Introduction

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# Introduction

## Data processing with the tidyverse

.center[<img src="img/00/logo-rworkshop.png" width="100px"/>]

### A. Ginolhac | rworkshop | 2021-09-08

---
class: middle

# Good morning!

### What you can do now:

.pull-left[

#### Check the material at the main site

.Large[https://rtidyverse2021.leibniz-psychology.org/]

#### Info and schedule

.Large[https://leibniz-psychology.org/rtidyverse2021/]

].pull-right[

#### Check your install

.large[https://rtidyverse2021.leibniz-psychology.org/install_tutorial.html]

]

---

# Overview

.large[
This 3-day-course provides an introduction to the **tidyverse**, a <svg aria-hidden="true" role="img" viewBox="0 0 581 512" style="height:30px;width:34.04px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:steelblue;overflow:visible;position:relative;"><path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"/></svg> dialect.

- Focusing on loading and cleaning data for exploratory visualizations
- Speeding data manipulation is the mission of this course
- This workshop is composed of 30 hours:
]

.flex[
.w-50.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mr1[
.large[.gbox[Lectures]]
 
- ~ 8 hours
- available online (<svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:25px;width:18.75px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M0 32l34.9 395.8L191.5 480l157.6-52.2L384 32H0zm308.2 127.9H124.4l4.1 49.4h175.6l-13.6 148.4-97.9 27v.3h-1.1l-98.7-27.3-6-75.8h47.7L138 320l53.5 14.5 53.7-14.5 6-62.2H84.3L71.5 112.2h241.1l-4.4 47.7z"/></svg> / <svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:25px;width:18.75px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M181.9 256.1c-5-16-4.9-46.9-2-46.9 8.4 0 7.6 36.9 2 46.9zm-1.7 47.2c-7.7 20.2-17.3 43.3-28.4 62.7 18.3-7 39-17.2 62.9-21.9-12.7-9.6-24.9-23.4-34.5-40.8zM86.1 428.1c0 .8 13.2-5.4 34.9-40.2-6.7 6.3-29.1 24.5-34.9 40.2zM248 160h136v328c0 13.3-10.7 24-24 24H24c-13.3 0-24-10.7-24-24V24C0 10.7 10.7 0 24 0h200v136c0 13.2 10.8 24 24 24zm-8 171.8c-20-12.2-33.3-29-42.7-53.8 4.5-18.5 11.6-46.6 6.2-64.2-4.7-29.4-42.4-26.5-47.8-6.8-5 18.3-.4 44.1 8.1 77-11.6 27.6-28.7 64.6-40.8 85.8-.1 0-.1.1-.2.1-27.1 13.9-73.6 44.5-54.5 68 5.6 6.9 16 10 21.5 10 17.9 0 35.7-18 61.1-61.8 25.8-8.5 54.1-19.1 79-23.2 21.7 11.8 47.1 19.5 64 19.5 29.2 0 31.2-32 19.7-43.4-13.9-13.6-54.3-9.7-73.6-7.2zM377 105L279 7c-4.5-4.5-10.6-7-17-7h-6v128h128v-6.1c0-6.3-2.5-12.4-7-16.9zm-74.1 255.3c4.1-2.7-2.5-11.9-42.8-9 37.1 15.8 42.8 9 42.8 9z"/></svg> )
- live **exercises** included
]

.w-50.bg-washed-blue.b--blue.ba.bw2.br3.shadow-5.ph3.ml1[
.large[.bbox[Practicals]]

- ~ 15 hours
- Using your own laptop
- Supplementary exercises if needed
]
]

---
class: vs1

# Speakers

.center[![](img/intro_2speakers.png)]

---

# Learning objectives

.flex[
.w-50.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mt3.ml6[
.large[.gbox[You will learn]]

.float-img[![](img/00/kt.png)]

.Large[
- <svg aria-hidden="true" role="img" viewBox="0 0 581 512" style="height:35px;width:39.72px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:steelblue;overflow:visible;position:relative;"><path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"/></svg> specificity
    + community
    + package ecosystem
    + vectorization
- opinionated tidyverse
- Rstudio layout
- basic data types (recap)
- basic data structures (recap)
]
]
]

---

# What is R?

.Large[
<svg aria-hidden="true" role="img" viewBox="0 0 581 512" style="height:35px;width:39.72px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:steelblue;overflow:visible;position:relative;"><path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"/></svg> is shorthand for ["GNU R"](https://www.r-project.org):

