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# Intermediate workshop on Reproducible Research in R <img src="images/apple-touch-icon.png" align="right" height=100/>

[![License: CC BY 4.0](https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

## Description

Reproducibility and open scientific practices are increasingly being requested
or required of scientists and researchers, but training on these practices has 
not kept pace. This course intends to help bridge that gap and covers the
fundamentals and workflow of data analysis in R.

This repository contains the lesson, lecture, and assignment material for the
course, including the website source files and other associated course
administration files. 

For more detail on the course, check out the [syllabus](https://r-cubed-intermediate.rostools.org/syllabus).

## Instructional Design

The lectures and lessons in this course are designed to be presented primarily
with a participatory live-coding approach. This involves an instructor typing
and running code in [RStudio](https://www.rstudio.com/) in front of the class,
while the class follows along using their own computers. Challenges are
interspersed in the lesson material, allowing participants to collaboratively
work on smaller coding problems for a few minutes. All lesson materials are
provided ahead of time on the course website for participants to refer to during
lectures. Throughout the course, participants work in small groups to complete
the exercises together.

## Lesson content

The teaching material is found mainly in the main project folder:

- `00-syllabus.Rmd`: Contains the syllabus and the schedule files.
- Files starting with a number: 
Contains the code-along teaching material, as well as
associated links to the lecture slides. 

The website is generated from [bookdown], 
so follows the file and folder structure
conventions from that package.

[bookdown]: https://bookdown.org/yihui/bookdown/

## Installing necessary packages

Packages used and depended on for this course are included in the `DESCRIPTION`
file. To install the packages, run this function in the root directory (where
the `r-cubed-intermediate.Rproj` file is located:

```r
# install.packages("remotes")
remotes::install_deps()
```

## Contributing

If you are interested in contributing to the course material, please refer to
the [contributing guidelines](CONTRIBUTING.md). Please note that the
project is released with a [Contributor Code of
Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to
abide by its terms.

## Acknowledgements

Much of the lesson material was taken and modified from multiple sources (most
of which I've created, been involved in, or contributed to), including:

- [UofTCoders Reproducible Quantitative Methods for EEB](https://uoftcoders.github.io/rcourse/) 
(which I helped develop and is the inspiration and basis for this course)
- [Software and Data Carpentry](https://carpentries.org/) workshop material
- [UofTCoders material](https://uoftcoders.github.io/studyGroup/lessons/)
and [AU CRU material](https://au-cru.github.io/site/material/),
from the peer led and contributed lessons
- Some material from my [*"Reproducible Quantitative Methods: Data analysis workflow using R"*](https://v1--dda-rcourse.netlify.com/)