Writing the Manuscript

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Reproducibility

In an effort to make all of the research process as transparent and reproducible as possible, we try to integrate our code and results into our manuscript writing in an automated process.

R Markdown

R Markdown allows you both to save and execute code and to generate reports and manuscripts with embedded code and figures in a single document. These .Rmd files are the most common way that we practice reproducibility here in the Drake Lab.

Check out this helpful manual for more information. What resource do we want to link?

Here's a good cheat sheet as well.

Other text editing software

Because research is collaborative now, it is best to use a text editing software that allows you collaborate with others, incorporate edits, and track changes.

	Pros	Cons
Google docs	version control, easy editing, accessible anywhere, not OS specific	must convert to other format(.doc, .tex) for journal submission
LateX/Overleaf	easy citation formatting and control, precise formatting, Overleaf allows online collaboration	not everyone knows LaTex, steep learning curve
Word (and other word processors)	WYSIWYG, more widely used, allows edits via track changes	doesn't work across OS, formatting can be a pain

Bibliographies and Reference Managers

• Zotero
• Mendeley
• Paperpile: For use with Google products, (3$/month as of Sept. 2018)

Existing Content Resources

• John's Fifteen Steps to writing a manuscript
• LaTeX cover letter template: zipped folder of everything you need
• CARS method of introductions
• Searchable phase book that might be useful when trying to structure information beyond comparisons. http://www.phrasebank.manchester.ac.uk/
• Writing tips from Pulitzer prizewinner Cormac McCarthy