Joining data & data communication using Quarto

CVEN 5999 - Summer 2025

Lars Schöbitz

Learning Objectives (for this week)

Learners can use Quarto and GitHub Pages to publish an HTML file.
Learners can add literature references to Quarto files using the navigation menu of RStudio visual editor.
Learners can cross-reference figures and tables within an Quarto file.
Learners can apply functions from the dplyr R Package to join multiple data sets.

Part 1: Joining data

We…

…have multiple data frames

…want to bring them together

professions <- read_csv(here::here("data/scientists/professions.csv")) 
dates <- read_csv(here::here("data/scientists/dates.csv")) 
works <- read_csv(here::here("scientists/works.csv"))

Data: Women in science

Information on 10 women in science who changed the world

name
Ada Lovelace
Marie Curie
Janaki Ammal
Chien-Shiung Wu
Katherine Johnson
Rosalind Franklin
Vera Rubin
Gladys West
Flossie Wong-Staal
Jennifer Doudna

name	profession
Ada Lovelace	Mathematician
Marie Curie	Physicist and Chemist
Janaki Ammal	Botanist
Chien-Shiung Wu	Physicist
Katherine Johnson	Mathematician
Rosalind Franklin	Chemist
Vera Rubin	Astronomer
Gladys West	Mathematician
Flossie Wong-Staal	Virologist and Molecular Biologist
Jennifer Doudna	Biochemist

name	birth_year	death_year
Janaki Ammal	1897	1984
Chien-Shiung Wu	1912	1997
Katherine Johnson	1918	2020
Rosalind Franklin	1920	1958
Vera Rubin	1928	2016
Gladys West	1930	NA
Flossie Wong-Staal	1947	NA
Jennifer Doudna	1964	NA

name	known_for
Ada Lovelace	first computer algorithm
Marie Curie	theory of radioactivity, discovery of elements polonium and radium, first woman to win a Nobel Prize
Janaki Ammal	hybrid species, biodiversity protection
Chien-Shiung Wu	confim and refine theory of radioactive beta decy, Wu experiment overturning theory of parity
Katherine Johnson	calculations of orbital mechanics critical to sending the first Americans into space
Vera Rubin	existence of dark matter
Gladys West	mathematical modeling of the shape of the Earth which served as the foundation of GPS technology
Flossie Wong-Staal	first scientist to clone HIV and create a map of its genes which led to a test for the virus
Jennifer Doudna	one of the primary developers of CRISPR, a ground-breaking technology for editing genomes

Desired output

name	profession	birth_year	death_year	known_for
Ada Lovelace	Mathematician	NA	NA	first computer algorithm
Marie Curie	Physicist and Chemist	NA	NA	theory of radioactivity, discovery of elements polonium and radium, first woman to win a Nobel Prize
Janaki Ammal	Botanist	1897	1984	hybrid species, biodiversity protection
Chien-Shiung Wu	Physicist	1912	1997	confim and refine theory of radioactive beta decy, Wu experiment overturning theory of parity
Katherine Johnson	Mathematician	1918	2020	calculations of orbital mechanics critical to sending the first Americans into space
Rosalind Franklin	Chemist	1920	1958	NA
Vera Rubin	Astronomer	1928	2016	existence of dark matter
Gladys West	Mathematician	1930	NA	mathematical modeling of the shape of the Earth which served as the foundation of GPS technology
Flossie Wong-Staal	Virologist and Molecular Biologist	1947	NA	first scientist to clone HIV and create a map of its genes which led to a test for the virus
Jennifer Doudna	Biochemist	1964	NA	one of the primary developers of CRISPR, a ground-breaking technology for editing genomes

Inputs, reminder

names(professions)

[1] "name"       "profession"

names(dates)

[1] "name"       "birth_year" "death_year"

names(works)

[1] "name"      "known_for"

nrow(professions)

[1] 10

nrow(dates)

[1] 8

nrow(works)

[1] 9

Joining data frames

something_join(x, y)

left_join(): all rows from x
right_join(): all rows from y
full_join(): all rows from both x and y
…

Setup

For the next few slides…

x <- tibble(
  id = c(1, 2, 3),
  value_x = c("x1", "x2", "x3")
  )

# A tibble: 3 × 2
     id value_x
  <dbl> <chr>  
1     1 x1     
2     2 x2     
3     3 x3

y <- tibble(
  id = c(1, 2, 4),
  value_y = c("y1", "y2", "y4")
  )

