---
output: github_document
---

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

# Website for Dairy Health Management at Utrecht University

## 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.  Make sure to have R tools installed.
3.  Open `bovi-analytics.Rproj` to open an [RStudio Project](https://r4ds.had.co.nz/workflow-projects.html).
4.  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.
5.  I had to run `renv::equip()` first to install some tools
6.  Then renv::activate() -\> re
7.  Make sure you update the lock file to the correct r version
8.  Run `renv::restore()` in the R console to install all the required packages for this project.
9.  `r emoji::emoji("tada")` All done! `r emoji::emoji("tada")` The complete website will be in a folder named `_site/`.

## How to activate git 'again'

## How to build the website

```{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 [Dairy Health Management](https://bovi-analytics.github.io/DairyHealthManagement/) by Dr. Miel Hostens and Dr. David Speksnijder.

`<a rel="license" href="http://creativecommons.org/licenses/by-nc/4.0/"`{=html}![Creative Commons License](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/"`{=html}Creative Commons Attribution-NonCommercial 4.0 International License</a>