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https://github.com/jchiquet/wildfires_inla

Submission paper for Computo: INLA and wildfires over Aquitaine region
https://github.com/jchiquet/wildfires_inla

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Submission paper for Computo: INLA and wildfires over Aquitaine region

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README 

        

# Computo template for R users



[![build and publish](https://github.com/computorg/template-computo-R/actions/workflows/build.yml/badge.svg)](https://github.com/computorg/template-computo-R/actions/workflows/build.yml)



Documentation and sample of a simple `R`-based submission for the [Computo journal](https://computorg.github.io), 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](https://computo.sfds.asso.fr/template-computo-R). :warning:



More information about submission and **guidelines for authors** can be found on the [dedicated page](https://computo.sfds.asso.fr/submit/).



## Process overview



Submissions to [Computo](https://computorg.github.io) 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](https://zenodo.org/) or [OSF](https://osf.io/) ). 



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](https://quarto.org/) installed on your computer, as well as the [Computo extension](https://github.com/computorg/computo-quarto-extension) to prepare your document. 

The latter can be installed as follows:



```.bash

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](https://computorg.github.io/template-computo-R/).



**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:



```.bash

quarto render template-computo-R.qmd # will render both to html and PDF

```



### Step 3: setup dependencies with `renv`



Use the [`renv` package manager](https://rstudio.github.io/renv/articles/renv.html) to setup a reproducible environment handling your `R` dependencies.



See [this page](https://computo.sfds.asso.fr/template-computo-R/#handle-r-dependencies-with-renv) 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](https://github.com/computorg/template-computo-R/blob/main/.github/workflows/build_n_publish.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](https://openreview.net/group?id=Computo).