Practical Artificial Intelligence for Medical Data Analyses with R

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# Practical **.orange[Artificial Intelligence] for **Medical Data Analyses** with **.orange[R]<br>Advanced

## **Efficient Reproducibility in R**<br>**.orange[A Journey from Patchworks to Projects]**

.orange[Biostatistics Month] 2025/05/14

[.orange[Corrado Lanera]](mailto:CorradoLanera@ubep.unipd.it) | [**Unit of Biostatistics, Epidemiology, and Public Health**](https://www.unipd-ubep.it/)
---
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<img src="img/profilo_CL.jpg" width="50%" />
# Find me at...

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[<svg aria-hidden="true" role="img" viewBox="0 0 496 512" style="height:1em;width:0.97em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M248,8C111.033,8,0,119.033,0,256S111.033,504,248,504,496,392.967,496,256,384.967,8,248,8ZM362.952,176.66c-3.732,39.215-19.881,134.378-28.1,178.3-3.476,18.584-10.322,24.816-16.948,25.425-14.4,1.326-25.338-9.517-39.287-18.661-21.827-14.308-34.158-23.215-55.346-37.177-24.485-16.135-8.612-25,5.342-39.5,3.652-3.793,67.107-61.51,68.335-66.746.153-.655.3-3.1-1.154-4.384s-3.59-.849-5.135-.5q-3.283.746-104.608,69.142-14.845,10.194-26.894,9.934c-8.855-.191-25.888-5.006-38.551-9.123-15.531-5.048-27.875-7.717-26.8-16.291q.84-6.7,18.45-13.7,108.446-47.248,144.628-62.3c68.872-28.647,83.183-33.623,92.511-33.789,2.052-.034,6.639.474,9.61,2.885a10.452,10.452,0,0,1,3.53,6.716A43.765,43.765,0,0,1,362.952,176.66Z"/></svg>](https://telegram.me/CorradoLanera)
**@CorradoLanera**

---

# How to .orange[follow] the workshops

#### Resources:

- .orange[Slides]: [https://corradolanera.github.io/ws-reproj/](https://corradolanera.github.io/ws-reproj/#1)

#### Coding:

1. If you like it **.orange[local]**: code **on your system**

- At any stage you can:<br>
  `usethis::use_course("CorradoLanera/<stage name>")`:
  - `<stage name>`s:
      - `bare.proj.01`
      - `foldered.02`
      - `changes.dry.03`
      - `structure.04`
      - `private.05`
      - `targets.06`

3. If you like it **.orange[remote]**: code (free of charge) **on Posit Cloud Workspace**:<br> [https://bit.ly/positcloud-ws-reproj](https://bit.ly/positcloud-ws-reproj)

<small>
.right[Whole .orange[project]: [https://github.com/CorradoLanera/ws-reproj](https://github.com/CorradoLanera/ws-reproj)
]
</small>

---
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# .orange[Outline]

- **.underline[Intro]**: definition of **.orange[AS]**AP, the anatomy of a **.orange[patchwork]**

- **.underline[Program]**: start **.orange[slow]**, do not waste **.orange[_time_]**

- **.underline[Step-by-step]**:
  - Setup an **R**/**RStudio** project: git, `{renv}`, and `{here}`.
  - Are you ready to **.orange[share]** and **.orange[collaborate]**? (welcome **GitHub**)
  - What about **.orange[folders]**?
  - What about **.orange[changes]**?
      + Data / **objects** (versions?)
      + Code / **Functions** (isolation, abstractions?)
      + **Bugs** (tests?)
  - Please, give me some **.orange[structure]**! The magic of the `DESCRIPTION` file
  - Oops! I have internal (**.orange[private]**) data for my (**.orange[public]**) project!
  - working with `{targets}`

- **.underline[All-in-one template]**: welcome [**`{laims.analysis}`**](https://github.com/UBESP-DCTV/laims.analysis)

- **.underline[Outro]**: definition of AS**.orange[AP]**, the anatomy of a **.orange[project]**

---
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# Intro: **.orange[AS]AP**

**Disclaimer**: ALL of the following is derived by personal experience, **.orange[failures]**, and lessons learnt in the last 11 years at UBEP as a biostatistician and data scientist, coding in R quite every single night 🌉.

---

# .orange[AS]AP

What usually happens...
.orange[As Soon] As Possible

- get the raw-data, manipulate them to .orange[directly fix easy-bugs]
- .orange[do the analysis]
--

- get updated data, overwrite previous, directly manipulate them to fix easy bugs (...some more **added**? some of them **forgotten**?)
- update (overwrite) the analysis
- add a copy **`analysis_v2.R`** of the script (just to be sure)
--

- find a bug, fix it and save third **`analysis_v2_ok.R`** version of analysis
- Searching for a faster execution, add an additional **`analysis_v2_ok_faster.R`** faster version (surely identical, console-checked!) to save full 15 seconds (after 2h of try-and-see coding experiments)
--

- > **send** the (hopefully) correct report 3 minutes **.underline[before]** **.orange[_by yesterday_!!!]**
--

- > get a .orange[**BUG** reported by the **BOSS**!] (... it's a **.orange[_B😨GSS_]** 🤦😭)
--

- But now we can not give up: produce a new version night-time (**.orange[without falling asleep]**)
- **.orange[AS]AP.orange[AS]AP.orange[AS]AP.orange[AS]AP**
--

.center[_... many new-files, new-versions, new-names, new-plots, new-fixes later..._]
--
<br>
.center[**SENT!**]

---
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...

