, which can be useful if you need to create a particular type of document frequently or want to customize the appearance of the final report. When you create a new R Markdown document from the RStudio menu File -> New File -> R Markdown, you will see a default example document (a template) in the RStudio editor.
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