ms_template

An example repository for automated rendering of scientific manuscripts in pdf and Microsoft Word format for submission to journals.

Rendering manuscripts

To render the manuscript, run render.R in the code folder: Rscript code/render.R.

Rendered output will show up in the results folder in pdf and docx format.

Adjusting styles

Adjust the csl (bibliography style), docx (MS Word format such as line spacing, fonts, etc), and sty (misc. latex formatting) files in the ms folder as needed to produce rendered manuscripts with appropriate styling for your journal of choice without the need to edit the Rmd file (hardly). The example style is set to New Phytologist.

For details, see the Rmd file and the rendered output of this example. Also, this blog post.

Dependencies

Basically, R, various R packages, pandoc, and latex. But see below.

Running with Docker

Rather than specify all the various dependencies needed in detail, I recommend using this Docker image from the Rocker project.

To use it, first install Docker and clone this repository.

Navigate to the cloned repository (where /path/to/repo is the path on your machine), and launch the container:

cd /path/to/repo
docker-compose up -d

Enter the container:

docker exec -it ms_template_rmd_1 bash

Inside the container, install the here package, then run render.R:

Rscript -e 'install.packages("here")'
Rscript code/render.R

When it's finished, exit the container and take it down:

exit
docker-compose down