Reproducible machine learning workflows with drake

class: left bottom hide-count
background-image: url(assets/images/bench-accounting-xxeAftHHq6E-unsplash.jpg)
background-size: 100%
background-position: top
background-color: #eff0f2

.talk-meta[
.talk-title[
# Reproducible machine learning workflows
]

.talk-author[
Patrick Schratz
]

.talk-date[
September 27th, 2019
]
]

---

class: top hide-count center middle

.f1.large[
<img class="icon-huge pr3" src="assets/images/desktop-download.svg" width="50px"/>
.code.moffitt-blue[usethis::use_course("mlr-org/mlr3-learndrake")]
]

.f1.large[
<img class="icon-huge pr3" src="assets/images/mark-github.svg" width="70px"/>
[github.com/.moffitt-orange[mlr-org/mlr3-learndrake]](https://github.com/mlr-org/mlr3-learndrake)
]

.f2.silver.center.mt5[Find someone to sit next to and share laptops]

.small[
(_Slide style and content borrowed from [Garrick Aden-Buie](https://github.com/gadenbuie/drake-intro)_ <i class="fas  fa-rocket "></i>)
]

---

class: inverse center middle hide-count

## What is drake?

![](assets/images/drake-meme.jpg)

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-16.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-17.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-18.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-19.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-20.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-21.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-22.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-23.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-24.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-25.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-26.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-27.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-28.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-29.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-30.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-31.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/messy-workflow-32.jpg')
background-size: contain

---

class: middle
background-image: url('assets/images/drawn/messy-workflow-32.jpg')
background-size: contain

.f2.moffitt-bg-light-blue-o90.white.pa5.shadow-3[
* Will this work when I come back to it later?

* What happens if I re-run _everything_?

* Am I certain that the results are still valid?
]

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/project-spectrum-33.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/project-spectrum-34.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/project-spectrum-35.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/project-spectrum-36.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-37.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-38.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-39.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-40.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-41.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-42.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-43.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-44.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-45.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-46.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-47.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-48.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-49.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-50.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-51.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-52.jpg')
background-size: contain

---

class: hide-count animated fadeIn
background-image: url('assets/images/drawn/drake-intro-53.jpg')
background-size: contain

---

layout: true
class: animated fadeIn
background-image: url('assets/images/drake-infographic.svg')
background-size: 100%
background-position: 40% left

(_borrowed from [ropensci/drake](https://github.com/ropensci/drake)_)

---

.bg-white.h-100.w-80.fixed.o-90.cover-2-3[

]

---

.bg-white.h-100.w-80.fixed.o-90.cover-3[

]

---

---
layout: false
class: inverse middle center

# drake Essentials

---
layout: false

# `_drake.R`

.flex[
.w-40[
The main settings file

- sources all R functions

- sources all "drake-plans" and binds them together

- sets the execution parameters in `drake_config()`

- called by `r_make()` at the start of every run
]

.w-70[

]
]

---

## .pkg[drake] "targets"

- _targets_ are simple R objects which **know their dependencies**

- _targets_ represent all intermediate or final results of your project

- _targets_ live in the **drake-cache** (`.drake` directory) and can from there be loaded into the global environment using `loadd()`

#### Advantages

- No need to use `saveRDS()`/`save()` anymore to store intermediate outputs

- Quick-load _targets_ under cursor in RStudio via addin

- visualize dependencies via `r_vis_drake_graph()`

---

# `r_vis_drake_graph()`

Shows how all _targets_ are connected

---

## How does drake help you in your daily work?

- Knows the execution order of your **complete** analysis
```r
r_vis_drake_graph()
```

- Enables **running** your complete project in **one call**
```r
r_make()
```

- Tracks metadata of each _target_ (runtime, etc.)

- If you make a substantial change downstream, all subsequent _targets_ will be updated (plots, tables, models, etc.)

---

## But wait, there's more!

There is a lot more that .pkg[drake] can do, including:

- [Predict total runtime](https://ropenscilabs.github.io/drake-manual/time.html#predict-total-runtime) of your plan

```r
r_predict_runtime()
```

- Support for [large plans](https://ropenscilabs.github.io/drake-manual/plans.html#large-plans) by using wildcards and functions `map()`, `cross()` and `combine()`

- [Parallel computation](https://ropenscilabs.github.io/drake-manual/hpc.html#parallel-backends) of _targets_ via packages

- .pkg[future]

- .pkg[clustermq] (HPC)

- Support for many HPC schedulers (SLURM, SGE, PBS, LSF) via package .pkg[clustermq]

