Put R in Production

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<a href="https://github.com/edgar-treischl/Workshop_reproducibleR" class="github-corner" aria-label="View source on GitHub"><svg width="80" height="80" viewBox="0 0 250 250" style="fill:#151513; color:#fff; position: absolute; top: 0; border: 0; right: 0;" aria-hidden="true"><path d="M0,0 L115,115 L130,115 L142,142 L250,250 L250,0 Z"/><path d="M128.3,109.0 C113.8,99.7 119.0,89.6 119.0,89.6 C122.0,82.7 120.5,78.6 120.5,78.6 C119.2,72.0 123.4,76.3 123.4,76.3 C127.3,80.9 125.5,87.3 125.5,87.3 C122.9,97.6 130.6,101.9 134.4,103.2" fill="currentColor" style="transform-origin: 130px 106px;" class="octo-arm"/><path d="M115.0,115.0 C114.9,115.1 118.7,116.5 119.8,115.4 L133.7,101.6 C136.9,99.2 139.9,98.4 142.2,98.6 C133.8,88.0 127.5,74.4 143.8,58.0 C148.5,53.4 154.0,51.2 159.7,51.0 C160.3,49.4 163.2,43.6 171.4,40.1 C171.4,40.1 176.1,42.5 178.8,56.2 C183.1,58.6 187.2,61.8 190.9,65.4 C194.5,69.0 197.7,73.2 200.1,77.6 C213.8,80.2 216.3,84.9 216.3,84.9 C212.7,93.1 206.9,96.0 205.4,96.6 C205.1,102.4 203.0,107.8 198.3,112.5 C181.9,128.9 168.3,122.5 157.7,114.1 C157.9,116.9 156.7,120.9 152.7,124.9 L141.0,136.5 C139.8,137.7 141.6,141.9 141.8,141.8 Z" fill="currentColor" class="octo-body"/></svg></a><style>.github-corner:hover .octo-arm{animation:octocat-wave 560ms ease-in-out}@keyframes octocat-wave{0%,100%{transform:rotate(0)}20%,60%{transform:rotate(-25deg)}40%,80%{transform:rotate(10deg)}}@media (max-width:500px){.github-corner:hover .octo-arm{animation:none}.github-corner .octo-arm{animation:octocat-wave 560ms ease-in-out}}</style>

<h1 style="font-family: 'Bangers', sans-serif; font-size: 65px; color: #ffff;">Put R in</h1>
<h1 style="font-family: 'Bangers', sans-serif; font-size: 65px; color: #ffff;">Production</h1>
<br/>
<p><a href="http://www.edgar-treischl.de" target="_blank" style="font-size: 35px; color: #ffff;">Edgar J. Treischl</a></p>

<br/>
.white[Last update: 2025-05-20]
<br/>
<h4 style = "color:#ffff; text-align: right;">Press ⭕ or ➡️</h4>

<div class="remark-footer"><a href="https://unsplash.com/de/@sajjadahmadi" target="_blank" style="color: gray;">Images: Sajjad Ahmadi</a></div>

---
## Agenda

.pull-left[

### 01 Develop 💭
### 02 Build 🚧
### 03 Document 📜
### 04 Deploy 🏃‍♀️

]

.pull-right[

]

---

class: middle, center, inverse

## Let's face the truth ...

---
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background-size: cover
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## .white[... develop, but get rid of bad habits first <br> 😄]

<div class="remark-footer"><a href="https://giphy.com/gifs/moodman-batman-smack-smacked-Qumf2QovTD4QxHPjy5" target="_blank" style="color: white;">Images source: MOODMAN</a></div>

---
## 01: Start with a clean slate and restart R

.pull-left[

- Do not save the workspace and do not load the workspace from an `.Rdata` file (Based on Bryan et al. 2021).

### The rm approach 🔫

- `rm(list = ls())` deletes user-created objects from the global workspace.

- **But**: The script may break due to hidden dependencies on things you ran in this R process before you executed: Attached packages are not detached, changed options are not restored, working directory is untouched!

]

.pull-right[
<figure>
    <img src="https://rstats.wtf/img/rstudio-workspace.png" style="width: 100%"/>
</figure>
]

---

## Don't Go Places Where You Don't Belong ...

---

## 01: Fix paths with the here package

#### Abandon absolute paths, they will break anyway ⚡

``` r
# Don't:
readr::read_csv("~/Documents/Berichte/orig/104_data.csv")
```

```
## Error: '~/Documents/Berichte/orig/104_data.csv' does not exist.
```

#### Ceate a project and use the `here` package:

``` r
# Here returns the path to the project
here::here()
```

```
## [1] "/Users/edgar/Documents/GitHub/Workshop_reproducibleR"
```

``` r
# Create a path to the file
here::here("data", "descriptive_title.csv")
```

```
## [1] "/Users/edgar/Documents/GitHub/Workshop_reproducibleR/data/descriptive_title.csv"
```