- An **interactive** programming language derived from **S** (**J. Chambers**, Bell Lab, 1976)
- Appeared in 1993, created by **R. Ihaka** and **R. Gentleman**, University of Auckland, NZ
- Focus on data analysis and plotting
- <svg aria-hidden="true" role="img" viewBox="0 0 581 512" style="height:35px;width:39.72px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:steelblue;overflow:visible;position:relative;"><path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"/></svg> is also shorthand for the ecosystem around this language
    + Book authors
    + Package developers
    + Ordinary useRs
  
Learning to use <svg aria-hidden="true" role="img" viewBox="0 0 581 512" style="height:35px;width:39.72px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:steelblue;overflow:visible;position:relative;"><path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"/></svg> will make you **more efficient** and **facilitate the use** of advanced data analysis tools
]

---

# Why using R?

.Large[
- It's *free!* and **open-source**
- easy to install / maintain
- multi-platform (Windows, macOS, GNU/Linux)
- can process big files and analyse huge amounts of data (db tools)
- integrated data visualization tools, *even dynamic* [`shiny`](https://shiny.rstudio.com/)
- fast, and even faster with *C++* integration via [Rcpp](http://dirk.eddelbuettel.com/code/rcpp/Rcpp-attributes.pdf) or [cpp11](https://cpp11.r-lib.org/).
- easy to get help
    + [huge R community in the web](https://support.rstudio.com/hc/en-us/articles/200552336-Getting-Help-with-R)
    + [stackoverflow](http://stackoverflow.com/questions/tagged/r) with a lot of tags like **r**, **ggplot2** etc.
    + [rbloggers](http://www.r-bloggers.com)
]

---

# About R is slow

.center[![](img/intro_r_releases_speed_calculation.png)]

.footnote[Source: [Jozef Hajnala](https://jozef.io/r921-happy-birthday-r/)]

---
    
# Twitter R community

.large[[`#rstats`](https://twitter.com/search?q=%23rstats) on twitter]

.center[![](img/intro_r_community.jpg)]

---

# Constant trend

.pull-left[![](img/intro_r_progression.png)

.footnote[Source: [Touchon & McCoy. _Ecosphere_. 2016](http://onlinelibrary.wiley.com/doi/10.1002/ecs2.1394/full)]

]
.pull-right[

![](img/intro_so_yearly_progression.png)

.footnote[Source: [D. Robinson, StackOverflow blog](https://stackoverflow.blog/2017/10/10/impressive-growth-r/)]
]

---

# Packages

.center[![](img/intro_packages_2021-05-04.png)]

.footnote[Source: [rdrr.io](https://rdrr.io/) on 2021-05-04]

.flex[
.w-33.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mt3.mr1[
.Large[.wbox[[CRAN](https://cran.r-project.org/web/packages/available_packages_by_date.html)]]

.large[**reliable**]: package is checked during submission process

[MRAN](https://mran.microsoft.com/packages/) for Windows users
]

.w-33.bg-washed-yellow.b--yellow.ba.bw2.br3.shadow-5.ph3.mt3.mr1[
.large[.wbox[[bioconductor](https://www.bioconductor.org/)]]

- dedicated to biology. [{limma} example](https://www.bioconductor.org/packages/release/bioc/html/limma.html)
- required dedicated package

typical install:

```r
# install.packages("BiocManager")
BiocManager::install("limma")
```
]

.w-33.bg-washed-red.b--red.ba.bw2.br3.shadow-5.ph3.mt3.mr1[
.large[.wbox[[GitHub](https://github.com/)]]

easy install thanks to [remotes](https://remotes.r-lib.org/).

```r
# install.packages("remotes")
remotes::install_github("tidyverse/readr")
```

could be a security issue
]]

---
class: hide_logo
# [R-universe](https://r-universe.dev/)

- [ropensci](https://ropensci.or) initiative, by [Jeroen Ooms](https://ropensci.org/author/jeroen-ooms/)
- [Video intro](https://ropensci.org/commcalls/may2021-r-universe/), everyone can have a domain for publishing their content
- Provides automated built vignettes and binary packages for <svg aria-hidden="true" role="img" viewBox="0 0 384 512" style="height:20px;width:15px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:black;overflow:visible;position:relative;"><path d="M318.7 268.7c-.2-36.7 16.4-64.4 50-84.8-18.8-26.9-47.2-41.7-84.7-44.6-35.5-2.8-74.3 20.7-88.5 20.7-15 0-49.4-19.7-76.4-19.7C63.3 141.2 4 184.8 4 273.5q0 39.3 14.4 81.2c12.8 36.7 59 126.7 107.2 125.2 25.2-.6 43-17.9 75.8-17.9 31.8 0 48.3 17.9 76.4 17.9 48.6-.7 90.4-82.5 102.6-119.3-65.2-30.7-61.7-90-61.7-91.9zm-56.6-164.2c27.3-32.4 24.8-61.9 24-72.5-24.1 1.4-52 16.4-67.9 34.9-17.5 19.8-27.8 44.3-25.6 71.9 26.1 2 49.9-11.4 69.5-34.3z"/></svg>  / <svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:20px;width:17.5px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:black;overflow:visible;position:relative;"><path d="M0 93.7l183.6-25.3v177.4H0V93.7zm0 324.6l183.6 25.3V268.4H0v149.9zm203.8 28L448 480V268.4H203.8v177.9zm0-380.6v180.1H448V32L203.8 65.7z"/></svg>  (also dev versions)
- No `remotes` / `devtools` / `rtools` required, design your rules outside **CRAN**

