The Repro Book

Description

Welcome to the Repro Book, an open-source online learning resource on reproducible research. The main goal of the Repro Book is to provide a companion online course text book for courses on reproducible research.

Repository Structure

Folders

.github/workflows is a folder that contains GitHub Actions workflows. Currently, two automatic workflows run automatically. This folder can be ignored by users who want to contribute to the book.

_extensions is a folder that contains Quarto extensions. Currently, this book only uses the fontawesome-extension to create icons like this: {{< fa folder >}}. This folder can be ignored by users who want to contribute to the book.

chapters is the heart of the book. The chapters folder contains all main chapters of the book. The content of each chapter is stored in its own .qmd file. If you want to contribute with content and modify chapters or create new ones, this is main the place where your adjustments take place.

images is a folder that does not contain images (yet). The images displayed in this book are stored in a NextCloud folder. If you want to contribute images to this book, please upload them to the NextCloud folder. For an explanation of how to use the images from NextCloud, see contributing.qmd.

renv is a folder that contains information about the R packages used in this book. If your contributions include the utility of an additional R package, see contributing.qmd for how to modify the relevant files.

Files

.Renviron is a file used in R that allows users to define environment variables.

.Rprofile is a file used in R that allows users to customize their R sessions by specifying code that should be executed every time R starts.

.all-contributorsrc is a file where the contributors of this project are listed. When you want to start working on this book, you will be included in this document. Content contribution is not affected by this file.

.codespellrc is a file connected to a an automated codespell check at GitHub. Content contribution is not affected by this file.

.gitignore is a file that specifies files and folders that should be ignored and not tracked by Git. It prevents certain files or directories that are not essential for the project or generated during the development process from being included in the version history. For more information about .gitignore, check out this link.

LICENSE is a file where you can see what others are and are not allowed to do with this project.

Makefile is a special text file that contains rules and instructions for automating the execution of software programs.

README.md is the file you are currently reading. It provides basic information about a project and a description of a repository.

_affiliations.yml is a metadata-file that contains information about the affiliations the contributors work at. If you contribute to this project and are affiliated to a different institution than University of Hamburg, you can extend the file for your institution.

_authors.yml is a metadata-file that contains information about the authors of this project. If you contribute to this project as an author, you can extend the file for your information.

_custom.scss is a used to customize the styling of Quarto documents by writing our own CSS (Cascading Style Sheets) rules.

_quarto.yml is a metadata-file that configures the project settings. For example, it configures the book title and subtitle and how the book chapters are arranged. If you contribute to this project with a new chapter, you have to add the location of the chapter in a meaningful way to the chapters-section in the _quarto.yml-file.

_quarto-pdf.yml is also a metadata-file that configures the project settings but only when we export the book to PDF.

_variables.yml is a metadata-file that specifies variables in a project. It is possible to use the variables in the files that constitute the chapters or similar.

acknowledgements.qmd is a closing book chapter where we describe which different tools we use for what.

contents.qmd is an opening book chapter where we describe what you can expect in each chapter.

index.qmd is a file that contains the content of the first site of the repro book. It serves as the cover of the book.

plausible.html is used to integrate Plausible Analytics, a privacy-focused web analytics tool. This file serves as a way to include the necessary HTML code to track website or document usage without compromising user privacy.

references.bib is a file that contains information about all the references we use in our book. It is written using BibTex. If you contribute to this book and add new references, please make sure that these references are stored in this file.

references.qmd is a closing chapter that lists all the mentioned references. It is automatically generated from the references.bib-file.

renv.lock is a file that saves R packages and their versions used in this book. If you contribute to this book and need additional R packages, please make sure that these packages are stored in this file.

repro-book.Rproj is a project file used by RStudio, an integrated development environment for R. It serves as a container for all files and settings related to a specific R project.

summary.qmd is a closing chapter of the book. It summarizes the most important insights.