# A tibble: 3 × 2
     id value_y
  <dbl> <chr>  
1     1 y1     
2     2 y2     
3     4 y4

`left_join()`

left_join(x, y)

# A tibble: 3 × 3
     id value_x value_y
  <dbl> <chr>   <chr>  
1     1 x1      y1     
2     2 x2      y2     
3     3 x3      <NA>

`left_join()`

professions %>%
  left_join(dates)

name	profession	birth_year	death_year
Ada Lovelace	Mathematician	NA	NA
Marie Curie	Physicist and Chemist	NA	NA
Janaki Ammal	Botanist	1897	1984
Chien-Shiung Wu	Physicist	1912	1997
Katherine Johnson	Mathematician	1918	2020
Rosalind Franklin	Chemist	1920	1958
Vera Rubin	Astronomer	1928	2016
Gladys West	Mathematician	1930	NA
Flossie Wong-Staal	Virologist and Molecular Biologist	1947	NA
Jennifer Doudna	Biochemist	1964	NA

`right_join()`

right_join(x, y)

# A tibble: 3 × 3
     id value_x value_y
  <dbl> <chr>   <chr>  
1     1 x1      y1     
2     2 x2      y2     
3     4 <NA>    y4

`right_join()`

professions %>%
  right_join(dates)

name	profession	birth_year	death_year
Janaki Ammal	Botanist	1897	1984
Chien-Shiung Wu	Physicist	1912	1997
Katherine Johnson	Mathematician	1918	2020
Rosalind Franklin	Chemist	1920	1958
Vera Rubin	Astronomer	1928	2016
Gladys West	Mathematician	1930	NA
Flossie Wong-Staal	Virologist and Molecular Biologist	1947	NA
Jennifer Doudna	Biochemist	1964	NA

`full_join()`

full_join(x, y)

# A tibble: 4 × 3
     id value_x value_y
  <dbl> <chr>   <chr>  
1     1 x1      y1     
2     2 x2      y2     
3     3 x3      <NA>   
4     4 <NA>    y4

`full_join()`

dates %>%
  full_join(works)

name	birth_year	death_year	known_for
Janaki Ammal	1897	1984	hybrid species, biodiversity protection
Chien-Shiung Wu	1912	1997	confim and refine theory of radioactive beta decy, Wu experiment overturning theory of parity
Katherine Johnson	1918	2020	calculations of orbital mechanics critical to sending the first Americans into space
Rosalind Franklin	1920	1958	NA
Vera Rubin	1928	2016	existence of dark matter
Gladys West	1930	NA	mathematical modeling of the shape of the Earth which served as the foundation of GPS technology
Flossie Wong-Staal	1947	NA	first scientist to clone HIV and create a map of its genes which led to a test for the virus
Jennifer Doudna	1964	NA	one of the primary developers of CRISPR, a ground-breaking technology for editing genomes
Ada Lovelace	NA	NA	first computer algorithm
Marie Curie	NA	NA	theory of radioactivity, discovery of elements polonium and radium, first woman to win a Nobel Prize

Putting it altogether

professions %>%
  left_join(dates) %>%
  left_join(works) |> 
  kable()

name	profession	birth_year	death_year	known_for
Ada Lovelace	Mathematician	NA	NA	first computer algorithm
Marie Curie	Physicist and Chemist	NA	NA	theory of radioactivity, discovery of elements polonium and radium, first woman to win a Nobel Prize
Janaki Ammal	Botanist	1897	1984	hybrid species, biodiversity protection
Chien-Shiung Wu	Physicist	1912	1997	confim and refine theory of radioactive beta decy, Wu experiment overturning theory of parity
Katherine Johnson	Mathematician	1918	2020	calculations of orbital mechanics critical to sending the first Americans into space
Rosalind Franklin	Chemist	1920	1958	NA
Vera Rubin	Astronomer	1928	2016	existence of dark matter
Gladys West	Mathematician	1930	NA	mathematical modeling of the shape of the Earth which served as the foundation of GPS technology
Flossie Wong-Staal	Virologist and Molecular Biologist	1947	NA	first scientist to clone HIV and create a map of its genes which led to a test for the virus
Jennifer Doudna	Biochemist	1964	NA	one of the primary developers of CRISPR, a ground-breaking technology for editing genomes

Part 2: Communicate results with Quarto

Why Quarto? -> Open Science

What is Quarto?