.center[
[![runi](img/intro_runiverse.png)](https://gadenbuie.r-universe.dev/ui#builds)
]

---

# Installation

.pull-left[

.bold[CRAN] install from Rstudio (autocompletion)

![](./img/intro_packages_install_panel.png)
]

.pull-right[

.bold[CRAN] install from Rstudio' console

![](./img/intro_packages_install_console.png)
]

.footnote[more in the article from [David Smith](http://blog.revolutionanalytics.com/2017/01/cran-10000.html)]

---

# Help pages

.pull-left[
2 possibilities for manual pages.

```r
?log
help(log)
```

Sadly, manpages are often unhelpful, 
**vignettes** or [**articles**](http://readxl.tidyverse.org/articles/sheet-geometry.html) better described workflow.
]

.pull-right[
In **Rstudio**, the help page can be viewed in the bottom right pane

![](img/intro_help_rstudio.png)
]

---

# Drawback: Steep learning curve

### Period of much suckiness

.vembedr[
<div class="vembedr">
<div>
<iframe src="https://www.youtube.com/embed/8SGif63VW6E?start=252" width="533" height="300" frameborder="0" allowfullscreen=""></iframe>
</div>
</div>
]

---
class: middle, center

.huge[
>The bad news is that when ever you learn a new skill you’re going to _suck_. It’s going to be _frustrating_. The .green.bold[good] news is that is .bold[typical] and happens to .bold[everyone] and it is only .bold[temporary]. You can’t go from knowing nothing to becoming an expert without going through a period of great _frustration_ and great _suckiness_.

.tr[
— _Hadley Wickham_]
]

.footnote[source: [Hadley Wickham dplyr tutorial at useR 2014](https://youtu.be/8SGif63VW6E?t=252)]

---

# R is hard to learn

.Large[**R base** is complex, has a long history and many contributors]

.flex[
.w-70.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph4.ml6[
.large[.gbox[Why R is hard to learn]]

- Unhelpful help `?print`
- generic methods `print.data.frame`
- too many commands `colnames, names`
- inconsistent names `read.csv, load, readRDS`
- un-strict syntax, was designed for interactive usage
- too many ways to select variables `df$x, df$"x", df[,"x"], df[[1]]`
- [...] see [r4stats' post](http://r4stats.com/articles/why-r-is-hard-to-learn/) for the full list
- the `tidyverse` curse
]]

.flex[
.w-70.bg-washed-yellow.b--yellow.ba.bw2.br3.shadow-5.ph2.mt2.ml6[

> Navigating the balance between `base` R and the `tidyverse` is a challenge to learn

.tr[
— _Robert A. Muenchen_]

]
]

.center[.footnote[source: [Robert A. Muenchen' blog](http://r4stats.com/articles/why-r-is-hard-to-learn/)]]

---
class: middle, center

.Large[
>The ambiguity [of the S language] is real and goes to a key objective: we wanted users to be able to begin in an .bold.red[interactive environment], where they did not consciously think of themselves as programming. Then as their needs became clearer and their sophistication increased, they should be able .blue.bold[slide gradually into programming], when the language and system aspects would become more important.

.tr[
— _John Chambers, "Stages in the Evolution of S"_]
]

.footnote[source: [Teaching R to New Users: from tapply to Tydiverse 2018](https://www.youtube.com/watch?v=5033jBHFiHE) by .bold[Roger D. Peng]]

---

## Tidyverse origin

.left-column[
.Large[H. Wickham]

[Hadley](http://had.co.nz) is Chief Scientist at **Rstudio**

- coined the _tidyverse_ at [userR meeting in 2016](https://twitter.com/drob/status/748196885307920385)
- developed and maintains most of the core _tidyverse_ packages

![](https://pbs.twimg.com/profile_images/905186381995147264/7zKAG5sY_200x200.jpg)

]

.right-column[
.Large[
We think the [**tidyverse**](http://tidyverse.org/) is better, especially for beginners. It is:

