My Writing Workflow

In this post, I outline my workflow for writing up reports, working papers, and manuscripts for journal submission.

My writing workflow

Following on from my previous post about my data workflow, I outline my basic writing workflow here. As mentioned in the previous post, I use Scapple as a tool to organise my thoughts, brainstorm, and plan my work, including basic outline for my write-up (background on the figure above).1

I start my initial drafts, particularly methods and results sections within RStudio, as it is where I do my data analysis and visualisation and it is simply easier to write about methods and results while they are being worked on. However, for most of my original writing, I use Scrivener, with Bookends as my reference manager. I can easily export Markdown written within RStudio in a format like RTF for Scrivener. Scrivener is one of the very best applications available for academic writing, possibly for any kind of writing, as it allows you to organise your writings in small segments, set targets (word count) and track the progress easily, as well as collate and organise research materials, such as relevant papers, snippets or any other kinds of materials. While I use my Mac for most of my writing, Scrivener is also available for Windows, I often work on Scrivener in Windows, especially in office where I have to use Windows PC. I normally use Dropbox to store my Scrivener projects so I can pick up from where I left off on any of my PCs, including on my iPad with Scrivener app. On the Mac Bookends works very well with Scrivener as a reference manager; however, if you are working on a Windows PC, you can easily use Endnote or Mendeley for reference management, and to insert citation into your write-up (as citation codes that can later be automatically scanned by reference manager like Endnote to create formatted bibliography).

Once I have a full draft of the paper/report, I export them from Scrivener to a specialised word processing application. If I am working alone on the project - and do not need others to edit the text, I often work on Mellel in my Mac. Mellel is one of the best and most stable word processing application on MacOS, especially when you are writing a long text document, such as a thesis; and it works perfectly with Bookends for reference management. For example, I finalised my PhD dissertation on Mellel with Bookends for reference management. When I needed my thesis chapters to be commented on, I sent them as RTF to my supervisors so they could comment on it using MS Word. But if you do not need others to directly edit the document, Mellel can export document as PDF directly from the main menu.

When I am working on a co-authored paper, I move from Scrivener to MS Word when I have to have other authors working on the paper as well, as everybody I work with uses Word and are comfortable working on it (I don’t know any of my co-authors who use Mellel for example). I have on occasions used Google Docs when I’ve wanted inputs from more than one co-authors at the same time, and also to make the versioning easier, however, being online-only makes Google Docs hard to use, especially when your collaborators are travelling or are in places with poor internet connection. Hence MS Word is usually the go-to application when working on a co-authored paper. In terms of reference manager, there are a number of options that work well with Word. Bookends works with Word as well on a Mac, but as it is not available on Windows OS, I either use Endnote or Mendeley for organising references and citation when working on co-authored papers.

Once the papers are finalised on Word (or Mellel), I convert them to PDF for submission to journals or for wider circulation if they are research reports or working papers.

  1. A note on the use of proprietary/for-cost applications, and availability of free/open-source alternatives. While I do like to use free and open-source applications as much as is possible, they also have to have the necessary features that you are after. Sometimes, you just want an application that works out-of-the-box without having to do much tweaking. For these reasons, I do have quite a few for-cost applications in my workflow; however, some of these applications do have potential free/open-source alternatives. While there are some free/open-source mind-mapping tools, I haven’t found one that is as easy to use and flexible as Scapple and that works seamlessly in both Mac and Windows. RStudio comes in free, open-source edition. For the main writing environment, again I don’t know of any free/open-source alternative to Scrivener with similar set of features. Scapple and Scrivener both have slightly cheaper Education licence. For reference management, Mendeley is free but requires an online account (free), and there are other similar free alternatives like Endnote basic or zotero. For final writing, free and open-source LibreOffice is more or less a complete replacement for MS Office suite, and its Writer can be used instead of MS Word

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