Quarto is a new, open-source,
scientific and technical
publishing system

the goal is to make the process of creating
and collaborating dramatically better

A schematic representing the multi-language input (e.g. Python, R, Observable, Julia) and multi-format output (e.g. PDF, html, Word documents, and more) versatility of Quarto.

Quarto for literate programming

diagram of converting a Qmd document via knitr/pandoc into markdown and then into output formats

diagram of converting a Quarto document via Jupyter/pandoc into markdown and then into output formats

What is a `.qmd`?

A Quarto document i.e. a .qmd is a plain text file

Metadata (YAML)

format: html
engine: knitr

format: html
engine: jupyter

Code

```{r}
library(dplyr)

mtcars |> 
  dplyr::group_by(cyl) |> 
  dplyr::summarize(mean = mean(mpg))
```

```{python}
from siuba import _, group_by, summarize
from siuba.data import mtcars
(mtcars
  >> group_by(_.cyl)
  >> summarize(avg_mpg = _.mpg.mean())
  )
```

Text

# Heading 1
This is a sentence with some **bold text**, some *italic text* and an 
![image](image.png){fig-alt="Alt text for this image"}.

Quarto makes moving between formats straightforward

Document

lesson-1.qmd

title: "Lesson 1"
format: html

Presentation

lesson-1.qmd

title: "Lesson 1"
format: revealjs

Website

_quarto.yml

project:
  type: website

website: 
  navbar: 
    left:
      - lesson-1.qmd

It is traightforward in Quarto to move between output formats
As an educator, there are two things that are important to me
- reproducibility, and
- ease of transitiion between output formats
I am using Quarto for everything, and it’s finally the tool let’s me go from one output type to anoher without the to change anything by the YAML metadata

For example, here are common things I produce

–> a lesson in document form
–> the same content in presentation form
–> the same content on a page in a website,

and you can see that all that needed to change going between these formats is a few lines in the yaml.

No slide breaks to remove, no citation style to change, no headings to re-level. This ease of transition has freed up time to focus my time on content, and that, folks, is the dream!

Comfort of your own workspace

A screenshot of a Quarto document rendered inside RStudio

A screenshot of a Quarto document rendered inside JupyterLab

A screenshot of a Quarto document rendered inside VSCode

Rich Documentation

Screenshot of the Quarto homepage at https://quarto.org/.

Live Coding Exercise: Write a report

Clone GitHub repository from GitHub

Open the GitHub Organisation for the course: https://github.com/cven5999-ss25
Locate the wk-06-writing repository with your username wk-06-writing-GITHUB-USERNAME
Follow along with me

Break

10:00

Cross-references

no space between {r} and #| tbl-cap: "A table"
spelling tbl not tab
no spaces (use dashes in label)

See Table 1…

```{r}
#| tbl-cap: "A table"
#| label: tbl-simple-table

tibble(
  id = c(1, 2, 3),
  name = c("X", "Y", "Z")
) %>% 
  knitr::kable()
```

Table 1: A table

id	name
1	X
2	Y
3	Z

Homework week 6

Homework due dates

All material on course website
Homework assignment & learning reflection due: 2025-07-11

Capstone Project Report

Information

All material on course website
Due date for report: 2025-07-25

Thanks! 🌻

Acknowledgements

A large proportion of these slides are taken from Mine Çetinkaya Rundel’s “Hello Quarto” presentation & Thomas Mock’s “Quarto for the Curious” presentation

Slides created via revealjs and Quarto: https://quarto.org/docs/presentations/revealjs/

Access slides as PDF on GitHub

All material is licensed under Creative Commons Attribution Share Alike 4.0 International.

Joining data & data communication using Quarto

Learning Objectives (for this week)

Part 1: Joining data

We…

Data: Women in science

Inputs

Desired output

Inputs, reminder

Joining data frames

Joining data frames

Setup

left_join()

left_join()

right_join()

right_join()

full_join()

full_join()

Putting it altogether

Part 2: Communicate results with Quarto

Why Quarto? -> Open Science

What is Quarto?

Quarto for literate programming

What is a .qmd?

Quarto makes moving between formats straightforward

Comfort of your own workspace

Rich Documentation

Live Coding Exercise: Write a report

Clone GitHub repository from GitHub

Break

Cross-references

Homework week 6

Homework due dates

Capstone Project Report

Information

Thanks! 🌻

Acknowledgements

`left_join()`

`left_join()`

`right_join()`

`right_join()`

`full_join()`

`full_join()`

What is a `.qmd`?