![]() ![]() In the short-term, however, the biggest practical difference between Rmarkdown and Word is the writing environment. In the long-term, the biggest practical difference between writing in Rmarkdown versus Word is to greatly increase the efficiency from data to professional looking output. All of this takes time, and these processes need to be repeated if something in the analysis changes affecting figures, tables, or summary statistics. Within-text values calculated from data need to likewise be copied into Word directly. Table elements from statistical output often need to be copied and pasted, or written from scratch. Figures need to be copied and pasted into the text (or attached separately). Page breaks and formatting can be difficult to specify as desired. And the prevalence of word processors makes the inconveniences associated with using them to do scientific writing go largely unrecognised we are used to it. There is nothing wrong with this, but Microsoft Word and other word processors are not written with scientific writing in mind. ![]() Most biologists write manuscripts in Miscrosoft Word. Practical differences between Rmarkdown and Word ![]() The essential tools for getting started can be learned in minutes, with the more advanced options being learned along the way fairly painlessly as needed. Having written manuscripts in all three, I am convinced that Rmarkdown is the most useful and most efficient way to do scientific writing. Before this, the options were pretty much limited to Microsoft Word and LaTeX. The ability to write high quality documents in Rmarkdown is possible because of the work of the Rstudio team, and especially the developer Yihui Xie. Rmarkdown is still fairly new, having been first released in 2012 (Xie, Allaire, and Grolemund 2018), not long after the initial release of Rstudio in 2011. I will explain this latter advantage in more detail in the next section, comparing how writing in Rmarkdown differs from writing in Word, in practice. Other advantages will be more subtle, and include the ability to integrate more easily with version control software such as git, and to focus more clearly on the process of writing rather than formatting the document. Some of these advantages will be obvious features of Rmarkdown, including the ability to do the following: integrate R code directly (avoiding the need to awkwardly copy-paste analyses, tables, or figures), use BibTeX (to easily add citations, properly formatted for a specific journal), integrate LaTeX equations, add links, and add HTML code and comments. My hope is that the advantages will become clear as I demonstrate how to write a manuscript in Rmarkdown. It is not immediately obvious what the advantage is for doing any of this, particularly for people who are already comfortable writing in Word (or LaTeX). In fact, when initialising a new Rmarkdown document within Rstudio (in Rstudio, select File > New File > R Markdown), some example text and R code is initialised to help demonstrated how it works this sample text can be immediately turned into an HTML, PDF, or DOCX using the ‘Knit’ icon in the Rmarkdown toolbar. Getting started with writing simple documents in Rmarkdown takes very little time in Rstudio. Rmd files can be opened and edited in Rstudio, and turned into HTML, PDF, or DOCX files with the push of a button. For now, all that is important to know is that. xml files, so something with these extensions cannot be opened in a text editor, but is not technically a binary). xml binary files include files with the extensions. Other examples of text files are files with the extensions. Text files are also easy to work with in version control and on GitHub because version control (e.g., git) can track the line by line changes over time in a way that cannot be done with non text files (i.e., binary files). Because Rmarkdown files are text files, they can be viewed and edited in any text editor (e.g., Notepad, gedit) or integrated development environment (e.g., Rstudio, vim, emacs). Within Rstudio, a document can be written in Rmarkdown, then converted seamlessly to high quality HTML, PDF, or DOCX formats. Rmarkdown is a type of file (extension ‘.Rmd’) that is used to make documents that are easily integrated with R. ![]()
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