Chapter 11 Collaborative & Formatting Tools

Other than the collaborative writing software or tools mentioned earlier(e.g., Google Docs, or the “tracked changes” tool in Microsoft Word), there exists a number of collaborative and formatting tools that can be very helpful in the manuscript writing process.

11.1 Rmarkdown

Below is a brief tutorial on how to use RMarkdown to mix code and text together to create a reproducible article, with citation, tables and figures, i.e., how to use Rmarkdown as a tool to write scientific documents.

11.2 GitHub

Below is a video about how to use GitHub in collaboration with RStudio and R to write and update scientific documents. In the description of the video, you can find a table of content, and able to click on the respective sections.

11.3 Formatting tools

Usually the formatting options are explained in the journal’s website, often providing necessary word and LaTeX templates. Rmarkdown users often use rticles that includes a suite of custom R Markdown LaTeX formats and templates for various journals.

There are some journals, that allows authors to submit in any format of their choice for the first submission. Here is an example of Your Paper, Your Way (YPYW) resource from Elsevier. For YOYW, only when a paper is requested for revision, authors are requested to use the format specified by the journal.