---

### Learn more with these resources

.flex[
.w-40.ph4[
Drake

* [User Manual](https://ropenscilabs.github.io/drake-manual/)
* [Package Docs](https://ropensci.github.io/drake/)
* [ropensci/drake](https://github.com/ropensci/drake)
* [drake-faq](https://ropenscilabs.github.io/drake-manual/faq.html)
* [wlandau/drake-examples](https://github.com/wlandau/drake-examples)
* [wlandau/learndrake](https://github.com/wlandau/learndrake)
* [mlr-org/mlr3-learndrake](https://github.com/mlr-org/mlr3-learndrake)
]
.w-60.ph4[
Functions

* [Advanced R: Functions](https://adv-r.hadley.nz/functions.html)
* [Functions - Nice R Code](https://nicercode.github.io/guides/functions/)
* [Programming with R: Creating Functions](https://swcarpentry.github.io/r-novice-inflammation/02-func-R/)
]
]

.small[
**Icons** by [Github octicons](https://octicons.github.com/) and the following [Noun Project](https://thenounproject.com/search/?q=Report&i=180805) icon creators:
[Kirby Wu, TW](https://thenounproject.com/search/?q=json&i=966215),
[Iga](https://thenounproject.com/search/?q=document&i=2711779),
[Lil Squid](https://thenounproject.com/search/?q=report&i=149914),
[Wichai Wi](https://thenounproject.com/search/?q=results&i=2294590),
[Nick Kinling](https://thenounproject.com/search/?q=detour&i=788361).

**Built with** [rmarkdown](https://rmarkdown.rstudio.com), [xaringan](https://slides.yihui.name/xaringan), [xaringanthemer](https://pkg.garrickadenbuie.com/xaringanthemer), [remark.js](http://remarkjs.com/), [tachyons.css](http://tachyons.io/), [animate.css](https://daneden.github.io/animate.css/)
]

---
layout: false

## Personal FAQ (1/2)

.small[
+ What is the difference between `drake::make()` and `drake::r_make()`?

> `r_make()` runs in a fresh R session via package .pkg[callr] and sources the config before every run. No need to source the config yourself and then run `make(config)`. See also [drake-manual/safer-interactivity](https://ropenscilabs.github.io/drake-manual/projects.html#safer-interactivity).

+ How do I parallelize code within targets?

> By passing `prework = quote(future::plan(future.callr::callr, workers = <n>))` or a similar parallel plan to `drake_config()` in `_drake.R`. Do not use `future::plan()` within scripts/functions.

+ I have no idea what the status of my running computation is. Is there a way to see it?

> Yes, either use `drake::progress()`, `drake::finished()` or `drake::failed()`. Optionally make the output more verbose using `drake::progress() %>% print(n = 200)`.
]

---
layout: false

## Personal FAQ (2/2)

.small[
+ Everything in the drake manual is forcing me to use functions but I am used to scripts mainly.
What is better with functions?

> Project structure and organization is eminently important. A function-based workflow enhances reproducibility and leads to a more clean project structure. See [this discussion](https://github.com/ropensci/drake/issues/994) for more information.

+ Is there a convenient way to load targets quickly?

> Yes! With the installation of .pkg[drake] there is an addin called "load targets under cursor" that lets you load the R object under your cursor when its bound to a keyboard shortcut. Mine is bound to "CTRL + L".

+ What about other addins and keyboard shortcuts?

> Take a look into the "Addins" menu in RStudio for a list of avaiable addins. I have the followings addin/shorcut bindings: `r_vis_drake_graph()` -> "CTRL + Shift + V"; `r_outdated()` -> "CTRL + Shift + O"; "load target under cursor" -> "CTRL +L"

]

.drake-logo {
  background-image: url('assets/images/drake-logo.svg');
  background-size: cover;
  background-repeat: no-repeat;
}

.talk-meta {
  font-family: Overpass;
  position: absolute;
  text-align: left;
  bottom: 10px;
  left: 25px;
}

.talk-author {
  color: #444;
    font-weight: bold;
  font-family: "Work Sans";
  font-size: 1.5em;
  line-height: 1em;
}

.talk-date {
  color: #666;
  font-size: 1.25em;
  font-family: "Work Sans";
  line-height: 0;
}

.icon-huge {
  position: relative; 
  top: 35px;
}

.icon-medium {
  position: relative; 
  top: 35px;
  widht: 50%;
}

.cover-2-3 {
  left: 33%;
}

.cover-3 {
  left: 66%;
}
</style>