What is R?

class: center, middle, inverse, title-slide

# What is R?
### The R Bootcamp Twitter: <a href='https://twitter.com/therbootcamp'>@therbootcamp</a>
### April 2018

---

# R

From [Wikipedia](https://en.wikipedia.org/wiki/Statistical_model) (emphasis added):

> R is an **open source programming language** and software environment for **statistical computing and graphics** that is supported by the R Foundation for Statistical Computing. The R language is **widely used among statisticians and data miners** for developing statistical software and data analysis. Polls, surveys of data miners, and studies of scholarly literature databases show that **R's popularity has increased substantially in recent years**.

> R is a GNU package. The source code for the R software environment is written primarily in **C, Fortran, and R**. R is freely available under the GNU General Public License, and pre-compiled binary versions are provided for various operating systems. While R has a command line interface, there are several **graphical front-ends available**.

---

# Programming language

From [Wikipedia](https://en.wikipedia.org/wiki/Statistical_model) (emphasis added):

> A programming language is a **formal language** that specifies a set of instructions that can be used to produce various kinds of output. Programming languages generally consist of **instructions for a computer**. Programming languages can be used to create programs that **implement specific algorithms**.

.pull-left4[
### Algorithm
1. Load data
2. Extract variables
3. Run analysis
4. Print result
]

.pull-right6[
### Implementation in R

```r
data <- read.table(link)
variables <- data[,c('group','variable')]
analysis <- lm(variable ~ group, data = variables)
summary(analysis)
```
]

<!-- ---

# A short history on R

From [Wikipedia](https://en.wikipedia.org/wiki/R_(programming_language) (emphasis added):

.pull-left6[
> R is an implementation of the **S programming language** combined with **lexical scoping** semantics [environments] inspired by Scheme. [...] There are some important differences, but much of the code written for S runs unaltered.

>R was created by **Ross Ihaka and Robert Gentleman** [...] and is currently developed by the **R Development Core Team** [...]. R is named partly after the first names of the first two R authors and partly as a play on the name of S. The project was conceived in 1992, with an initial version released in 1995 and a **stable beta version in 2000**.
]

.pull-right6[
<img src="http://www.estatisticacomr.uff.br/wp-content/uploads/2014/11/Criadores.jpg" height="350px" style="display: block; margin: auto;" />

Robert Gentleman and Ross Ihaka 
source: https://i0.wp.com/r4stats.com/

]
-->
---

# R is purpose specific

R has been build for **statistical computing and graphics** and that is basically it:

.pull-left5[
### Use R (today) for...
1. Importing and exporting data
2. Handle and process data
3. Run cutting-edge analyses
4. Analyze big data
5. Create publication-ready figures
6. Prepare reproducible reports
]

.pull-right5[
### Don't use R for...
1. OS programs
2. GUIs
3. Complex websites
]

---

# R is widely used

.pull-left3[
R steadily **grows in popularity**.

Today, R is one of the **most popular languages for data science** and overall.

In terms of the number of data science jobs, **R beats SAS and Matlab**, and is on par with Python:
]

.pull-left65[
<img src="https://i0.wp.com/r4stats.com/wp-content/uploads/2017/02/Fig-1a-IndeedJobs-2017.png" height="370">

source: https://i0.wp.com/r4stats.com/
]

---

# R is so popular because

There are many good reasons to prefer R over superficially more user friendly software such as **Excel** or **SPSS** or more complex programming languages like **C++** or **Python**.

.pull-left45[
### Pro
1. **It's free**
2. Relatively **easy**
3. **Extensibility** ([CRAN](https://cran.r-project.org/), packages)
4. **User base** (e.g., [stackoverflow](https://stackoverflow.com/))
5. [**Tidyverse**](https://www.tidyverse.org/) (`dplyr`, `ggplot`, etc.)
6. [**RStudio**](https://www.rstudio.com/)
7. **Productivity** options: [Latex](https://www.latex-project.org/), [Markdown](https://daringfireball.net/projects/markdown/), [GitHub](https://github.com/)
]

.pull-right45[
### Con
Sometimes slow and awkward, but...

[Tidyverse](https://www.tidyverse.org/)
[Rcpp](http://www.rcpp.org/), [BH](https://cran.r-project.org/web/packages/BH/index.html): Links R to C++ and high-performance C++ libraries 
[rPython](http://rpython.r-forge.r-project.org/): Links R to Python 
[RHadoop](https://github.com/RevolutionAnalytics/RHadoop/wiki): Links R to Hadoop for big data applications. 
]

<!---

Move to Efficient projects

# Project management

RStudio facilitate project management via the use of *projects*. Projects support:

.pull-left5[
1. **File management** by automatically setting the working directory (see `setwd()`)
 
2. **Project transitioning** by saving re-opening scripts, history, and workspace.
 
3. **Customization** by enabling project specific settings.
 
4. **Version control** by linking projects to repositories (e.g., using [GitHub](https://github.com/))
]
.pull-right5[

]

--->

---

# Packages

.pull-left35[

R features a vast and cutting-edge collection of **packages** provided on [**CRAN**](https://cran.r-project.org/) and [**Git/GitHub**](https://github.com/hadley) by R's large and highly active user base and the work of .

```r
# To install a package
install.packages('package_name')

# load a package
library(package_name)
require(package_name)

#Note: 
# Don't forget that packages 
# must also be loaded.
```

]

.pull-right55[

<a href="https://www.rdocumentation.org/trends">https://www.rdocumentation.org/trends</a>
]
---

# The almighty **tidyverse**

Among its many packages, R newly contains a collection of high-performance, user-friendly packages (libraries) known as the [tidyverse](https://www.tidyverse.org/). The tidyverse includes:
1. `ggplot2` -- creating graphics.
2. `dplyr` -- data manipulation.
3. `tidyr` -- tidying data.
4. `readr` -- read wild data.
5. `purrr` -- functional programming.
6. `tibble` -- modern data frame.

---

# RStudio: R's favorite environment

Next to many useful packages, R users greatly benefit from R's integrated development environment [**RStudio**](https://www.rstudio.com/). Rstudio is a **graphical user interface** that allows you to (a) edit code, (b) run code, (c) access files and history, and (d) create plots. RStudio also helps you with **project management**, **version control** via [Github](https://github.com/), writing **reports** using [markdown](http://rmarkdown.rstudio.com/authoring_basics.html) and [knitr](https://yihui.name/knitr/), and many other aspects of working with R.

---

# Essentials of the R language

.pull-left5[
>"To understand computations in R, two slogans are helpful:
 
>###(1) Everything that exists is an object and 
>###(2) everything that happens is a function call."
]

.pull-right5[
<img src="https://statweb.stanford.edu/~jmc4/CopyPhoto.jpg" width="350" align="center">
John Chambers Author of S and developer of R 
<a href="https://statweb.stanford.edu/~jmc4/">statweb.stanford.edu</a>

]

---

# Calls, assignments, and expressions

R programs evolve through functions: Every action entails **passing on arguments (aka objects) to a function**, **calling (aka executing) the function**, and **printing or storing its output**. And this goes deep, many operations are functions in disguise.

.pull-left45[

```r
# a prototypical function
some_function <- function(argument_1, argument_2){ 
 
 # do something with arguments
 result <- argument_1 + argument_2 
 
 # return result
 result
 }
```

]

.pull-right45[

```r
# Expressions
some_function(2, 2)
```

```
## [1] 4
```

```r
2 + 2
```

```
## [1] 4
```

```r
# Assignments
my_object1 <- some_function(2, 2)
my_object2 <- 2 + 2 
```
]

<!---
# Object-orientation

R is an object-oriented language. For us this entails: 
>(a) **Everything is an object** (including functions). 
>(b) **Generic functions** that respond to the **object's class**. 
>(c) R **always copies deep**, implying that we always need to assign the output of a result.

.pull-left45[

```r
# creating a vector and testing its class
my_vector <- c(1, 5, 2)
class(my_vector)
```

```
## [1] "numeric"
```

```r
# testing the class of an object
print(my_vector)
```

```
## [1] 1 5 2
```
]

.pull-right45[

```r
# Sorting a vector
sort(my_vector)  
```

```
## [1] 1 2 5
```

```r
print(my_vector) # still unsorted
```

```
## [1] 1 5 2
```
]

--->

---

# Syntax style

Programming languages have different expressive styles. R uses...

.pull-left35[
+ **Comment** symbol `#`
<br2>
+ **Quotations** with either `" "` or ' '
<br2>
+ Curly brackets `{}` **enclose expressions** explicitly
<br2>
+ Parentheses `()` **call functions**
<br2>
+ Semicolon `;` **separates expressions**
<br2>
+ `<`,`>`,`|`,`&`,`==`, `!=` define **logical statements**
]

.pull-right55[

```r
# This is a comment

# