An example repository for automated rendering of scientific manuscripts in pdf
and Microsoft Word format for submission to journals.
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.
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.
Basically, R, various R packages, pandoc, and latex. But see below.
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