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# Repository for the Reproducible Manuscripts Quarto Workshop
# Code Publishing Tutorial

This repository is for day 2 of the self-paced Reproducible Manuscripts Quarto Workshop.
The repository is structured as follows:
This repository contains a tutorial on code publishing created for the LMU Open Science Center.
It can be viewed online at <https://lmu-osc.github.io/code-publishing/>.

1. The folder "01_Example" contains a **minimal reproducible example** with a Quarto manuscript using the Palmer Penguins data set. All necessary files are there, including the .qmd-file, the data in .csv format, a .bib-file with references, and a citation style csl.-file.
2. The folder "02_Practise" contains the data in .csv format, a .bib-file with references, a .cls-file for *apaquarto*, and a citation style .csl-file. These are necessary components to **recreate the minimal reproducible example as a practise**, and would have to be copy-pasted anyway. Other files, like the .RProj-, renv-, and .qmd-files will be created by the participants during the practise in this folder.
3. The folder "03_Supplement" contains a **checklist** that participants can use to go over their project at the end and see which reproducibility measures they were able to implement and how to take it one step further.
4. The file "Instructions.qmd" contains the detailed instructions for day 2, i.e. how to execute the example, recreate it, apply the techniques to own data, and use the checklist, step-by-step.
The tutorial pages are contained in the `*.qmd` files in the root folder.
All images are contained in the folder `images`.

If you encounter any issues during the workshop that you cannot resolve through a quick Google search, please approach the workshop instructors.
## Previewing and rendering the tutorial

The tutorial is written in Markdown and uses [Quarto][quarto] to render it as a website.
To render the tutorial on your own computer, you need to have Quarto installed.

[quarto]: (https://quarto.org/)

Further, the R package [`renv`][renv] is used to track the project's dependencies

[renv]: https://cran.r-project.org/package=renv

One can install `renv` by running the following:

```r
install.packages("renv")
```

Then, one can restore the dependencies tracked with `renv` by running the following:

```r
renv::restore()
```

While you are working on the tutorial, you can preview it by running:

```sh
quarto preview
```

This will open the tutorial in your browser.
If you make any changes, the website will automatically reload.

If you are done editing and would like to render the tutorial to a static website,
run the following:

```sh
quarto render
```

## Contributing

If you are contributing to this tutorial,
please read the [contributing notes](CONTRIBUTING.md) before.

## License

Except where noted otherwise, the narrative text in this tutorial is licensed under [CC BY-SA 4.0][cc-by-sa];
the code without any narrative text is also (at your option) available under [CC0 1.0][cc0].

[cc-by-sa]: https://creativecommons.org/licenses/by-sa/4.0/
[cc0]: https://creativecommons.org/publicdomain/zero/1.0/

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