Analysis

Topics

Code Chunks
Inline Code
Sourcing Scripts

Code Chunks

What are Code Chunks?

Specified place for code
Executable
Weaved between between text
May print output or create new variables, for example

```{r}
#| echo: true
1993 + 2023
```

[1] 4016

Anatomy of a Code Chunk

On each end of the code chunk: 3 backticks: ``` **
Curly brackets: engine: {r} or {python} **
Top of chunk: Code chunk options, with hashpipe: #|

```{r}
#| label: cars-r
#| echo: false
mtcars %>% 
  distinct(cyl)
```

```{python}
#| label: car-py
#| echo: false
distinct_cyl = mtcars.drop_duplicates(subset=['cyl'])
```

** not needed in a code cell in a Jupyter notebook!

Code Chunk Options

Useful code chunk options:

#| eval: true: Evaluates code chunk.
#| echo: true: Includes source code in output.
#| output: true: Includes results of code execution in output.
#| warning: true: Includes warnings in output.
#| include: false: Catch all for preventing anything from being included.
#| label: something-meaningful: Good practice to always include!

Options for figure-creating code chunks:

#| fig-cap: "your figure's caption" : caption of the figure
#| fig-width: 8 : width of the figure
#| fig-height: 6 : height of the figure

Code Chunk Options

Options for all code chunks: include in yaml (top of the document).

For example…

---
format: html
execute:
  echo: false
---

… hides all code in the output!

Inserting Code Chunks

Option 1: Type it out

Option 2: Visual editor: Insert > Code cell

Option 3: Shortcuts:

RStudio: Ctrl+Alt+I
VS Code: Ctrl+Shift+I
Jupyter Lab: B

Exercise

Go to the Code Chunks chapter in the workshop book and do the exercise.

You will be pasting some code from a dummy script into code chunks in your document!

15:00

Inline Code

Inline code: what & why?

Insert results or (quick) calculations into running text, without additional text formatting.

Why?

report and describe results reproducibly
minimizes errors: no manual copy-pasting results
automatic updating when data or code changes

Inline code: how?

In R

There are `r sum(penguins$Species=='Adelie')` 
penguins of the Adelie species in the dataset.

There are 152 penguins of the "Adelie" species in the dataset.

In Python (Quarto >= 1.4)¹

```{python}
x = 5 + 5
```

The answer to 5 + 5 is `{python} x`

Exercise

Take a couple of minutes to play around with the possibilities of inline code!

Go to the Inline code chapter in the workshop book to complete the exercise.

10:00

Sourcing Scripts

Sourcing external files: what & why?

For example: R and Python scripts, .qmd or .ipynb files.

Why separate scripts from the manuscript?

minimizes errors: no manual copy-pasting code
easier code debugging
making the Quarto document easier to digest
modular coding = good coding practice

Sourcing external files: how?

.qmd files: use the chunk option #| file: "your-script.ext".
.ipynb files: import the script as module or run it.

```{r}
#| file: "your-script.R"
#| eval: true 
```

Python:

```{python}
#| echo: false
%run your-script.py
```

Or: Add an empty __init__.py file to your scripts folder and run:

```{python}
#| echo: false
from your-script import function
```

Exercise

The workshop-materials contain 2 example scripts: do_addition.R and do_addition.py. You will use one of them to include the code in your Quarto document.

Go to the Sourcing code chapter in the workshop book and complete the exercise!

10:00

Other options

Other options not discussed here:

Use parts of an external script within the Quarto document, for example to only run a few selected lines.
Run a script before or after rendering a Quarto document to a manuscript: Quarto Docs: Project Scripts
Use code chunks from existing Quarto documents or Jupyter notebooks: Quarto v1.4 Release
Include entire Quarto documents or Jupyter notebooks within your current Quarto document: Quarto Docs: Includes