5  Preparing a manuscript

Steps to prepare a manuscript for copyediting.

5.1 Create a working folder for your article

If you don’t have a dedicated working folder for your article, create one.

If you’re going to use RStudio, create a project for the article with File > New Project…. Use ‘Existing directory’ if your project already has a folder, otherwise “Create project in a new directory” to create one.

5.2 Place original materials in a preserved folder

A submission comes with a manuscript file and possibly others: bibliography, PDF version, figures, etc. It’s handy to have those in your working folder for the article, but you want to keep them safe. Place them either in a subfolder called original or history. (The history folder will then be used to keep track of your exchanges with the author.)

5.3 Convert to markdown

Two options: conversion box (RStudio) or with Pandoc. The first is easy if you’re not familiar with the terminal and allows you to do a bunch of manuscripts at once. The second is faster for a single manuscript once you’ve learnt how to do it.

5.3.1 With the conversion box and RStudio

Requires RStudio and a conversion-box folder at the root of journal’s working folder.

  1. Delete any manuscript already present in the conversion-box folder: Word files (.docx, .doc), LaTeX files (.tex), markdown or quarto files (.md, .qmd). This is a temporary folder, whomever left it there has made copies.
  2. Copy your original manuscript (MS Word, LaTeX) in the conversion-box folder. You can copy several if you want to convert multiple manuscripts in one go.
  3. Rename the manuscript file(s) if necessary: manuscript filenames must not contain spaces, colons, question or exclamation marks.
  4. Open conversion-box.Rproj in the conversion-box folder. This opens RStudio in the ‘conversion box’ project.
  5. In RStudio, do Build > Build All, or equivalently hit Shift-Ctrl-B (Win. Linux) or Shift-Cmd-B (Mac). This converts any MS Word or LaTeX file in the folder to markdown.
  6. Copy the resulting markdown file from the conversion-box to your article’s working folder.

5.3.2 With Pandoc only

Open a terminal. If using RStudio or VSCode, there is a Terminal tab. This opens a terminal already located in your article’s working folder. If you’re opening a terminal from your system, you need to navigate (using cd, change directory commands) to your article working folder.

If you need help with using the terminal see section Appendix A.

Run the following command:

pandoc -s original/manuscript.docx -o manuscript.md
  • original/manuscript.docx is the path and filename of the original manuscript. Here I’m assuming that the submission is called manuscript.docx and placed in a folder original. On Windows we use backlash to mark folders so that would be original\mansucript.docx instead.
  • -o manuscript.md tells pandoc to convert to markdown (.md) and save the result as manuscript.md in your cuurent folder.
  • -s, short for --standalone, tells Pandoc to produce a “standalone” document, i.e. include a header with any metadata it is able to extract from the source.

For instance, if your terminal was not located in your article working folder but in its original subfolder, and you wanted to write the result in the main sufolder (i.e. one folder up), you’d use instead:

pandoc -s mansucript.docx -o ../manuscript.md

Where ../ (..\ on Windows) means “one folder up”.

5.3.2.1 LaTeX manuscripts: check the bibliography field

Converting from LaTeX is the same, but pay attention to the bibliography file location. The resulting markdown file may have a bibliography key:

bibliography: original/references.bib

bibliography: C:/Windows/Users/Zotero/references.bib

Update these if needed. Here original is the subfolder for preserving the original: I should instead copy the .bib file to the main article folder and replace this key with bibliography: references.bib. The second one, C:/Windows... is a location in the author’s computer as it was cited in their LaTeX file, it should be removed.

5.3.2.2 More options for Pandoc conversion

See Pandoc’s Manual: reader options for more options.