Bookdown contest submission: a template for Copernicus academic journals

bookdown
bookdown-contest

#1

This is a submission to the 1st bookdown contest. (The link to the announcement should be here. But as a new user of RStudio community, I am only allowed to use 2 links in one post...)

Highlights

  • Write academic papers of Copernicus journals with R markdown syntax.
  • Support ~ 40 Copernicus journals.
  • Support both the two-columned pdf version and the discussion version.
  • Create multiple file formats, including .pdf, single .html, gitbook, .md, .epub, docx.

Introduction

Copernicus Publications is a publisher of scientific literature which publishes around 40 peer-reviewed open access scientific journals and other publications on behalf of the European Geosciences Union (EGU). Many years ago, one of my manuscripts was submitted to the academic Biogeosciences (BG). I wrote it with LaTeX. BG is one of the top journals in my research area. I believe I will submit to BG again in the future and I would not use LaTeX again. Therefore I created the bookdown template for Copernicus.

The bookdown-copernicus template was firstly included in the bookdownplus package in 2017. It used to be named as 'article' and 'discussion'. For the 1st bookdown contest I merged them into one and improved the structure of the files for easier use.

An Example with Its Repo

Repo: https://github.com/pzhaonet/bookdown-copernicus

Copernicus journal papers are open-access. A submitted manuscript, if accepted, is firstly published online as a discussion version, the layout of which is easy for computer monitors. Here is my example:

After successful discussions, the manuscript is published in a two-column printed version:

As a new user of the RStudio community, I am only allowed to insert one image in a post. More images could be found in the repo mentioned above.

Users can easily specify the layout in the yaml of the bookdown-copernicus template.

Users can view mdpi.docx, mdpi.epub, mdpi.html, mdpi.pdf, and mdpi.tex as well.

Technical details

Copernicus provides a LaTeX template which is free for using. I modified it as 'tex/template_article.tex', i.e. something was moved from the original LaTeX template to the yaml of 'index.Rmd'. Users could simply compare them and then get an idea how to convert a LaTeX template into a bookdown template.

Re-use

  • Download the GitHub Repo.
  • Revise 'index.Rmd' and 'body.Rmd' as your own manuscript.
  • Build the book with R bookdown.

Any suggestions are welcome. Just PR the repo!


#2

Well, that's amazing. I wish that, considering that R is so strong in many academic fields, main publishers (Wiley, Nature-Springer etc) should put a bit of effort on making these kind of templates available. It would save a lot of time and efforts both to us us, as academics, and to them, as publishers....

I have not gone thougly to your template, as I do not use copernicus in my area of research, but the only suggestion I can do, is that, it you have not already did, write copernicus and show them the template

Cheers
Fer


#3

Thanks for your suggestion. It would be great if the journal can accept a bookdown template. However, I am a little worried about how many people would like to use it. There seem not many bookdown users in academia. I am the only one among the people Iiving around me.

I do not think it is time to show the template to the journal. We need a large user group who has the demand for bookdown. If I were the journal, I would insist on LaTeX submission, as bookdown creates LaTeX files.


#4

Interesting work! I have not used bookdown much, but have done something similar for the rticles package: https://github.com/rstudio/rticles/pull/172 Great effort, hope your template will find many users and increase uptake for reproducible documents in geosciences.


#5

Wow, you did a great job! I should not have created the bookdown template for Copernicus (and MDPI, Elsevier) if I had known that they are already available in rticle!