Appendix B — Tools Used to Make This Book

This appendix provides a comprehensive guide to replicating the environment and code used in this book. To get started, you’ll need to install the R programming language along with RStudio IDE. Additionally, we’ll walk through the steps for setting up a Quarto book project, integrating it with GitHub for version control, and ensuring reproducibility with the {renv} package. This setup will allow you to restore the project’s environment exactly as it was during the book’s creation, ensuring that all code examples run seamlessly.

B.1 RStudio Installation

First, you’ll need to download and install R and RStudio Desktop. You can do this by visiting the following link: RStudio Desktop Download.

B.2 How to Set Up This Project with Quarto

Quarto is the next-generation version of RMarkdown, designed for a wide range of publishing tasks, including creating notes, presentations, websites, and books. This book has been developed using Quarto, with the project versioned on GitHub. For more details on how to publish a Quarto book, refer to the official Quarto documentation.

To set up your project:

In RStudio, create a new project in a new directory.
Enable Git for version control.
Select “Quarto Book Project” as the project type. This will automatically generate a _quarto.yml file with the following structure:

---
project:
  type: book
---

To preview your book, use the terminal to run quarto preview. This command will generate a _book directory containing the compiled book files.

B.2.0.1 GitHub Useful Commands

You can manage your project using GitHub directly from RStudio or via command line. To connect your project with GitHub:

After creating your project, initiate a Git repository with:

git init
git remote add origin https://github.com/yourusername/your-repo.git

Commit your files and push them to the GitHub repository:
```
git branch -M main
git push -u origin main
```

B.2.0.2 Publish Your Book on GitHub Pages

To publish your Quarto book on GitHub Pages:

Modify the _quarto.yml file to specify the output directory as docs:
```
---
project:
  type: book
  output-dir: docs
---
```
Add a .nojekyll file to prevent GitHub Pages from ignoring files:
```
touch .nojekyll
```
Render your book with:
```
quarto render
```
This command will create a docs folder where the compiled book will be stored.

B.2.0.3 Adding a Package

If you want to add a custom R package to your book project, follow these steps:

Create a new package using devtools:
```
devtools::create("yourpkg")
```
Add raw data processing scripts:
```
usethis::use_data_raw()
```
This command creates a .R script in the data-raw directory for processing your data.
Save processed data for use in the package:
```
usethis::use_data(yourdata)
```
Document your package functions and datasets:
```
usethis::use_r("yourdataset")
devtools::document()
```
Use vignettes for additional documentation:
```
vignette("rd-other") # For datasets
vignette("rd")
```
Finally, build your package to include all new data and functions:
```
devtools::load_all(".")
```

B.2.0.4 Ensuring Reproducibility with renv

To ensure that all analyses and code examples in the book are reproducible, we’ve utilized the renv package. This package captures the specific versions of all R packages used in the project, storing them in an renv.lock file located in the root directory of the book’s GitHub repository.

To restore the project environment to its original state:

Clone the project repository.
Run the following command in your R console:
```
renv::restore()
```
This command reads the renv.lock file and reinstalls all packages with the exact versions used during the book’s development.

Using renv ensures that all code examples work as intended, regardless of future package updates, making it easier for readers to replicate analyses or adapt the code to their datasets.