%%{
init: {
"theme": "dark",
"themeCSS": ".label foreignObject, .cluster-label foreignObject { font-size: 90%; overflow: visible; }"
}
}%%
flowchart LR
A1[qmd] --> C{"knitr<br>(R)"}
A1[qmd] --> B{"Jupyter<br>(Python)"}
A2[ipynb] --> B{"Jupyter<br>(Python)"}
B --> D[md]
C --> D[md]
D --> E{Pandoc}
E --> F[pdf]
E --> G[docx]
E --> H[html]
E --> I[...]
subgraph engine [Engine]
B
C
end
QTM 350 - Data Science Computing
Lecture 08 - Reproducible Research with Quarto
25 September, 2024
Quiz 01
What do you think of it?
- How did you do? What did you find challenging, if anything?
- Too long, too short, too easy, too hard?
- What did you like about it (if anything 😅)?
- Feedback is always welcome! 🙏
Checking git diff
Checking git diff
Today’s plan 📅
- Why is reproducible research so important in data science (and elsewhere too)?
- The idea of literate programming and how it can help you write better code
- An introduction to Quarto and how it can help you write reproducible research
- Using Quarto to write reports in many formats (HTML, PDF, Word, etc.)
- How to use Quarto to write code
The reproducibility crisis
- Reproducibility is the ability of an entire experiment or study to be duplicated, either by the same researcher or by someone else working independently
- The reproducibility crisis is a term used to describe the inability of researchers to replicate the results of a study using the same data and methods
- The crisis is not limited to data science, but it’s particularly acute in fields like psychology and medicine
- The crisis is caused by a combination of factors, including poor experimental design, publication bias, and the use of p-values
- Here we will focus on the role of code and data in reproducibility, which is the most relevant to us
Amy Cuddy demonstrating her theory of “power posing”. It could never be replicated. Ted Talk with 72 million views!
The reproducibility crisis in medicine
The reproducibility crisis in psychology
Why does it matter? We all write code, right? 🤔
Code is reproducible by default, isn’t it?
Literate programming
- Literate programming is a programming paradigm introduced by Donald Knuth in 1984
- The idea is to treat code as a form of literature, where the code is interspersed with explanations and documentation
- The goal is to make the code more readable and understandable to humans
- Requires two processing steps: weaving and tangling
- Weaving: converts the literate programme into a document
- Tangling: extracts the code from the document
- Literate programming improves code quality by requiring programmers to articulate their reasoning, thus showing flawed design choices
Some Quarto examples
Company reports
Some Quarto examples
Interactive dashboards
Some Quarto examples
Books
Some Quarto examples
Websites
Downloading and installing Quarto
Downloading and installing Quarto
Additionally, you can download and install Quarto using:
Writing with your favourite editor
Quarto projects: default
Quarto projects: website
Quarto projects: blog
Quarto projects: book
Quarto projects: manuscript
knitr
---
title: "ggplot2 demo"
format:
html:
code-fold: true
---
## Meet Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
```{r}
#| label: plot-penguins
#| echo: false
#| message: false
#| warning: false
library(tidyverse)
library(palmerpenguins)
ggplot(penguins,
aes(x = flipper_length_mm, y = bill_length_mm)) +
geom_point(aes(color = species, shape = species)) +
scale_color_manual(values = c("darkorange","purple","cyan4")) +
labs(
title = "Flipper and bill length",
subtitle = "Dimensions for penguins at Palmer Station LTER",
x = "Flipper length (mm)", y = "Bill length (mm)",
color = "Penguin species", shape = "Penguin species"
) +
theme_minimal()
Jupyter
---
title: "Palmer Penguins Demo"
format:
html:
code-fold: true
jupyter: python3
---
## Meet Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
```{python}
#| echo: false
#| message: false
import pandas as pd
import seaborn as sns
from palmerpenguins import load_penguins
sns.set_style('whitegrid')
penguins = load_penguins()
g = sns.lmplot(x="flipper_length_mm",
y="body_mass_g",
hue="species",
height=7,
data=penguins,
palette=['#FF8C00','#159090','#A034F0']);
g.set_xlabels('Flipper Length');
g.set_ylabels('Body Mass');
Quarto tooling
:::
Writing using the Visual Editor
Contents of a Quarto document
- A Quarto document contains three types of content: a YAML header, code chunks, and Markdown text
- We will cover Markdown in more detail in the next lecture
YAML
Code chunks
- Code chunks begin and end with three backticks (usually)
- Code chunks are identified with a programming language in between
{} - Can include optional chunk options, in YAML style, identified by
#|at the beginning of the line
Multiple figures
Put two plots side by side:
