Setting up isolated project-libraries using {renv}

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# Setting up isolated project-libraries using {<code>renv</code>}
## <br>
### Catherine Blatter
### RRTM, 15.03.2022

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<div class="footer">Catherine Blatter | Setting up isolated project-libraries using {`renv`} | RRTM, 15.03.2022 </div>
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# Have you ever...

<br>

- written code that produced beautiful output until suddenly it didn't?

<br> 
- ran a statistical model that - out of the blue - throws a warning?

<br>

- copied code from a colleague that just does not work on your computer?

<br>

** <svg viewBox="0 0 448 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> Time-consuming and frustrating issue** *(typically after updating)*

<br> 
- Popular solution: **.mint[*"If there is one thing I have learnt in R is to never ever update anything!"*]**

.fn-r[*quote from and with permission of Lauriane*]

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# Goals of today's research flash

<br>

> Describe the internal setup and interrelations between R, RStudio, R packages and their versions

<br>

> Present a conceptual solution & technical framework designed to tackle the issue:  
-   Isolated project-libraries with {`renv`}

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#  R, RStudio and R packages

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#  R, RStudio and R packages

.fn-r[.reddark[Versions] to report in a publication]

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# R, RStudio and R packages

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# The R System library

- Directory.sup[1] where packages are **stored**.sup[2] and **looked up**.sup[3] for an analysis

.fn-r[.sup[1]use `.libPaths()` to check where, .sup[2]stored = `install.packages()`, .sup[3]looked up = `library()` ]

--
<br>
- Installation/update of a package == **removal** of a previous version  
   *e.g. update to* {`ggplot2`} 3.3.5 == <span style="text-decoration:line-through; color: var(--reddark);">2.3.9</span>

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# R package dependencies

- Packages can be **linked** to other packages (*dependent*): e.g. {`ggplot2`} has got 30 dependencies:
<img src='ggplot-dependency-graph.jpg' >

.fn-r[*Fig.source:* [RStudio](https://www.rstudio.com/blog/challenges-in-package-management/), February 2022]

- Installation/update of 1 package == updates **all dependencies** as well

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# What does this mean for an analysis?

.huge[Example]

- Explicit use of 3 packages (by `library()`):

```r
library(ggplot2) # powerful plotting library
library(lme4) # multi-level modelling
library(naniar) # dealing with missing values
```

- <svg viewBox="0 0 448 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> R implicitly uses 41 packages

.huge[Usual analysis]

- Explicit use of 10-15 packages

- .reddark[*Issue*]: (recommended) update <svg viewBox="0 0 448 512" style="height:1em;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> unintended consequence

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# The conceptual solution

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# The conceptual solution

> .mintdark[Isolated] project-libraries (*also called environments*)

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# The conceptual solution

> .mintdark[Isolated] project-libraries (*also called environments*)

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# Isolated libraries (environments)

--
<br>

- Standard practice in programming languages, e.g. Python

.fn-r[further info: https://environments.rstudio.com/, https://peps.python.org/pep-0405/]
--

- ...one of the main reasons that non-programmers do not proceed with Python

<br>
- Fundamentally different to 'usual' interaction with a computer:

- Imagine the need to define *how* to use MS Word before creating a new Word-document
 
<br>

- R user = academic researcher, often without any formal training in programming -  
  lack of knowledge on situation and solution

---

# The technical framework: {`renv`}

- R package designed to create **.mintdark[*r*]**eproducible **.mintdark[*env*]**ironments  
  by initiating isolated project-libraries

<br>

.fn-l[Kevin Ushey (2022). renv: Project Environments. R package version 0.15.2.]

<br>

- What do I see when using {`renv`}? 
  
  - a subfolder `renv` that contains the isolated library  
    (*useful on your computer*)  
  
  - a lockfile `renv.lock` where all versions are documented  
    (*useful for creating the same library on another computer*)

---

# Reflection & key points

- {`renv`} is not a uniform solution to computational reproducibility   
<br>

- Alternatives are available - require more technical know-how 
<br>

--
<br>

- {`renv`} offers a lightweight & manageable solution to

- setup and use multiple libraries across your computer 
    
  - easily document all versions and dependencies of packages
    
  - share your environment-setup with other collaborators

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# Thank you for your attention

<div>

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# Setup {`renv`}

Official documentation: https://rstudio.github.io/renv/articles/renv.html

1) Open the `.Rproj`-file of the desired analysis-folder

2) Call `install.packages("renv")`

3) Call `renv::init()`   
  > *this creates the subfolder and the `renv.lock`-file *
  
  > {`renv`} interacts with you in the console & prints what it does

4) Continue working as usual - if you need to install further packages, they are installed in the project-library

5) From time to time: call `renv::snapshot()` 
  
  > *adds all the packages used in this project to the `renv.lock`-file *

.fn-l[Setup tested with {`renv`} 0.15.2, R Version 4.1.3 on Mac OS X 12.2.1]
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# Alternatives

<br>

- https://annotater.liomys.mx/ - annotates the version or R packages used 
  in a script (*downside:* no dependencies, manual installation)

<br>

- https://github.com/MilesMcBain/capsule - mimics the lockfile, not the isolated library (*downside*: need to set-up the environment every time you work on the analysis)

<br>

- Setting up everything by hand with {`base`}-R

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# Why {`renv`} ?