7  Copyeditor workflow

Your article folder should contain a copyediting checklist and a revision tracker. Use the checklist on your first round of copyediting the article. Use the revision tracker to keep track of unfinished tasks and communications with the author (changes that you need to notify the author of, questions you need to ask them, record of their answers).

For instance, use a subfolder history and put in it files checklist.md for the checklist and r1.md, r2.md for revision rounds.

Below are examples of checklist and revision document for you to copy/paste.

7.1 Copyediting workflow

  1. Pre-conversion changes (optional). Fix the author’s MS Word or LaTeX document for better conversion results. In MS Word: use headings styles, metadata sections, and optionally use equations for formulas and special symbols. In LaTeX: usually nothing is needed, but sometimes unnecessary LaTeX commands and packages need to be removed (e.g., framed boxes).
  2. Convert to markdown.
  3. Metadata. Fill in the metadata.
  4. Section headings. Check that section headings are encoded, given them identifiers for crossreferences (optional).
  5. Format elements. Apply markdown formatting to blockquotes, lists, statements, formulas, etc.
  6. Cross-references. Encode cross-references within the document (to section headings, footnotes, statements etc.).
  7. Citations. Encode citations in Markdown. If using Zotero: create a (sub)collection for the paper, look up the citations online and add them to the collection using Zotero’s browser plugin. Export the collection as a BibTeX file (.bib) in your article folder. Insert the citations in the document, ideally using a Zotero-markdown plugin for your editor (e.g. Citation Picker for Zotero in VS code).
  8. Add a # References heading at the end of the document.
  9. Render the output and proofread.
  10. Go through the checklist.

7.2 The checklist

## Importing and Preparing the Original Document, Setting up Workspace

- [ ] Create working folder. If using Rstudio, create a project.
- [ ] Copy original manuscript in the folder (`original` subfolder).
- [ ] Prepare manuscript for conversion (headings styles, footnotes, formulas), so that pandoc recognizes most of the things. 
- [ ] Convert to markdown with `pandoc -s <originalfile> -o <outputfile.md>`. 
- [ ] Create revison tracker files: create `history` folder, create a file `r1.md` in it and copy this checklist into it.

## Formatting

- [ ] Complete metadata block: title, author, affiliation, abstract, thanks, bibliography, nocite (if needed).
- [ ] Sections: are they formatted correctly at all levels?
- [ ] Footnotes: are they formatted correctly?
- [ ] Quotations: are they formatted correctly? (as blocks when needed, etc.)
- [ ] Quotation marks: check that quotation marks are coherently used: single or double; punctuation inside/outside.
- [ ] Quotes vs. italics: is their usage for emphasis/highlights as per Chicago Manual (scare-quotes vs. so-called vs. key terms, etc.)?
- [ ] Dashes: is the usage as hyphens, en-, em-dashes correct?
- [ ] Bold: avoid bold unless absolutely needed.
- [ ] Statements: check that claims, examples, theorems etc. are formatted
    as statements. Arguments with labelled premises are custom-labelled
    lists. Block equations are display maths. Use identifiers if statements or list items are crossreferenced.
- [ ] Math content: check that math content (incl. schematic letters like $A$) is coded as inline or display formulas.
- [ ] Special symbols: are they special symbols? Encode them as such (HTMLentities, copy/paste) rather than LaTeX unless absolutely necessary.

## Proofreading

- [ ] Fix minor typos and grammatical mistakes. No need to notify the author.
- [ ] Ungrammatical, poor English, otherwise flawed sentences (e.g. we can't tell what a pronoun refers to): correct or ask the author to correct. If you correct, include in a list of changes notified to the author.
- [x] No need to advise on the content (poor structure or presentation, redudant point, obscure ideas, etc.). This was the referee's job.
- [ ] One final pass with spell & grammar checker

## Crossreferences and Citations

- [ ] Crossreferences: check that you have identified the crossreferences in the text and added labels wherever needed (references to sections, footnotes, claims, premises, arguments, etc.)
- [ ] Create a `.bib` file from the author’s bibliography
- [ ] Identify all the references in the text and replace them with keys from your .bib file. 
- [ ] Use normal vs inline citations where appropriate? Use year-only sparingly. Use multiple inline citations (`@doe [@smith;@jones]`) and normal citations with long prefixes and suffixes (`[this is also discussed in @doe and other places]`) where appropriate. Treat borderline cases consistently across the paper (e.g., whether to use year-only or normal when the author is already named in the sentence).  
- [ ] Is the author’s bibliography correct? (wrong title, wrong year of publication, etc.)
- [ ] Add "References" heading at the end of the document.

## Rendering in output formats

- [ ] Special symbols: do they render correctly in all outputs?
- [ ] First-line indentation: paragraphs that *continue* after a block
    quote, table or list should not have an indentation. Add `\noident`
    codes where needed.
- [ ] Math and LaTeX: check that it renders correctly in HTML output. Use *Imagify* if needed.
- [ ] Tables: are the tables a faithful rendering of the original tables by the author?
- [ ] Figures: do they render correctly in all outputs?
- [ ] Bibliography: does it looks good? do the citation links work?

## Send to the author

- [ ] Compile list of questions and notifications for the author.
- [ ] Have a last look at the paper.
- [ ] Send to the author for revisions and/or approval.

7.3 The Revision Tracker

Here’s an example of revision-tracking file. We use a new one for each back-and-forth with the author.

## TO DO 

- things you still have to do
- item 

## TO ASK

- things to ask about or notify the author

## IGNORE

- things you've considered but decided against
- including author requests

## GET HELP

- things you need to ask editors 
- or the template editor about