---
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## 01: R vs. Rmd

### 🖐️ Code lives in R, Code and Text in Rmd files

If you need to create a document from a source code, run:

``` r
#spin converts an R script to an Rmd file
knitr::spin("script.R")
```

- Roxygen comments will be treated as text (more about that later)
- Add yaml header to the script to control the output

If you need to extract the code from an Rmd file, run:

``` r
#Extracts R code chunks from Rmd files
knitr::purl()
```

- Adjust the level of extraction with the `documentation` parameter (e.g., code only)
- Set `purl = FALSE` to avoid the extraction of code chunks (see Xie 2024)

---
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# .red[Keep your version under control]

<div class="remark-footer"><a href="https://giphy.com/gifs/love-batman-heart-10YHLXWAUpGUZq" target="_blank" style="color: black;">Source: adeanormal</a></div>

---
background-image: url(https://github.githubassets.com/assets/GitHub-Mark-ea2971cee799.png)
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## 01: Git(Hub)

### Track changes over time

---
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## 01: Develop With Style(r)

.pull-left[

<div class="info-box">
  <i>🦜️️</i> "styler formats your code according to the tidyverse style guide (https://style.tidyverse.org) (or your custom style guide) so you can direct your attention to the content of your code" (Müller and Walthert 2024).
</div>

#### ⚡ Easily apply tidyverse style or adjust and and apply your own style guide

]

.pull-right[

``` r
styler::style_text(
  "myFunction<-function( x,y){
  if(sum( x , y )==10){
    print( 'Sum is correct!' )
  }
}"
)
```

```
## myFunction <- function(x, y) {
##   if (sum(x, y) == 10) {
##     print("Sum is correct!")
##   }
## }
```

]

#### There a goodies ❤️ if you develop an R package:

``` r
#Stlye your package code, but automate via GitHub Actions
styler::style_pkg()
```

---
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## 01: Lintr

.pull-left[

<div class="info-box">
  <i>🦜️</i>"lintr provides static code analysis for R. It checks for adherence to a given style, identifying syntax errors and possible semantic issues, then reports them to you so you can take action" (Hester et al. 2024).
</div>

]

.pull-right[

``` r
lintr::lint(text = 'myFunction <- function(x, y) {
  if (sum(x, y) == 10) {
    print("Sum is correct!")
  }
}')
```

```
## <text>:1:1: style: [object_name_linter] Variable and function name style should match snake_case or symbols.
## myFunction <- function(x, y) {
## ^~~~~~~~~~
```

]

There are even more goodies 🦹 if you develop an R package:

``` r
#lintr::lint_dir(path = "R")
lintr::lint_package()
```

---
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## .white[Let's build ... 🦹]

<div class="remark-footer"><a href="https://gifer.com/de/8rTu" target="_blank" style="color: black;">Source: Mark Hamill</a></div>

---
## 02: R Packages

### I will not create something like ggplot2, so why should I create a package anyway? 😜

.pull-left[

- *Reusability and Distribution*: Make sure everything needed to run is available. Plus: simplifies version control, dependency management, and installation.
- *Organization and Maintainability*: A package encourages a clean and organized code, making it easier to maintain, update, and extend over time.

- *Documentation*: A package allows to include automatic documentation (help files, website, vignettes) , making it much easier for others - and the future yourself - to understand how it works.

]

.pull-right[
<figure>
    <a href="https://r-pkgs.org" target="_blank"><img src="https://r-pkgs.org/images/cover-2e-small.png" alt="www.edgar-treischl.de" width="65%"/>
</figure>
]

---
## 02: devtools does the heavy lifting 🏋️

<div class="info-box">
  <i>🦜</i> "The aim of devtools is to make package development easier by providing R functions that simplify and expedite common tasks. R Packages is a book based around this workflow." (Wickham et al. 2022)
</div>

.pull-left[

]

.pull-right[
<figure>
    <a href="https://devtools.r-lib.org" target="_blank"><img src="https://devtools.r-lib.org/logo.svg" alt="www.edgar-treischl.de" width="55%" align="center"/>
</figure>
]

---
## 02: usethis

<div class="info-box">
  <i>🦜</i> "usethis is a workflow package: it automates repetitive tasks that arise during project setup and development, both for R packages and non-package projects." (Wickham et al. 2022)
</div>

.pull-left[

``` r
#Create a new package
usethis::create_package("path/to/package")
```

``` r
#Add a package in the DESCRIPTION file
usethis::use_package("ggplot2")
```

``` r
#Add a readme file
usethis::use_readme_rmd()
```

]

.pull-right[
<figure>
    <a href="https://usethis.r-lib.org/" target="_blank"><img src="https://usethis.r-lib.org/logo.png" alt="www.edgar-treischl.de" width="55%" align="center"/>
</figure>
]

---
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## 02: Github Actions

.pull-left[

Continuous Integration/Continuous Deployment:

1. *Reliability via Automated Testing*: We can automatically run tests on every commit, ensuring that code changes don't break functionality.

2. *Consistent Environments*: CI/CD pipelines define reproducible environments, ensuring that the code runs the same way on every machine, regardless the local setup.

3. *Effortless Deployment*: With GitHub Actions, you can automate the deployment of R Markdown reports, Shiny apps, R packages, and so on.

]

.pull-right[

```yaml
# Workflow from: https://github.com/r-lib/actions/tree/v2/examples

on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: R-CMD-check

jobs:
  R-CMD-check:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes
    steps:
      - uses: actions/checkout@v3

...
```

]

---
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## 02: Github Actions and usethis

Usethis has predefined workflows for:

``` r
usethis::use_github_action()

# Which action do you want to add? (0 to exit)
# (See <https://github.com/r-lib/actions/tree/v2/examples> for other options) 
# 
# 1: check-standard: Run `R CMD check` on Linux, macOS, and Windows
# 2: test-coverage: Compute test coverage and report to https://about.codecov.io
# 3: pr-commands: Add /document and /style commands for pull requests
```

---
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# .black[... but don't forget to test 👻]

<div class="remark-footer"><a href="https://gifer.com/de/8Bx3" target="_blank" style="color: black;">Source: Gifer</a></div>

---
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## 02: testthat

<br/>

<div class="info-box">
  <i>🦜</i> "Testing your code can be painful and tedious, but it greatly increases the quality of your code. testthat tries to make testing as fun as possible, so that you get a visceral satisfaction from writing tests. Testing should be addictive, so you do it all the time. (Wickham 2011)"
</div>

<br/>

.pull-left[

``` r
#Set up the test infrastructure
# And build a test
usethis::use_test("name")
```

]

.pull-right[

]

---
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## 02: covr

.panelset[

.panel[.panel-name[Test Coverage]

.pull-left[

<div class="info-box">
  <i>🦜️</i>"Track test coverage for your R package and view reports locally or (optionally) upload the results to codecov or coveralls. (Hester 2023)"
</div>

``` r
# Inspect the test coverage
covr::report()
```

]
.pull-right[

]

.panel[.panel-name[Tracked Source]
 <img src="images/covr.png" style="width: 90%"/>
]

]

---
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background-size: cover
class: bottom, center

## .red[Documentation]

<div class="remark-footer"><a href="https://www.sarah-johnson.com/personal-art" target="_blank" style="color: black;">Source: Sarah Johnson</a></div>

---
background-image: url(https://roxygen2.r-lib.org/logo.png)
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background-size: 8%
## 03 Document: roxygen2

.pull-left[

### Describe your functions and ...

<div class="info-box">
  <i>🦜️</i> "... roxygen2 will process your source code and comments to automatically generate .Rd files in man/, NAMESPACE, and, if needed, the Collate field in DESCRIPTION.". (Wickham and Csárdi 2024)
</div>

- Help files for your functions will be available

- The pkgdown package will use the roxygen2 comments to create a website for your package

]

.pull-right[

``` r
#' Function title
#' 
#' @description What does this `add` function.
#' 
#' @param x Function parameter.
#' @param y Function parameter.
#'
#' @return A number.
#'
#' @examples
#' add(1, 1)

#' @export
add <- function(x, y) {
  x + y
}
```

]

---

## 03 Document: pkgdown

.pull-left[

<div class="info-box">
  <i>🦜️</i> "The goal of pkgdown is to make it easy to make an elegant and useful package website with a minimum of work. You can get a basic website up and running in just a couple of minutes. If you’re using GitHub, we recommend setting up pkgdown and GitHub actions to automatically build and publish your site". (Wickham et al. 2024)
</div>

]

.pull-right[
<figure>
    <a href="https://pkgdown.r-lib.org" target="_blank"><img src="https://pkgdown.r-lib.org/logo.png" alt="https://pkgdown.r-lib.org" width="50%" align="center"/>
</figure>
]

<br>

---
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## 03 Document: pkgdown
<br>
<div style="position:relative; padding-bottom:56.25%; height:0; overflow:hidden; max-width:97%;">
  <iframe src="https://pkgdown.r-lib.org" width="500" height="315" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen style="position:absolute; top:0; left:0; width:100%; height:100%;"></iframe>
</div>

---
background-image: url(https://pkgdown.r-lib.org/logo.png)
background-position: 90% 5%
background-size: 8%

