- I use Mendeley to organize and annotate PDF files of academic articles.
- Mendeley can automatically generate
.bibfiles that contain citation info of all or part of your Mendeley library. .cslfiles 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.- 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.
- I usually write in Scrivener and export the text as
.md, so that version control can be done easily withgitandgithub. .mdtext can be converted to APA-formatted documents viapandocalong with appropriate specifications, including a.bibfile, a.cslfile (in APA style), and a APA-formatted template (in my case, a.docx).- Alternatively, to more easily include analyses and results in the manuscript, one can write in
.Rmdto incorporateRcode and outputs, and usepapaja(anRpackage based onpandoc; recommended to use inR Studio) to convert the.Rmdinto even more sophisticated version of APA documents then the previously mentioned regularpandocapproach.
-
You will find examples of converting markdown (
.md) or Rmarkdown (.Rmd) files into APA-formatted, publication-ready documents (e.g.,.docx,.pdf,.tex), usingpandocorpapaja. -
Specific instructions can be found in
example_pandoc.mdandexample_papaja.Rmd -
APA_template.docxis modified from the template provided bypapaja -
APA_ML.cslis modified from theapa.cslobtained from Zotero, such that in press articles can be correctly cited with Mendeley.- Enter in press in the
Short titlefield in Mendeley, which is equivalent to theshorttitlevariable in.bibfiles - Note: If references are not managed via Mendeley, the regular
apa.cslcan be used with thestatusvariable specified as in press for a given entry in.bibfiles
- Enter in press in the
-
See
example.bibfor 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- unpublished manuscripts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
- Mendeley: https://www.mendeley.com/
- BibTeX (.bib): http://www.bibtex.org
- Citation Style Library (.csl): http://citationstyles.org/
- 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/
- pandoc: https://pandoc.org/
- scrivomatic: https://github.com/iandol/scrivomatic
- R Studio
- papaja: https://github.com/crsh/papaja
- bookdown: https://bookdown.org/yihui/bookdown/
- git: https://git-scm.com/
- github: https://github.com/
- hub: https://github.com/github/hub
- tig: https://github.com/jonas/tig