Getting Started

Once you have followed all the steps for Installation and setup, you can start to create the Quarto document that you will be working in during the workshop.

1. Create an RStudio Project

  • In RStudio, click File > New Project > Existing Directory.
  • Browse to your folder my-reproducible-manuscript in which you have saved the workshop materials.
  • Check the Open in new session option.
  • Click Create Project. This will create a my-reproducible-manuscript.Rproj file.

2. Document your project for reproducibility

Your project already contains pre-made folders, a README file and a License. Open the README.md file and fill it with a few relevant details, for example:

  • Purpose and contents of the project
  • Your name (Author)
  • The date of creation
  • Etc.

3. Create a Quarto document for your manuscript.

  • In RStudio, click File -> New File -> Quarto Document
  • Give your document a title, such as My Reproducible Manuscript.
  • Add yourself as an author.
  • For now, the default output format (HTML) and engine (knitr) are fine.
  • Uncheck the Use visual markdown editor option.
  • Click Create. A new Quarto document opens.

4. Render the Quarto document to HTML

  • Save the Quarto document in the docs folder within the my-reproducible-manuscript folder.
    Give the file a clear name, without using spaces. For example, my-reproducible-manuscript.qmd.
  • Once everything has been saved correctly, click the Render button in the menu bar.
  • The rendered HTML copy of your document will appear in your web browser or alongside the editor in RStudio. You will also see a my-reproducible-manuscript.html file appear in the docs folder.

1. Open the my-reproducible-manuscript folder in Visual Studio Code

In VS Code, click File > Open Folder… > my-reproducible-manuscript > Select folder.

2. Document your project for reproducibility

Your project already contains pre-made folders, a README file and a License. Open the README.md file and fill it with a few relevant details, for example:

  • Purpose and contents of the project
  • Your name (Author)
  • The date of creation
  • Etc.

3. Create a Quarto document for your manuscript.

  • In the Command Palette of VS Code (usually at the top of the screen, looks like a search bar), type > Quarto: New Document. This will open up a new empty Quarto document.
  • Give your new document a Title, such as My Reproducible Manuscript.
  • Copy the following block of text and code into your Quarto document:
## Quarto

Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.

## Running Code

When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:

```{python}
1 + 1
```

You can add options to executable code like this

```{python}
#| echo: false
2 * 2
```

The `echo: false` option disables the printing of code (only output is displayed).

4. Render the Quarto document to HTML

  • Save the Quarto document in the docs folder within the my-reproducible-manuscript folder.
    Give the file a clear name, without using spaces. For example, my-reproducible-manuscript.qmd.
  • In VS Code, click Terminal -> Split Terminal
  • In the newly created Terminal, run the following command:
quarto render my-reproducible-manuscript.qmd

The rendered HTML copy of your document will appear in your web browser or alongside the editor in VS Code. You will also see a my-reproducible-manuscript.html file appear in the docs folder.

1. Open the my-reproducible-manuscript folder in Jupyter Lab

  • Open Anaconda Navigator > Jupyter Lab.
  • Start a clean environment: close running kernels and non-relevant files you have open.
  • In the files section of Jupyter Lab, navigate to the location where you stored the my-reproducible-manuscript folder.

2. Document your project for reproducibility

Your project already contains pre-made folders, a README file and a License. Open the README.md file and fill it with a few relevant details, for example:

  • Purpose and contents of the project
  • Your name (Author)
  • The date of creation
  • Etc.

3. Open the Jupyter Notebook

  • Navigate to the docs folder.
  • Open the my-reproducible-manuscript.ipynb file.
  • Give your new document a Title, such as My Reproducible Manuscript and save your changes.

4. Render the Quarto document to HTML

  • In Jupyter Lab, click File -> New -> Terminal
  • Set the working directory to your project folder in the terminal, such as (use tab for autocompletion):
cd .\path\to\my-reproducible-manuscript\
  • In the newly created Terminal, run the following command:
quarto render docs/my-reproducible-manuscript.ipynb

You will see a my-reproducible-manuscript.html file appear in the docs folder. Click on it to open it.