## 03 Document: pkgdown

### Create a pkgdown website via:

.pull-left[

``` r
#usethis creates config file: => _pkgdown.yml config file
usethis::use_pkgdown()

#Build the website via:
pkgdown::build_site()
```

### 🚀 via GitHub Actions:

``` r
#Add corresponding GHA to deploy each time you push to GitHub
usethis::use_pkgdown_github_pages()
```

]

.pull-right[

```yaml
# _pkgdown.yml
url: https://edgar-treischl.github.io/ProjectX/
template:
  bootstrap: 5
  bootswatch: litera
  bslib:
    base_font: {google: "Solway"}
    heading_font: {google: "Solway"}
navbar:
...
```

]

---
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background-size: contain
class: bottom, center

<br>
## .white[Deploy]

<div class="remark-footer"><a href="https://giphy.com/gifs/batman-robin-laundry-l1J9JOEZqVI4JFEk0" target="_blank" style="color: black;">Source: Threadless</a></div>

---
## 04: renv

<div class="info-box">
  <i>🦜</i> "The renv package helps you create reproducible environments for your R projects. Use renv to make your R projects more isolated, portable and reproducible" (Ushey and Wickham 2024).
</div>

.pull-left[

- Isolated: Installing a new or updated package for one project won’t break your other projects, and vice versa.

- Portable: Easily transport your projects from one computer to another, even across different platforms.

- Reproducible: renv records the exact package versions you depend on, and ensures those exact versions are the ones that get installed." (Ushey and Wickham)

]

.pull-right[
<figure>
    <a href="https://rstudio.github.io/renv/index.html" target="_blank"><img src="https://rstudio.github.io/renv/logo.svg" alt="The renv package" width="65%"/>
</figure>
]

---
background-image: url(https://rstudio.github.io/renv/logo.svg)
background-position: 90% 5%
background-size: 8%

## 04: renv

.pull-left[

- Use `renv::init()` to initiate a new project:
  - Gives you the power of isolation because it creates a project library 
  - Creates a .Rprofile file to load the renv library as long as renv is active
  - The package creates a renv.lock with metadata about every project package so that it can be installed on a new machine

- Use `renv::snapshot()` to create a snapshot of the project environment

- Use `renv::restore()` to restore the project environment

]

.pull-right[

]

---
## 04: renv lockfile

```shell
  "R": {
    "Version": "4.4.1",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://cloud.r-project.org"
      }
    ]
  },
  "Packages": {
    "markdown": {
      "Package": "markdown",
      "Version": "1.0",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "4584a57f565dd7987d59dda3a02cfb41"}
    }
```

---
## 04: Docker

.pull-left[

Create, deploy, and run applications in containers:

- Container: A standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another.

- Dockerfile: A text document that contains all the commands a user could call on the command line to assemble an image.

- Rocker: A project that provides different Docker images for R. Those bundles include the OS, R, (RStudio), and packages.

]

.pull-right[

]

---
background-image: url(https://rocker-project.org/img/rocker.png)
background-position: 90% 5%
background-size: 8%

## 04: Docker and Rocker

<div class="info-box"><i>🦜</i> The Rocker Project provides a collection of (Linux) containers suited for different needs. Find a base image to extend or images with popular software and optimized libraries pre-installed. (Rocker website) </div>

```shell
# Use a base R image from rocker project (official R Docker image)
FROM rocker/r-ver:4.4.1

# Set a working directory in the container
WORKDIR /app

# Copy a simple R script into the container
COPY hello.R .

# Install necessary R packages (e.g., ggplot2)
RUN R -e "install.packages(c('ggplot2'), repos='https://cloud.r-project.org/')"

# Set the entry point to run the R script
ENTRYPOINT ["Rscript", "hello.R"]
  
```

---
## 04: sessioninfo

``` r
mysession <- sessioninfo::session_info()
mysession$platform
```

```
##  setting  value
##  version  R version 4.4.2 (2024-10-31)
##  os       macOS Sequoia 15.4.1
##  system   aarch64, darwin20
##  ui       X11
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       Europe/Berlin
##  date     2025-05-20
##  pandoc   3.4 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
##  quarto   1.6.39 @ /usr/local/bin/quarto
```

Set the parameter: `to_file = "session.log"`  to export a log file

---
## 04: sessioninfo

``` r
sessioninfo::session_info(info = "external")
```

```bash
═ Session info ═══════════════════════════════════════════════════════════════
─ External software ──────────────────────────────────────────────────────────
 setting        value
 cairo          1.17.6
 cairoFT
 pango          1.50.14
 png            1.6.40
 jpeg           9.5
 tiff           LIBTIFF, Version 4.5.0
 tcl            8.6.13
 curl           8.7.1
 ...
──────────────────────────────────────────────────────────────────────────────

```

---
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## Thank you for your attention!

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## Licence

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