03-methods.qmd

# Methods

<br>

This section describes the tools and methods used to create and utilize this template.

This template itself is the "method". It prescribes a specific way to organize and execute a reproducible research project.

## Core Technologies

1.  [**Quarto:**]((https://quarto.org)) The primary authoring tool. It uses Markdown syntax for text and integrates executable code chunks (primarily R, but also Python, Julia, etc.). Key features used:
    -   **Book Format:** Organizes the article into chapters/sections.
    -   **Code Chunks:** Embed R code directly (`{r}`) for analysis and visualization.
    -   **Citations:** Managed via `references.bib` (BibTeX) and formatted using `apa7ed.csl`. You can use [Zotero](https://www.zotero.org/) in RStudio for this.
    -   **Embedding Outputs:** Results from scripts in `Scripts/` can be embedded into the narrative using `{{< embed >}}` (see Results section).
2.  [**R & RStudio:**](https://posit.co/download/rstudio-desktop/) The computational engine and integrated development environment (IDE). R/RStudio is used for statistical analysis, data manipulation, and creating visualizations within Quarto documents.
3.  **Git & GitHub:**
    -   [**Git:**](https://git-scm.com/) Provides version control locally. Every significant change to your project files is tracked.
    -   [**GitHub:**](https://github.com/) Hosts the repository online, enabling collaboration, sharing, backup, and to publish the dynamic document (Github Pages). It also integrates with GitHub Actions.
4.  **Environment Management:**
    -   [**renv:**](https://rstudio.github.io/renv/) (Proper Reproducibility) Tracks and restores specific R package versions used in the project. The `renv.lock` file is the key component.
    -   [**Docker:**](https://www.docker.com/) (Full Reproducibility) Packages the entire software environment (R, RStudio, Quarto, packages, LaTeX) into a container. This guarantees that the environment is identical for anyone running the project. The `docker/` folder contains the necessary configuration (`Dockerfile`, `docker-compose.yml`, `start/stop` scripts).
    -   [**MyBinder**](https://mybinder.org/): Cloud platform for reproducibility verification.  Provides one-click browser-based access to a complete computational environment, enabling verification without local installation (`.binder/Dockerfile`)
5.  **Sharing & Publication:**
    -   [**OSF:**](https://osf.io/) A platform for registering, storing, and sharing research materials openly.
    -   [**GitHub Pages:**](https://pages.github.com/) A free service to host the rendered HTML version of your Quarto book/article directly from your GitHub repository. The `.github/workflows/deploy.yml` file automates this process.

## Workflow Integration

If you need to learn a little more about Reproducible Research with [R/RStudio](https://posit.co/download/rstudio-desktop/), there are excellent free e-books:

-   [R for Data Science](https://r4ds.hadley.nz/)
-   [Building reproducible analytical pipelines with R](https://raps-with-r.dev/)
-   [The Open Science Manual: Make Your Scientific Research Accessible and Reproducible](https://arca-dpss.github.io/manual-open-science/)

The typical workflow using this template for Full Reproducibility involves:

1.  Setting up the environment using Docker (`docker/start.sh` or `start.bat`).
2.  Working within the RStudio container to edit `.qmd` files, run code chunks, and manage R packages (tracked by `renv`).
3.  Rendering the document using `quarto render` in the RStudio Terminal.
4.  Stopping the Docker environment when done (`docker/stop.sh` or `stop.bat`).
5.  Using Git locally to commit and push changes to your GitHub repository.
6.  Optionally, pushing to the `main` branch triggers the GitHub Actions workflow to automatically publish the updated HTML site to GitHub Pages.