index.qmd

# Welcome! {.unnumbered}

{{< include /includes/_badges.qmd >}}

```{r write-packages-to-bib}
#| include: false
# automatically create a bib database for R packages
knitr::write_bib(
  unique(desc::desc_get_deps()$package[-1]),
  here::here("includes/packages.bib")
)
```

Reproducibility and open scientific practices are increasingly in demand
and needed by scientists and researchers in modern research
environments. More frequently, our work, as researchers, includes a high
level of collaboration on scientific projects. Consequently, many new
challenges arise that we lack the training or knowledge to resolve.

These challenges include:

-   Designing and structuring code for an analysis that follows some
    basic principles that make it easier to write, to do more with less
    code, and to collaborate on;
-   Establishing common coding styles and standards to make it easier to
    read or review each other's code;
-   Documenting the software dependencies of a project to synchronize
    computing environments among collaborators and potentially with
    servers;
-   Documenting (and automating) the steps taken to process, analyze,
    and present data and findings in a way that allows collaborators to
    regenerate the most recent results.

Training and awareness of the skills and knowledge necessary to create
reproducible and transparent data analysis pipelines are still
significantly lacking among researchers. Partly due to this gap, how
*exactly* an analysis is done (including data processing and wrangling)
to produce a given result are often poorly, if at all, described in
scientific studies. This can have a major impact on the reproducibility
and, ultimately, the reliability of studies.

This 3-day workshop is designed to address these issues by using
participatory live-typing or "code-alongs", where the teacher
demonstrates the tasks on their computer connected to a projector while
learners type along on their own computer. The workshop also includes
reading tasks, discussion activities, hands-on exercises using a
real-world dataset, and group work on a project to apply the skills
gained from the workshop.

This website contains all of the material for the workshop, including
readings, exercises, presentations, live-typing material, and images. It
is structured as a book, with "chapters" as sessions, in order of
appearance. We make heavy use of the website throughout the workshop
where "type-along" sessions almost identically follow the material on
the website (with slight modifications for time or more detailed
explanations).

Check out the overview section of the workshop, starting with the
[Syllabus](/overview/syllabus.qmd).

If you plan on attending the workshop, please make sure to complete the
[Pre-workshop tasks](/pre-workshop/overview.qmd) to get set up and ready
for the workshop. The pre-workshop tasks include a survey that you need
to fill out before the workshop starts.

{{< include /includes/_star-us.qmd >}}

## Target audiences

This website and its content are targeted to three groups:

1.  For the **learners** to use during the workshop, both to follow
    along and also to use as a reference after the workshop ends. A more
    detailed description of who the learner is can be found in [Is this
    for you?](/overview/is-this-for-you.qmd)
2.  For the **teachers** to use as a guide for when they do the
    type-along sessions.
3.  For those who are **interested in teaching**, who may not have much
    experience or may not know where to start, to use this website as a
    guide to running and teaching their own workshops.

## Re-use and licensing

The workshop material is licensed under the [Creative Commons
Attribution 4.0 License](LICENSE.md), so the material can be used,
re-used, and modified, as long as there is attribution to this source.
Check out the [For teachers](/appendix/for-teachers.qmd) section for
more details and tips on using this material for teaching.

## Contributing

Want to contribute to this workshop? Look through our
[CONTRIBUTING](CONTRIBUTING.md) page for contribution guidelines on how
to get started.

### Contributors

{{< include /includes/_contributors.qmd >}}

## How the website is made

The workshop material is created using [Quarto](https://quarto.org) to
write the material and create the book format,
[GitHub](https://github.com/) to host the [Git](https://git-scm.com/)
repository of the material, and [GitHub
Actions](https://github.com/features/actions) with
[Netlify](https://www.netlify.com/) to build and host the website. The
original source material for this workshop is found on the
[`{{< meta gh.repo >}}`](https://github.com/{{< meta gh.org >}}/{{< meta gh.repo >}})
GitHub repository.

## Acknowledgements

Illustration cover is by [Storyset](https://storyset.com/work).

The [Danish Diabetes and Endocrinology
Academy](https://www.ddeacademy.dk/) hosts, organizes, and sponsors this
workshop. A huge thanks to them for their involvement and support!
[Steno Diabetes Center Aarhus](https://www.stenoaarhus.dk/) and [Aarhus
University](https://au.dk) employs Luke Johnston, who is the developer
of this open educational resource and is (usually) the lead instructor
when running this workshop.

::: {layout-ncol="3"}
![](images/logo-sdca.png){width="100px"
alt="Logo for Steno Diabetes Center Aarhus"}

![](images/logo-ddea.png){width="260px"
alt="Logo for Danish Diabetes and Endocrinology Academy"}

![](images/logo-au.png){width="220px" alt="Logo for Aarhus University"}
:::