Documentation and sample of a simple R
-based submission for the Computo journal, using our Quarto-based template and renv
for handling dependencies.
It shows how to automatically setup and build the HTML and PDF outputs, ready to submit to our peer-review platform.
:warning: All important information about writing and preparing an article to be submitted to Computo, and related technicalities are detailed in the template manuscript. :warning:
More information about submission and guidelines for authors can be found on the dedicated page.
Submissions to Computo require both scientific content (typically equations, codes and figures, data) and a proof that this content is reproducible. This is achieved by means of i) a notebook system, ii) a virtual environment fixing the dependencies and iii) continuous integration (plus, if needed, an external website to store large data files such a Zenodo or OSF ).
A Computo submission is thus a git(hub) repository like this one containing
.qmd
file + a BibTeX .bib
file + some statics files, e.g. figures or small .csv
data tables)In this template, we focus on R
users and detail a solution based on
knitr
kernel of Quarto for rendering the document,renv
package for setting the virtual environment,Use this repository as a template via the "use this template" button on the top of this page.
Note: You can use Gitlab for submitting for Computo. We hope giving more support in the future.
You need quarto installed on your computer, as well as the Computo extension to prepare your document. The latter can be installed as follows:
quarto add computorg/computo-quarto-extension
Write your notebook as usual, as demonstrated in the template-computo-R.qmd
sample.
Note: Make sure that you are able to build your manuscript as a standard notebook on your system before proceeding to the next step.
To build your document (both in PDF and HTML by default), you can run the command quarto render
, e.g. for the template:
quarto render template-computo-R.qmd # will render both to html and PDF
renv
Use the renv
package manager to setup a reproducible environment handling your R
dependencies.
See this page for more details about R
dependency setup.
Put everything together and check that your work is indeed reproducible. To this end, you need to rely on a github action, whose default is pre-configured and found here: .github/workflows/build.yml
This action will
renv
, using your renv.lock
fileNote: Gitlab CI can be used to obtained similar results.
Once step 4 is successful, you should end up with an HTML version published as a gh-page, as well as a PDF version (see "Other format" at the end of the table of content of the rendered HTML). This PDF version can be submitted to the OpenReview platform.