My Writing Workflow

markdown, pandoc, and more!

1. I use Mendeley to organize and annotate PDF files of academic articles.
2. Mendeley can automatically generate .bib files that contain citation info of all or part of your Mendeley library.
3. .csl files specify what citation style (e.g., APA) the references will be formatted in. It can be extracted from Mendeley or easily obtained from the internet.
4. Scrivener is a writing program I use for organizing my writing projects. It's good for making outline, moving things around, focusing on selective parts of a manuscript, taking notes, gathering research materials, exporting to various file formats etc.
   • Note: Scrivener is a paid software. There is an open-source alternative that I heard of, called Manuskript. I have not personally tried it, but it seems cool.
5. I usually write in Scrivener and export the text as .md, so that version control can be done easily with git and github.
6. .md text can be converted to APA-formatted documents via pandoc along with appropriate specifications, including a .bib file, a .csl file (in APA style), and a APA-formatted template (in my case, a .docx).
7. Alternatively, to more easily include analyses and results in the manuscript, one can write in .Rmd to incorporate R code and outputs, and use papaja (an R package based on pandoc; recommended to use in R Studio) to convert the .Rmd into even more sophisticated version of APA documents then the previously mentioned regular pandoc approach.

In this repository

• You will find examples of converting markdown (.md) or Rmarkdown (.Rmd) files into APA-formatted, publication-ready documents (e.g., .docx, .pdf, .tex), using pandoc or papaja.

• Specific instructions can be found in example_pandoc.md and example_papaja.Rmd

• APA_template.docx is modified from the template provided by papaja

• APA_ML.csl is modified from the apa.csl obtained from Zotero, such that in press articles can be correctly cited with Mendeley.

  • Enter in press in the Short title field in Mendeley, which is equivalent to the shorttitle variable in .bib files
  • Note: If references are not managed via Mendeley, the regular apa.csl can be used with the status variable specified as in press for a given entry in .bib files

• See example.bib for ways to specify different types of manuscripts, including:

  • published journal articles
  • published books
  • published book chapters
  • in press manuscripts
  • manuscripts submitted for publication
  • unpublished manuscripts
  • master's theses or doctoral dissertations

Useful links

reference management

• Mendeley: https://www.mendeley.com/
• BibTeX (.bib): http://www.bibtex.org
• Citation Style Library (.csl): http://citationstyles.org/

text editing

• interface
  • Scrivener: https://www.literatureandlatte.com/scrivener/overview
  • Manuskript: http://www.theologeek.ch/manuskript/
  • vim: https://www.vim.org/
  • vimwiki: https://github.com/vimwiki/vimwiki
  • MacDown: https://macdown.uranusjr.com/
  • R Studio: https://www.rstudio.com/
• filetypes
  • Markdown (.md): https://www.markdownguide.org/
  • Rmarkdown (.Rmd): https://rmarkdown.rstudio.com/

file conversion / formatting

• pandoc: https://pandoc.org/
• scrivomatic: https://github.com/iandol/scrivomatic
• R Studio
  • papaja: https://github.com/crsh/papaja
  • bookdown: https://bookdown.org/yihui/bookdown/

version control

• git: https://git-scm.com/
• github: https://github.com/
• hub: https://github.com/github/hub
• tig: https://github.com/jonas/tig