Computo template for R users

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.

⚠️ All important information about writing and preparing an article to be submitted to Computo, and related technicalities are detailed in the template manuscript. ⚠️

More information about submission and guidelines for authors can be found on the dedicated page.

Process overview

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

• the source files of the notebook (a quarto .qmd file + a BibTeX .bib file + some statics files, e.g. figures or small .csv data tables)
• configuration files to set up the dependencies in a virtual environment
• configuration files to set up the continuous integration rendering the final documents

In this template, we focus on R users and detail a solution based on

• The knitr kernel of Quarto for rendering the document,
• The renv package for setting the virtual environment,
• Github actions for handling the continuous integration.

Step-by-step procedure

Step 0: setup a git repository

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.

Step 1. setup Quarto and Computo extension on your system

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

Step 2. write your contribution

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

Step 3: setup dependencies with 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.

Step 4: proof reproducibility

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

1. Check out repository on the ubuntu-latest machine
2. Install quarto and dependencies, including the Computo extension for Quarto
3. Install R and dependencies with renv, using your renv.lock file
4. Render your .qmd file and Publish the results on a gh-page (both HTML and PDF)

Note: Gitlab CI can be used to obtained similar results.

Step 5. submit

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.