- recent (both an issue and an advantage)
- allows [doing powerful things quickly](http://varianceexplained.org/r/teach-tidyverse/)
- unified
- consistent, one way to do things
- give strength to learn base R
- criticisms will come later

]]

---

## Tidyverse, core packages

.center[![](img/intro_tidyverse_components.png)]

---

# Top download

.center[<img src="img/intro_top_download_metacran_2020-11-09.png", width="55%">]

.left[.footnote[source: [METACRAN, top downloaded](https://www.r-pkg.org/downloaded) (2020-11-09)]]

---

# Rstudio / tidyverse hard to ignore

.center[<img src="img/intro_top_download_metacran_2020-11-09_tv.png", width="55%">]

.left[.footnote[source: [METACRAN, top downloaded](https://www.r-pkg.org/downloaded) (2020-11-09)]]

---

# 18<sup>th</sup> of May, R 4.1

.pull-left[
### Tidyverse

.huge[
- pipe 
<img src="https://raw.githubusercontent.com/tidyverse/magrittr/master/man/figures/logo.png" style="height:70px;"/>

- lambda: `~ .x`
]
.large[
- `c(factor("a"), factor("b"))` is `[1] a b`
<img src="https://raw.githubusercontent.com/r-lib/vctrs/master/man/figures/logo.png" style="height:70px;"/>
]
]

.footnote[[lambda](https://en.wikipedia.org/wiki/Anonymous_function) functions are .bold[anonymous]. Classic syntax is `(function(x) x + 2)(2)`
</br>.bold[v4.0] brought `stringsAsFactors = FALSE` that `tibbles` have]

.pull-right[
### <svg aria-hidden="true" role="img" viewBox="0 0 581 512" style="height:60px;width:68.09px;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"/></svg> v4.1

.huge[
- native pipe `|>`
- lambda: `\(x)`
- combine factors also works (before: `[1] 1 1`)
]

]

---
class: inverse, center, middle

![](img/00/logo_rstudio.png)

---

# What is it?

.Large[[RStudio](https://www.rstudio.com/products/RStudio/)] is an Integrated Development Environment
It makes working with R much easier

.left-column[
## .red[Warning]

.large[Don't mix up **R** and **RStudio**.  
**R** needs to be installed first.]
]

.right-column[
## Features

.large[
- _Projects_ to ease files organisation
- _Console_ to run **R**, with syntax highlighter
- full support for _Rmarkdown_ docs & chunks
- _Viewer_ for data / plots / website
- _Package management_ (including building, tests and development)
- _Autocompletion_ using <kbd>TAB</kbd>
- [_Cheatsheets_](https://www.rstudio.com/resources/cheatsheets/) (**New** [2021-08-23](https://blog.rstudio.com/2021/08/23/cheat-sheet-updates/))
- _Git_ integration for versioning
- _Inline_ outputs
- _Keyboard shortcuts_
- integrated _Terminal_
- _Jobs_ for running long runs in a separated session
]]

---

# The 4 panels layout

.center[![](img/intro_rstudio_layout.jpg)]

---

# Four panels

.pull-left[
### scripting

- could be your main window
- should be a **Rmarkdown** doc
- tabs are great

### Console

- could be hidden with **inline** outputs
- `Rmarkdown` output logs
- optional, embed a nice `Terminal` tab
- optional,`Jobs` tab

]
.pull-right[
### Environment

- **Environment**, display loaded objects and their `str()`
- History is useless IMO
- nice `git` integration
- **Build** for development
- database **connections** interface
- **Tutorial** integration of [`learnr`](https://rstudio.github.io/learnr/)

### Files / Plots / Help

- **Packages** management tab
- unnecessary **Plots** panel when using **inline** outputs
- **Help** tab
- Viewer for animations
]

---
class: hide_logo
# Rearrange panels

![](https://www.pipinghotdata.com/posts/2020-09-07-introducing-the-rstudio-ide-and-r-markdown/gifs/move-panels.gif)

.footnote[[source:Shannon Pileggi](https://www.pipinghotdata.com/posts/2020-09-07-introducing-the-rstudio-ide-and-r-markdown/#rmd)]

---
class: hide_logo

# For reproducibility

#### .green[Options to activate / deactivate]

.pull-left[
![](img/intro_rstudio_settings.png)
]
.pull-right[
 `rm(list = ls())` is not recommended

- does **not** make a fresh R session
    + `library()` calls remain
    + working directory not set!
    + modified functions, [evil](https://github.com/romainfrancois/evil.R) `==` <- `!=`
- knitting `Rmarkdown` files solves it

.footnote[[source: Jenny Bryan article](https://www.tidyverse.org/articles/2017/12/workflow-vs-script/)]
]

