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!


#6

It is common to see duplicated effort in open source, which is fine. Indeed rticles has included many journal templates, and we definitely wish more users can contribute more templates to the package, or improve the existing templates! Thanks!


#7

I learnt rmarkdown first, and then bookdown. Somehow I missed and skipped rticles, which should not have happened...