**.orange[_B😨GSS_]** 🤦😭

The project is then passed to a new analyst

... **.orange[AS]AP.orange[AS]AP.orange[AS]AP.orange[AS]AP** ...<br>**.orange[ASAY]** (**.orange[A]s .orange[S]oon .orange[A]s .orange[Y]ESTERDAY**)

But they can't understand **ANYTHING** of the work already done...!

So they prefer to **RESTART** from scratch<br>(adding sub-folders, sub-files, sub-version, sub-plots, sub-fixes to the project!)

<br>

**.orange[DONE!]**, and before dinner! 😎😎😎

...

**.orange[_B😱GSS_]** 🤦😭

---
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#### BOSS:

"I would have spend less time if did it by myself!"

"Ok, I will do it!"

"mmm 🤔 ... which are the original/last data?!" ...

...

😨🤦😭

.orange[**THE END.**]

---
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Go Tidyverse (but...)

[tidyverse.tidyverse.org/articles/paper.html](https://tidyverse.tidyverse.org/articles/paper.html)

---
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---
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---
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# .orange[Don't waste **time**]

---

# .orange[Whose] **time** <small><small>you don't have to waste</small></small>?!

- Your time?!

- My time?!

- Boss' time?!

<br>

**.center[.orange[Project time] = ]**

`$$\sum_{i = 1}^{\#\ correct\ version!}\left(\sum_{p\in team}\sum_{t\in tasks} time_i(by = p, for = t, include\_breaks = TRUE)\right)$$`

--
<br>
<br>

.center[
**AS.orange[AP]** `$:= argmin(Project\ time)$`

(**.orange[CL] personal** definition!)

]

---
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# .orange[Start **slow**]

---

# **If** you need it, .orange[do it]!

- Don't do things you don't need > **you will .orange[waste] time**!

- Be prepared to add features/components > **you will .orange[save] time**!

In the following step-by-step project development, we aim to show how to add features accordingly to sequential requirements.

- change **.orange[the order]** at your convenience
 - change **.orange[the tools]** at your convenience (or as they will improve/change)
 - don't implement stages you don't need (until you need them...!)

> This won't be a workshop about the tools we will show. It will be a workshop about the processes, the structures, and the motivations in using them.

---
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# **.orange[Step**-by-**step]**

---

# Create a project

We start from just a bare project

> create new RStudio project (including git and {renv} ticks)

> `usethis::use_course("CorradoLanera/bare.proj.01")`

> Posit Cloud: 01 - Bare project

- let's talk about `{here}` (and a `00-setup.R` script)

- let's talk about RStudio projects and `{renv}`

- let's talk about git

---

# Start some analysis

- analysis.R

- report.rmd

> Where do we put input data and output files? How do we reach them?

---
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.orange[Live session]

Start from:

`usethis::use_course("CorradoLanera/bare.proj.01")`

Posit Cloud: 01 - Bare project

---

# Changes?

.orange[DRY]: Do Not Repeat Yourself!

> What if some input/output file changed?

> What about repeated code?

> What if you find some bugs?

---
class: inverse, middle, center, hide-count

.orange[Live session]

Start from:

`usethis::use_course("CorradoLanera/foldered.02")`

Posit Cloud: 02 - Foldered

---

# All this code .orange[together] is really really HORRIBLE and .orange[confusing]!

> what about a clear structure?

> what about error-prone repeated code?

---
class: inverse, middle, center, hide-count

.orange[Live session]

Start from:

`usethis::use_course("CorradoLanera/changes.dry.03")`

Posit Cloud: 03 - Changes & DRY

---

# Data Protection...

> What if I have private data (in a centralized folder, and visible by colleagues only)?

> What if I would like to share the code (but not the data)?

