An org mode template for submissions to Peer Community In journals

This repository provides a minimal org mode template for writing scientific articles, with a convenient formatting for each journal from Peer community in.

You’ll find in this repository one directory for each journal. To use the template matching your disciplinary field, simply download the corresponding folder and work directly in this folder, by writing your main text in the file main.org. The output after a C-c C-e l o on the file main.org should correspond to the file main.pdf, provided here as a reference.

Additional instructions are available in each specific folder.

Disclaimer

• All the files from this repo (except the main.* files) are taken from PCI official website. I do not provide any support for those files, in particular for their LaTeX template, preambule_*.tex. The org template only tries to offer a convenient org mode adaptation to their LaTeX file.
• Each preambule_*.tex file (which has been created by the PCI team, and is available on their website) has been slightly modified to allow an easier org export.

org-ref

This org mode template supposes that you are using org-ref to handle your bibliography. To install and use org-ref, simply add the following lines to your .emacs (latexmk must be installed on your computer):

(use-package org-ref
  :ensure t
  :after org
  :init
  (setq org-latex-pdf-process (list "latexmk -shell-escape -bibtex -f -pdf %f")))

If you do not wish to use org-ref, simply remove the related parts in the org template.

:ignore: tag

The :ignore: tag used for some org headlines is provided by the package ox-extra. If you want to use it, you’ll have to download this file in a folder that can be found by Emacs (i.e., a folder which is in its load-path), and to add the following lines in your .emacs:

(require 'ox-extra)
(ox-extras-activate '(ignore-headlines))

Useful resources

Writing a reproducible paper with org mode is incredibly convenient and pleasant; however, it may be challenging for beginners. If you are not really familiar with org-mode, the following resources may be useful:

• Using Emacs, Org-mode and R for Research Writing, a great tutorial by Vikas Rawal
• Literate programming with Org mode, a blog post by Greg J. Stein
• A (non exhasutive!) list of scientific papers prepared with org mode