---

# Code diagnostics, highly recommended

using  `Global Options -> Code -> Diagnostics` editing panel:

.pull-left[
![](img/intro_diag_rstudio.png)
.bottom-footnote[source: [Kevin Ushey' article](https://support.rstudio.com/hc/en-us/articles/205753617-Code-Diagnostics?version=1.1.133&mode=desktop)] 
]
.pull-right[
- check argument calls

![](img/intro_rstudio_check_args.png)

- missing arguments

![](img/intro_rstudio_check_missing.png)

- variable definitions

![](img/intro_rstudio_check_vars.png)

+ unused variables & style recommendations

]

---
# Symbol and their names for this course

.flex[
.w-70.bg-washed-yellow.b--yellow.ba.bw2.br3.shadow-5.ph2.mt2.mr3[
.bbox[Common operators]
.large[
`=` - equal

`.` - dot

`,` - comma

`>` - greater than

`<` - less than

`~` - twiddle

`*` - star

`-` - hyphen

`_` - underscore
]]

.w-70.bg-washed-yellow.b--yellow.ba.bw2.br3.shadow-5.ph2.mt2.mr3[
.bbox[Quotation and comments]
.large[

`"` - double quotation marks

`'` - single quotation marks

`` ` `` - backticks

`#` - hash

<code>&#124;</code> - (vertical) bar

`/` - (forward) slash

`\` - backslash
]
]

.w-70.bg-washed-yellow.b--yellow.ba.bw2.br3.shadow-5.ph2.mt2[
.bbox[Enclosures]
.large[

`()` - parentheses 
 
`[]`- (square) brackets
 
`{}` - (curly) braces
 
`<>` - chevrons 
 
]

.bbox[R-specific operators]
.large[
`<-` - assignment (left)

`->` - right assignment

`%>%` - (magrittr) pipe

`|>` - (base) pipe

]
]

]
---
## Arithmetic operations

.large[
.pull-left[

- `+`: addition  
- `-`: subtraction  
- `*`: multiplication  
- `/`: division  
- `^` or `**`: exponentiation 
- `%%`: modulo (remainder after division)
- `%/%`: integer division
]

.pull-right[

#### **Remember** that **R** will:

- first perform **exponentiation**
- then multiplications and/or divisions
- and finally additions and/or subtractions.

###  prioritization

change the priority in evaluation:

- parentheses `(` and `)` to group calculations
]
]

---

## Using `library()`, ensure function' origin

.pull-left[
with only `base` loaded

```r
x <- 1:10
filter(x, rep(1, 3))
```

```
Time Series:
Start = 1 
End = 10 
Frequency = 1 
 [1] NA  6  9 12 15 18 21 24 27 NA
```

]
.pull-right[

.bold.red[Conflict]: 2 packages export same function

with the same name, the latest loaded wins

```r
library(dplyr)
filter(x, rep(1, 3))
```

```
Error in UseMethod("filter"): no applicable method for 'filter' applied to an object of class "c('integer', 'numeric')"
```

**Solution**: use `::` to call functions from a specific package

```r
stats::filter(x, rep(1, 3))
```

```
Time Series:
Start = 1 
End = 10 
Frequency = 1 
 [1] NA  6  9 12 15 18 21 24 27 NA
```

Or use the [`conflicted`](https://github.com/r-lib/conflicted) package
]

---
class: inverse, middle, center

# Data types and structures
## R base

---

# Getting started

Let's get ready to use **R** and **RStudio**

.flex[
.w-70.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mt3.ml5[
.large[.gbox[do the following]]

- Open up RStudio
- Maximize the RStudio window
- Click the Console pane, at the prompt (`>`) type in `3 + 2` and hit enter

```r
> 3 + 2
```
]]

