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---
title: "Sharpening the Axe"
subtitle: "Reproducible Data Analysis at the Speed of Thought"
abstract: |
This talk is all about workflows and tools.
We will learn about `Quarto`, the next iteration of Rmarkdown
and integrate it into our workflow.
We will see the `targets` R package in action to help us
keep track of complicated analysis pipelines and produce
verifiably reproducible results.
Lastly, we will venture into uncharted territory to find
out first hand, why it always pays off to learn the intricacies
of your tools with a live demonstration of using `Quarto` and
`targets` in `Neovim`.
date: December 19, 2023
author: Jannik Buhr
institute: Heidelberg Institute for Theoretical Studies
format:
revealjs:
# embed-resources: false
title-slide-attributes:
data-background-image: ./img/hand-axe.png
data-background-size: contain
data-background-position: left
auto-animate-unmatched: false
code-copy: true
citations-hover: true
reference-links: false
progress: true
slide-number: true
chalkboard:
buttons: true
multiplex: false
preview-links: auto
theme: [default, theme.scss]
css: ./styles.css
footer: |
<https://jmbuhr.de/2023-workflow>
bibliography: ./references.bib
nocite: ""
execute:
warning: false
eval: true
echo: true
engine: knitr
---
# Welcome
```{r}
#| echo: false
library(tidyverse)
library(palmerpenguins)
```
<html>
<script>
document.head.appendChild(Object.assign(document.createElement("link"), {rel: "icon", href: "data:image/svg+xml,<svg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 100 100'><text y='.9em' font-size='90'>🦦</text></svg>"}))
</script>
</html>
## Otters have a favorite Rock 🪨
:::: {layout="[1,1]"}
:::{#quote}
{#otter-pound}
> "The mean number of **blows** necessary **to open a mussel** was **35.5** [...].\
> The **same stone** was frequently **retained** for several successive food items, [...]"
>
> --- @hallToolUsingBehaviorCalifornia1964
:::
::::
:::footer
Image sources: <https://en.wikipedia.org/wiki/Tool_use_by_sea_otters>, <https://en.wikipedia.org/wiki/Tool_use_by_sea_otters>
:::
## Otters have a favorite Rock 🪨
> "Give me six hours to cut down a tree and I will spend the first four sharpening the axe."
>
> --- Abraham Lincoln
## Otters have a favorite Rock 🪨
> "Give me six minutes to open a mussel and I will spend the first four finding the perfect rock."
>
> --- ~~Abraham~~ Otterham Lincoln
## Humans are toolmakers 🪓
{.fl width=38%}
:::{#textbox}
**Humans** don't just **use** tools.
We **shape** and **perfect** them.
:::
. . .
{.fr width=38%}
:::footer
Image sources: <https://www.pexels.com/photo/person-holding-a-stone-2957058/>, <https://en.wikipedia.org/wiki/Hand_axe>
:::
## Who am I? 🦦
:::{#jannik .fr}
:::
Hi, I'm Jannik!
Computational Biochemist at\
HITS and Heidelberg University
I use **Quantum Mechanical Simulations** to study how **Collagen** breaks under force
{width=60%}
I love building and teaching tools 🧰
:::profile
- \@jmbuhr
- [](https://github.com/jmbuhr){.bi-github}
- [](https://jmbuhr.de){.bi-house}
- [](https://mastodon.online/@jmbuhr){.bi-mastodon}
- [](https://www.youtube.com/@jmbuhr){.bi-youtube}
- [](https://www.linkedin.com/in/jmbuhr/){.bi-linkedin}
:::
{{< qrcode https://github.com/jmbuhr.de/2023-workflow qr width=124 height=124 colorDark='#1E4287' >}}
## The Tools Today 🧰
::: {.columns}
::: {.column width="30%"}
{width=100%}
{width=50%}
{width=100%}
:::
::: {.column width="70%"}
### Quarto
<https://quarto.org/>
Next iteration of `Rmarkdown`.
### Targets
<https://docs.ropensci.org/targets/>
R package for reproducible workflows.
### Neovim
<https://neovim.io/>
hyperextensible Vim-based text editor
:::
:::
# Warmup!
## Remember these letters
```{r}
#| echo: false
countdown::countdown(minutes = 0, seconds = 7)
```
[xfwiadcnanvrqybceawgjdczlyhlwoovxxce]{#letters}
## Remember these letters
How many of these letters do you remember?
## Remember these letters
```{r}
#| echo: false
countdown::countdown(minutes = 0, seconds = 7)
```
[The quick brown fox jumps over the lazy dog]{#letters}
## Remember these letters
Do you remember the sentence on the previous slide?
. . .
Of course you do, it's just **one** sentence!
. . .
But it has the **same number of letters** as the random letters.
## The Magic 7 ± 2
One piece of information is a **chunk**.
We can keep **7** (± 2) **chunks** in our **working memory** [@millerMagicalNumberSeven1956a].
We gain space by combining thoughts and **concepts**
Letters → Words → Sentences → Concepts
# Optimize Your Workflow
## Quarto: Structure Thoughts
:::tr
:::
<https://quarto.org/>
An open-source scientific and technical publishing system.
- Keep **thoughts, code and results** close
- Cater to different **output formats**
- web, pdf, docx, ppt ...
- Fully **reproducible**
{#rstudio}
## {background-image="./img/choose.png" background-size=70% background-position=top}
|
|
|
|
|
`qmd` files are just plain text!
````
---
title: "quarto demo"
format:
html:
code-fold: true
---
## Air Quality
@fig-airquality further explores the impact of temperature on ozone level.
```{{r}}
#| label: fig-airquality
#| fig-cap: "Temperature and ozone level."
library(ggplot2)
ggplot(airquality, aes(Temp, Ozone)) +
geom_point() +
geom_smooth(method = "loess"
)
```
````
## Quarto: Structure Thoughts
:::tr
:::
:::sidenote
🖥️📱📰
:::
::: {.incremental}
- **Why** did I perform this operation?
- Read a detailed **explanation** of past-me right **next** to the code!
- Different and changing **output formats**?
- Just let quarto **generate** them for you!
- Could you increase the fontsize in **all your plots**?
- Sure, just **change** one number and **re-render**!
:::
. . .
> "I have a machine learning model that takes 6 hours to calculate. [...] how do I put this in a Quarto notebook?"
. . .
Well, **don't!**
## Targets: Organize Workflows
:::tr
{width=50%}
:::
<https://docs.ropensci.org/targets/>
Function-oriented Make-like **declarative workflows** for R.
```{r}
#| echo: false
#| out-width: 90%
targets::tar_visnetwork()
```
Aim for **pure functions** that take **inputs** and produce **outputs**
without side effects.
## NeoVim: Not just for Speed!
## NeoVim: Not just for Speed!
## NeoVim: Not just for Speed!
**Modal editing** allows us to **communicate** with the editor.
**Complicated operations** become one **chunk**.
**Free up resources** for the important questions.
|
|
- modes
- normal, insert, visual
- verbs
- change, delete, paste etc.
- nouns (text objects)
- word, sentence, paragraph, block, parenthesis, function etc.
- movements
- "to end of line", "to beggining of the document", "down 3 lines" etc.
# Demo
Demo Time!
{width=80%}
::: {.aside}
Artwork by \@allisonhorst
:::
# Take Home Messages
## Take Home Messages
Keyboard shortcuts are for thoughts, not just speed ⌨️
. . .
Reproducibility and Interactivity can go hand in hand ▶️
. . .
Find your favorite rock 🪨
. . .
And sharpen the axe 🪓
. . .
Slides: <https://jmbuhr.de/2023-workflow>
{{< qrcode https://github.com/jmbuhr.de/2023-workflow qr2 width=200 height=200 colorDark='#1E4287' >}}
:::profile
- \@jmbuhr
- [](https://github.com/jmbuhr){.bi-github}
- [](https://jmbuhr.de){.bi-house}
- [](https://mastodon.online/@jmbuhr){.bi-mastodon}
- [](https://www.youtube.com/@jmbuhr){.bi-youtube}
- [](https://www.linkedin.com/in/jmbuhr/){.bi-linkedin}
:::
## References
:::{#refs}
:::
# Backup Slides
## Aside: Pure Functions
```{dot}
//| echo: false
//| fig-height: 3
digraph functions {
rankdir=LR;
node [shape=circle];
A -> B [label="f"];
B -> C [label="g"];
A -> C [label="h"];
}
```
$$
g \circ f = h\
$$
::: {.columns}
::: {.column width=""}
**pure**
```{r}
#| eval: false
f = function(data, cutoff) {
data |>
filter(x < cutoff) |>
mutate(x = x * pi)
}
```
:::
::: {.column width=""}
vs. **Side Effects**
```{r}
#| eval: false
f_prime = function(cutoff) {
data <<- data |>
filter(x < cutoff) |>
mutate(x = x * pi)
}
```
:::
:::