---
class: inverse, middle, center, hide-count

.orange[Live session]

Start from:

`usethis::use_course("CorradoLanera/structure.04")`

Posit Cloud: 04 - structure

---
# Clear pipeline and automation

+ automatic discovering and saving of intermediate/final computed objects

+ automatic discovering of functions' and objects' dependencies
  
+ automatic update of all the outdated dependencies for updates (and only those)

> let's talk about `{targets}`:

---
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.orange[Live session]

Start from:

`usethis::use_course("CorradoLanera/private.05")`

Posit Cloud: 05 - private

---
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.orange[Final result]

Take as reference:

`usethis::use_course("CorradoLanera/targets.06")`

Posit Cloud: 06 - targets

---
# A comprehensive .orange[template]

[https://github.com/UBESP-DCTV/laims.analysis](https://github.com/UBESP-DCTV/laims.analysis) <small>- _You will need a (free) GitHub account_</small>

All explored features, plus:

- an **.orange[`explore.R`]** script specifically designed to host completely **unruled** exploratory code, i.e., ugly, un-styled, un-commented, un-usual, un-working, temporary code (which can be easily deleted time-after-time, maintaining their evidence and lesson-learnt thanks to git!)

- **.orange[`targets` objects directly usable]**: on computations, reports, and tests (maintaining their privacy if shared storage system is implemented)

- a **.orange[qmd report template]**: including logos, authorship with OrcID, citations, marginal notes, custom size for figures, ... (and more as powered by Quarto<sup>*</sup>)
- **.orange[test coverage]**: _**Percentage** of "**do-something**" code tested._
- **.orange[lint checks]**: _How **good** is your code "**statically**"?_
- **.orange[GitHub Action]**: _**automatic** execution of tests/lint/CRAN checks at **every push**!_
- **.orange[R-package structure]**: _make functions available as a **ready-to-use** r-package._

<small>
.footnote[[*] We didn't talk about Quarto today, if interested see: [https://quarto.org/](https://quarto.org/), and [https://books.ropensci.org/targets/literate-programming.html#quarto-targets](https://books.ropensci.org/targets/literate-programming.html#quarto-targets).]
</small>

---
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# Outro: **AS.orange[AP]**

---

# AS.orange[AP]

As Soon .orange[As Possible]

- Start .orange[easy] and .orange[slow] but keep your eyes on your final results!

- If your results are not correct, all your _high-speed_ goes down to zero!

- **Bugs will be there**. For sure! <br>The greatest error you can do is to assume your code is going to be error-free

- Do/check .orange[only] what you really need to do/check

- Enforce .orange[standards] and a coherent .orange[style]

- Use **templates**:   .orange[Conventions] are all about making repetitive stuff **.orange[invisible]**!

---

# Technical recap

- Track
  + changes (git)
  + environment (`{renv}`)
- Use portable paths (`{here}`)

- Use **standard** folder and files (keep structure .orange[invisible])

- .orange[Refactor] your code to extract logic by progressive layers of abstraction  **DRY**

- Use `DESCRIPTION` to activate R/RStudio super-powers (functions, tests, ...)

- Environmental vars (from function call, `.gitignore`d) for private locations

- Let `{targets}` manage project dependencies, efficient runs, and efficient storage of your objects

- Use GitHub (or similar) to share code (not data  nor secrets!) with collaborators, journals, public, ...!

.center[**If you know you need all of above, use templates! Like .orange[`laims.analysis`].**]

.center[
Go for AS**.orange[AP]** `$:= argmin(Project\ time)$` !!
]

---
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.bg-washed-green.b--dark-green.ba.bw2.br3.shadow-5.ph4.mt5[
.left[
_**.orange[The best]** is the enemy of the good!_ <br> .center[... and ...] <br> .right[_The only way to go fast is to **.orange[go well!]**_]
]

.tr[
— Voltaire + Uncle Bob
]
]

# Thank .orange[you] for the attention!

Slides: [https://CorradoLanera.github.io/ws-reproj](https://CorradoLanera.github.io/ws-reproj/#1)

Repo: [https://github.com/CorradoLanera/ws-reproj](https://github.com/CorradoLanera/ws-reproj)

<br>

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[<svg aria-hidden="true" role="img" viewBox="0 0 496 512" style="height:1em;width:0.97em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M248,8C111.033,8,0,119.033,0,256S111.033,504,248,504,496,392.967,496,256,384.967,8,248,8ZM362.952,176.66c-3.732,39.215-19.881,134.378-28.1,178.3-3.476,18.584-10.322,24.816-16.948,25.425-14.4,1.326-25.338-9.517-39.287-18.661-21.827-14.308-34.158-23.215-55.346-37.177-24.485-16.135-8.612-25,5.342-39.5,3.652-3.793,67.107-61.51,68.335-66.746.153-.655.3-3.1-1.154-4.384s-3.59-.849-5.135-.5q-3.283.746-104.608,69.142-14.845,10.194-26.894,9.934c-8.855-.191-25.888-5.006-38.551-9.123-15.531-5.048-27.875-7.717-26.8-16.291q.84-6.7,18.45-13.7,108.446-47.248,144.628-62.3c68.872-28.647,83.183-33.623,92.511-33.789,2.052-.034,6.639.474,9.61,2.885a10.452,10.452,0,0,1,3.53,6.716A43.765,43.765,0,0,1,362.952,176.66Z"/></svg>](https://telegram.me/CorradoLanera)
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