---

# 4 main types

.pull-left[

<table class="huxtable" style="border-collapse: collapse; border: 0px; margin-bottom: 2em; margin-top: 2em; ; margin-left: auto; margin-right: auto;  " id="tab:unnamed-chunk-19">
<col><col><tr>
<th style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0.4pt 0.4pt 0.4pt; border-top-color: rgb(255, 255, 255);  border-right-color: rgb(255, 255, 255);  border-bottom-color: rgb(255, 255, 255);  border-left-color: rgb(255, 255, 255); padding: 6pt 6pt 6pt 6pt; background-color: rgb(229, 229, 229); font-weight: bold;">Type</th><th style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0.4pt 0.4pt 0.4pt; border-top-color: rgb(255, 255, 255);  border-right-color: rgb(255, 255, 255);  border-bottom-color: rgb(255, 255, 255);  border-left-color: rgb(255, 255, 255); padding: 6pt 6pt 6pt 6pt; background-color: rgb(229, 229, 229); font-weight: bold;">Example</th></tr>
<tr>
<td style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0.4pt 0.4pt 0.4pt; border-top-color: rgb(255, 255, 255);  border-right-color: rgb(255, 255, 255);  border-bottom-color: rgb(255, 255, 255);  border-left-color: rgb(255, 255, 255); padding: 6pt 6pt 6pt 6pt; background-color: rgb(242, 242, 242); font-weight: normal;">numeric</td><td style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0.4pt 0.4pt 0.4pt; border-top-color: rgb(255, 255, 255);  border-right-color: rgb(255, 255, 255);  border-bottom-color: rgb(255, 255, 255);  border-left-color: rgb(255, 255, 255); padding: 6pt 6pt 6pt 6pt; background-color: rgb(242, 242, 242); font-weight: normal;">integer (2), double (2.34)</td></tr>
<tr>
<td style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0.4pt 0.4pt 0.4pt; border-top-color: rgb(255, 255, 255);  border-right-color: rgb(255, 255, 255);  border-bottom-color: rgb(255, 255, 255);  border-left-color: rgb(255, 255, 255); padding: 6pt 6pt 6pt 6pt; background-color: rgb(229, 229, 229); font-weight: normal;">character (strings)</td><td style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0.4pt 0.4pt 0.4pt; border-top-color: rgb(255, 255, 255);  border-right-color: rgb(255, 255, 255);  border-bottom-color: rgb(255, 255, 255);  border-left-color: rgb(255, 255, 255); padding: 6pt 6pt 6pt 6pt; background-color: rgb(229, 229, 229); font-weight: normal;">'tidyverse!'</td></tr>
<tr>
<td style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0.4pt 0.4pt 0.4pt; border-top-color: rgb(255, 255, 255);  border-right-color: rgb(255, 255, 255);  border-bottom-color: rgb(255, 255, 255);  border-left-color: rgb(255, 255, 255); padding: 6pt 6pt 6pt 6pt; background-color: rgb(242, 242, 242); font-weight: normal;">boolean</td><td style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0.4pt 0.4pt 0.4pt; border-top-color: rgb(255, 255, 255);  border-right-color: rgb(255, 255, 255);  border-bottom-color: rgb(255, 255, 255);  border-left-color: rgb(255, 255, 255); padding: 6pt 6pt 6pt 6pt; background-color: rgb(242, 242, 242); font-weight: normal;">TRUE / FALSE</td></tr>
<tr>
<td style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0.4pt 0.4pt 0.4pt; border-top-color: rgb(255, 255, 255);  border-right-color: rgb(255, 255, 255);  border-bottom-color: rgb(255, 255, 255);  border-left-color: rgb(255, 255, 255); padding: 6pt 6pt 6pt 6pt; background-color: rgb(229, 229, 229); font-weight: normal;">complex</td><td style="vertical-align: top; text-align: left; white-space: normal; border-style: solid solid solid solid; border-width: 0.4pt 0.4pt 0.4pt 0.4pt; border-top-color: rgb(255, 255, 255);  border-right-color: rgb(255, 255, 255);  border-bottom-color: rgb(255, 255, 255);  border-left-color: rgb(255, 255, 255); padding: 6pt 6pt 6pt 6pt; background-color: rgb(229, 229, 229); font-weight: normal;">2+0i</td></tr>
</table>

### Missing data and special cases

```r
NA   # not available, missing data
NA_real_
NA_integer_
NA_character_
NA_complex_
NULL # empty
-Inf/Inf # infinite values
NaN # Not a Number
```
]

.pull-right[

```r
2L
```

```
[1] 2
```

```r
typeof(2L)
```

```
[1] "integer"
```

```r
2.34
```

```
[1] 2.34
```

```r
typeof(2.34)
```

```
[1] "double"
```

```r
"tidyverse!"
```

```
[1] "tidyverse!"
```

```r
TRUE
```

```
[1] TRUE
```

```r
2+0i
```

```
[1] 2+0i
```

]

---

# Structures

.pull-left[

### Vectors

`c()` is the function for **concatenate**

```r
4
```

```
[1] 4
```

```r
c(43, 5.6, 2.90)
```

```
[1] 43.0  5.6  2.9
```

### Factors

convert strings to factors, `levels` is the dictionary

```r
factor(c("AA", "BB", "AA", "CC"))
```

```
[1] AA BB AA CC
Levels: AA BB CC
```

