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index.qmd
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# Welcome! {.unnumbered}
```{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:
- 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 course is designed to address these issues through code-along
sessions (instructor and learners coding together), reading activities,
discussion activities, and exercises using a real-world dataset. This
website contains all the course materials, from reading content to
exercises. It is structured like a book, with "chapters" serving as
lessons presented in order of appearance. We make extensive use of the
website throughout the course, with code-along sessions closely
following the website material (with slight modifications for time
constraints or more detailed explanations).
The course material was created using [Quarto](https://quarto.org/) to
write the lessons 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 create and host the website. The
original source material for this course is found on the
[`r-cubed-advanced`](https://github.com/rostools/r-cubed-advanced)
GitHub repository.
Want to contribute to this course? Check out the
[README](https://github.com/rostools/r-cubed-advanced/blob/main/README.md)
file as well as the
[CONTRIBUTING](https://github.com/rostools/r-cubed-advanced/blob/main/CONTRIBUTING.md)
file on the GitHub repository for more details. The main way to
contribute is by using [GitHub](https://github.com/) and creating a [new
Issue](https://github.com/rostools/r-cubed-advanced/issues/new) to make
comments and give feedback for the material.
## Re-use and licensing {#licensing}
<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img src="https://i.creativecommons.org/l/by/4.0/80x15.png" alt="Creative Commons License" style="border-width:0"/></a>
The course is licensed under the [Creative Commons Attribution 4.0
International License](https://creativecommons.org/licenses/by/4.0/) so
the material can be used, re-used, and modified, as long as there is
attribution to this source.
## 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 course. 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 lead
instructor and curriculum developer.
::: {layout-ncol=2}
{width="120px" alt="Logo for Steno Diabetes Center Aarhus"}
{width="300px" alt="Logo for Danish Diabetes and Endocrinology Academy"}
:::