README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include=FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# Website for Digital Agriculture (Dier & Data) at Utrecht University

<https://bovi-analytics.github.io/DigitalAgriculture/>

[Miel Hostens](https://www.bovi-analytics.com/) • Faculty of Veterinary Medicine • Utrecht University

## After updating R

[Source](https://inbo.github.io/tutorials/tutorials/r_renv_update/)

``` r
renv::upgrade() # upgrades renv, if new version is available 
renv::hydrate(update = "all") 
renv::snapshot() # inspect the message before confirming to overwrite renv.lock
```

## How to build the site

1.  Install [RStudio](https://www.rstudio.com/products/rstudio/download/#download) version 2022.07.1 or later since it has a [Quarto](https://quarto.org/) installation embedded in it. Otherwise, download and install [Quarto](https://quarto.org/) separately.
2.  Open `bovi-analytics.Rproj` to open an [RStudio Project](https://r4ds.had.co.nz/workflow-projects.html).
3.  If it's not installed already, R *should* try to install the [{renv} package](https://rstudio.github.io/renv/) when you open the RStudio Project for the first time. If you don't see a message about package installation, install it yourself by running `install.packages("renv")` in the R console.
4.  Run `renv::restore()` in the R console to install all the required packages for this project.
5.  `r emoji::emoji("tada")` All done! `r emoji::emoji("tada")` The complete website will be in a folder named `_site/`.

```{bash}
quarto publish gh-pages --no-browser --no-prompt	
```

The pipeline does major tasks:

-   **Build Quarto website**: This project is a [Quarto website](https://quarto.org/docs/websites/), which compiles and stitches together all the `.qmd` files in this project based on the settings in [`_quarto.yml`](_quarto.yml). See the [Quarto website documentation](https://quarto.org/docs/websites/) for more details.

-   **Upload resulting `_site/` folder to github pages**: This project is published using github pages using the `quarto publish gh-pages --no-browser` command

## Licenses

**Text and figures:** All prose and images are licensed under Creative Commons ([CC-BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/))

**Code:** All code is licensed under the [MIT License](LICENSE.md).

## Issues

If ' 'gh-pages' is already checked out' error occurs -\> remove any folder in the .git/worktree folder

## Attribution

Much of the content is based on [Digital Agriculture](https://bovi-analytics.github.io/DigitalAgriculture/) by Dr. Miel Hostens.

<a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/"><img src="https://i.creativecommons.org/l/by-nc/4.0/88x31.png" alt="Creative Commons License" style="border-width:0"/></a><br />This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/">Creative Commons Attribution-NonCommercial 4.0 International License</a>