]
.pull-right[

### Lists

very important as it can contain .Large[anything]

```r
list(f = factor(c("AA", "AA")),
     v = c(43, 5.6, 2.90),
     s = 4L)
```

```
$f
[1] AA AA
Levels: AA

$v
[1] 43.0  5.6  2.9

$s
[1] 4
```
]

---

## Data frames are special lists

.pull-left[

###  `data.frame`

same as list **but** where all objects _must_ have the **same** length

```r
data.frame(
  f = factor(c("AA", "AA", "BB")),
  v = c(43, 5.6, 2.90),
  s = rep(4, 3))
```

```
   f    v s
1 AA 43.0 4
2 AA  5.6 4
3 BB  2.9 4
```
]

.pull-right[
### Example, missing one element in `v`

```r
data.frame(
  f = factor(c("AA", "AA", "BB")),
  v = c(43, 5.6),
  s = rep(4, 3))
```

```
Error in data.frame(f = factor(c("AA", "AA", "BB")), v = c(43, 5.6), s = rep(4, : arguments imply differing number of rows: 3, 2
```
]

---

## Concatenate atomic elements

.pull-left[

### collection of simple _things_

- _things_ are the smallest elements: **atomic**
- **must** be of same **mode**: .red.bold[automatic] coercion
- indexed, from **1** to `length(vector)`
- created with the **`c()`** function

```r
c(2, TRUE, "a string")
```

```
[1] "2"        "TRUE"     "a string"
```
]

.pull-right[
#### Manual coercion

```r
as.character(c(2, TRUE, "a string"))
```

```
[1] "2"        "TRUE"     "a string"
```

```r
as.double(c(2, TRUE, "a string"))
```

```
[1]  2 NA NA
```

```r
as.double(c(2, 2.456, "a string"))
```

```
[1] 2.000 2.456    NA
```

]

---

## Assignment

.large[operator is `<-`, associate a _name_ to an object]

.pull-left[

```r
my_vec <- c(3, 4, 1:3)
my_vec
```

```
[1] 3 4 1 2 3
```

.flex[
.w-80.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mt3.mr1[
.large[.gbox[tip]]
Rstudio has the built-in shortcut <kbd>Alt</kbd>+<kbd>-</kbd> for `<-`
]
]
]

.pull-right[
### Rationale
.large[
if you don't assigned a name to a created object it is only temporary.
Assigning allows to save and re-use the object for a downstream step.]
]

---
class: hide_logo

# Binding names to values

.pull-left[
### Object has no name
<blockquote class="twitter-tweet"><p lang="en" dir="ltr">In <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a>, it&#39;s surprisingly important to realise that names have objects; objects don&#39;t have names <a href="https://t.co/bEMO1YVZX0">pic.twitter.com/bEMO1YVZX0</a></p>&mdash; Hadley Wickham (@hadleywickham) <a href="https://twitter.com/hadleywickham/status/732288980549390336?ref_src=twsrc%5Etfw">May 16, 2016</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

]

.pull-right[

#### vector is bind to the name `x`

```r
x <- 1:3
```

![](img/intro_binding_1.png)
####same vector is also bind to the name `y`

```r
y <- x
```

![](img/intro_binding_2.png)

.footnote[source: **H. Wickham** - [Adv _R_](https://adv-r.hadley.nz/names-values.html), [licence CC](http://creativecommons.org/licenses/by-nc-nd/3.0/us/)]
]

---

# Hierarchy

.pull-left[

.center[![](img/intro_data_structures_overview.png)]

]

.footnote[source: **H. Wickham** - [_R_ for data science](http://r4ds.had.co.nz/vectors.html), [licence CC](http://creativecommons.org/licenses/by-nc-nd/3.0/us/)]

.pull-right[

```r
is.vector(c("a", "c"))
```

```
[1] TRUE
```

```r
is.vector(list(a = 1))
```

```
[1] TRUE
```

```r
is.atomic(list(a = 1))
```

```
[1] FALSE
```

```r
is.data.frame(list(a = 1))
```

```
[1] FALSE
```
]

---

# Subsetting vectors

.flex[
.w-30.bg-washed-red.b--red.ba.bw2.br3.shadow-5.ph3.mt3.mr1[
.large[.rbox[important <svg aria-hidden="true" role="img" viewBox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:currentColor;overflow:visible;position:relative;"><path d="M569.517 440.013C587.975 472.007 564.806 512 527.94 512H48.054c-36.937 0-59.999-40.055-41.577-71.987L246.423 23.985c18.467-32.009 64.72-31.951 83.154 0l239.94 416.028zM288 354c-25.405 0-46 20.595-46 46s20.595 46 46 46 46-20.595 46-46-20.595-46-46-46zm-43.673-165.346l7.418 136c.347 6.364 5.609 11.346 11.982 11.346h48.546c6.373 0 11.635-4.982 11.982-11.346l7.418-136c.375-6.874-5.098-12.654-11.982-12.654h-63.383c-6.884 0-12.356 5.78-11.981 12.654z"/></svg>]]
.center.large[
unlike **python** or **Perl**, vectors use **1-based** index!!
]
]

.w-33.bg-green-red.b--green.ba.bw2.br3.shadow-5.ph3.mt3.mr1[
.large.ybox[.Large[`:`] operator]

generate integer sequence

```r
3:10
```

```
[1]  3  4  5  6  7  8  9 10
```
]
.w-33.bg-washed-gren.b--green.ba.bw2.br3.shadow-5.ph3.mt3.mr1[
.large.ybox[extract > 1 element]

select elements from position **3** to **10**:

```r
LETTERS[3:10]
```

```
[1] "C" "D" "E" "F" "G" "H" "I" "J"
```
]]

.flex[
.w-30.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mt3.mr1.ml6[
.large.ybox[break in sequence, use `c()`]

```r
LETTERS[c(2:5, 7)]
```

```
[1] "B" "C" "D" "E" "G"
```
]
.w-30.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mt3.mr6[
.large.ybox[negative selection]

```r
LETTERS[-(2:21)]
```

```
[1] "A" "V" "W" "X" "Y" "Z"
```
]]

---
class: slide-practical

## Vectorized operation, one of the best R feature

.flex[
.w-33.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mt3.mr1[

```r
my_vec <- 1:8
my_vec
```

```
[1] 1 2 3 4 5 6 7 8
```

```r
my_vec + 2
```

```
[1]  3  4  5  6  7  8  9 10
```
]
.w-33.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mt3.mr1[
#### try this one

```r
my_vec / 2
```
]
.w-33.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mt3.mr1[
#### and this one, how does it work?

```r
my_vec + 1:4
```
]]

---

## Answers

.pull-left[

.flex[
.w-100.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph1.mt3.mr1[

```r
my_vec / 2
```

```
[1] 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0
```

```r
my_vec + 1:4
```

```
[1]  2  4  6  8  6  8 10 12
```

.Large[`R`] is .bold[recycling] (*silently*) the shorter vector.

.bold[But], incompatible lengths create a *warning* !

```r
my_vec + 1:3 
```

```
Warning in my_vec + 1:3: longer object length is not a multiple of shorter
object length
```

```
[1]  2  4  6  5  7  9  8 10
```

]
]
]

.pull-right[
.flex[
.w-100.bg-washed-red.b--red.ba.bw2.br3.shadow-5.ph1.mt3.mr1[
#### Avoid writing loops (and do .red[not] grow a vector)

```r
res <- vector(mode = "numeric", length = length(my_vec))
for (i in seq_along(my_vec)) {
  res[i] <- my_vec[i] + 2
}
res
```

```
[1]  3  4  5  6  7  8  9 10
```
]
]
]

---

## Pipes

### Output the result of one function as input for the next one

.pull-left[
#### .Large[R base], classic parenthesis syntax

```r
set.seed(12)
round(mean(rnorm(5)), 2)
```

```
[1] -0.76
```

And pipes are into .large.bold[R base] since version .bold[4.1] as .large[`|>`]*.

For **tidyverse** functions (`data` first argument), both pipes work similarly. Base being faster.

.footnote[*: [Luke Tierney useR!2020](https://youtu.be/X_eDHNVceCU?t=4084)]
]

.pull-right[
####.Large[[`magrittr`](https://cran.r-project.org/web/packages/magrittr/vignettes/magrittr.html)] pipeline,  (originally by Stefan M. Bache)

```r
set.seed(12)
rnorm(5) %>%
  mean() %>%
  round(2)
```

```
[1] -0.76
```

Of note, `magrittr` needs to loaded with either:

```r
library(magrittr)
library(dplyr)
library(tidyverse)
```
]

---

## Before we stop

.flex[

.w-60.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mt2.ml1[
.large[.gbox[You learned to:]

.float-img[![](img/00/kt.png)]

- Introduction
    + R
    + Rstudio
    + tidyverse rationale
- data types
    + main categories
    + coerce
- data structures
    + main categories
    + sub-setting
    + vectorization
]
]
.w-40.bg-washed-green.b--green.ba.bw2.br3.shadow-5.ph3.mt2.ml2[
.large[.bbox[Acknowledgments  🙏 👏]]
* Roland Krause
* Hadley Wickham
* Robert Muenchen
* Romain François
* Jenny Bryan
]]

.w-60.pv2.ph3.mt1.ml6[
.huge[.bbox[Thank you for your attention!]]
]