session9.Rmd

---
title: "Creating targets-based scientific workflows"
subtitle: "Reproducible Scientific Workflows in R - Part 2"  
author: 
  - "Ernest Guevarra"
date: '2024-02-12'
output:
  xaringan::moon_reader:
    css: xaringan-themer.css
    nature:
      slideNumberFormat: "%current%"
      highlightStyle: github
      highlightLines: true
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---

```{r setup, include=FALSE}
options(htmltools.dir.version = FALSE)
knitr::opts_chunk$set(
  fig.width=9, fig.height=3.5, fig.retina=3,
  out.width = "100%",
  cache = FALSE,
  echo = TRUE,
  message = FALSE, 
  warning = FALSE,
  hiline = TRUE
)

if (!require(remotes)) install.packages("remotes")
if (!require(fontawesome)) remotes::install_github("rstudio/fontawesome")
if (!require(tweetrmd)) remotes::install_github("gadenbuie/tweetrmd")
if (!require(webshot2)) remotes::install_github("rstudio/webshot2")
```

```{r xaringan-themer, include=FALSE, warning=FALSE}
library(xaringanthemer)
style_mono_light(
  base_color = "#002147",
  title_slide_background_image = "",
  title_slide_background_size = "cover",
  header_font_google = google_font("Fira Sans"),
  text_font_google   = google_font("Fira Sans Condensed"),
  text_font_size = "1.2em",
  link_color = "#214700",
  header_h1_font_size = "50px",
  header_h2_font_size = "40px",
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  code_font_google   = google_font("Fira Mono"),
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  footnote_font_size = "0.5em"
)
```

# Outline

* Concepts on scientific workflows

* The `{targets}` package

* Practical session

---

class: inverse, center, middle

# Concepts on scientific workflows

---

class: inverse, center, middle

# Concept #1: Reproducibility, reproducibility, reproducibility!

---

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```{r tweet1, echo = FALSE, eval = FALSE}
tweetrmd::tweet_screenshot(
  tweet_url("kwbroman", "667735926915731457"),
  hide_media = TRUE,
  theme = "dark"
)
```

# Most important tool for Reproducible Research is the mindset, when starting, taht the end product will be reproducible.

[Keith Baggerly](http://odin.mdacc.tmc.edu/~kabaggerly/), via [@kwbroman](https://twitter.com/kwbrowman) [tweet](https://twitter.com/kwbroman/status/667735926915731457)

---

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# Concept #2: Organisation

---

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# File organization and naming are powerful weapons against chaos.

[@JennyBryan](https://twitter.com/jennybryan)

---

background-color: #FFFFFF
background-image: url(images/file_organisation.png)
background-size: 90%

---

class: inverse, center, middle

# Concept #3: DRY - Don't repeat yourself

---

class:: center, middle

# Don't repeat yourself. It's not only repetitive, it's redundant, and people have heard it before.

Lemony Snicket

---

background-color: #FFFFFF

```{r, echo = TRUE, eval = FALSE}
# Overlay maps of Niger and Nigeria to clean-up the map 
par(new=TRUE)
plot(nigeria, axes = FALSE, xlim = mapXLimits, ylim = mapYLimits, border = "white", col = "white")

par(new = TRUE)
plot(boundaries, axes = FALSE, xlim = mapXLimits, ylim=mapYLimits, lwd = 0.5, border = "black")

par(new = TRUE)
plot(n1, axes = FALSE, xlim = mapXLimits, ylim=mapYLimits, lwd = 0.25, col = "blue")

par(new = TRUE)
plot(n4, axes = FALSE, xlim = mapXLimits, ylim=mapYLimits, lwd = 0.25, col = "blue")

par(new = TRUE)
plot(n5, axes = FALSE, xlim = mapXLimits, ylim=mapYLimits, lwd = 0.25, col = "blue")

par(new = TRUE)
plot(n6, axes = FALSE, xlim = mapXLimits, ylim=mapYLimits, lwd = 0.25, col = "blue")

par(new = TRUE)
plot(n6.27, axes = FALSE, xlim = mapXLimits, ylim=mapYLimits, lwd = 0.25, col = "blue")

par(new = TRUE)
plot(n7, axes = FALSE, xlim = mapXLimits, ylim=mapYLimits, lwd = 0.25, col = "blue")

par(new = TRUE)
plot(n14, axes = FALSE, xlim = mapXLimits, ylim=mapYLimits, lwd = 0.25, col = "blue")
```

---

# Sisyphean loop

.pull-left[
<img src="https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Nekyia_Staatliche_Antikensammlungen_1494_n2.jpg/582px-Nekyia_Staatliche_Antikensammlungen_1494_n2.jpg" width="450px" style="vertical-align:middle" /> 
]

.pull-right[
1. Launch the code.
2. Wait while it runs.
3. Discover an issue.
4. Restart from scratch.
]

---

class: inverse, center, middle

# Concept #3: Frequency reduces difficulty

---

class: center, middle

```{r tweet2, echo = FALSE, eval = FALSE}
tweet_screenshot(
  tweet_url("JennyBryan", "1087795259872927744"),
  hide_media = TRUE,
  theme = "dark"
)
```

# If it hurts, do it more often.

[@martinfowler](https://twitter.com/martinfowler), via [@JennyBryan](https://twitter.com/JennyBryan) [tweet](https://twitter.com/JennyBryan/status/1087795259872927744)

---

# The `{targets}` package

.pull-left[
<img src="https://github.com/ropensci/targets/raw/main/man/figures/logo.png" width="400px" style="vertical-align:middle" />
]

.pull-right[
* a pipeline toolkit for Statistics and data science in R
* maintain a reproducible workflow without repeating yourself
* learns how your workflow fits together
* skips costly runtime for tasks that are already up-to-date
* runs only the necessary computation
* supports implicit parallel computing
* abstracts files as R objects
* shows tangible evidence that the results match the underlying code and data
]

---

# `{targets}` file organisation

.pull-left[
.center[![](images/targets_file_organisation.png)]
]

.pull-right[
* this is a typical file structure with user-defined components of any project-oriented workflow
* the `_targets.R` file, however, is special and specific to a `{targets}` workflow - it is the target script file
* the target script file should be in the project's root directory
]

---

# `{targets}` script file

.pull-left[
.center[![](images/target_script.png)]
]

.pull-right[
* Load the packages required (1)
* Load custom functions (1)
* Define individual targets - intermediate step of the workflow (2)
* End with a list of targets objects
]

---

background-color: #FFFFFF
background-image: url(images/workflow.png)
background-size: 60%

# `{targets}` workflow

---

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# Questions?

---

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# Practical session

## We will all continue to go through Exercise #1 in the [Practical R for Epidemiologists](https://practical-r.org/exercise1.html) book

---

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# Questions?

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# Thank you!

Slides can be viewed at https://oxford-ihtm.io/open-reproducible-science/session9.html

PDF version of slides can be downloaded at https://oxford-ihtm.io/open-reproducible-science/pdf/session9-reproducible-scientific-workflows.pdf

R scripts for slides available [here](https://github.com/OxfordIHTM/open-reproducible-science/blob/main/session9.Rmd)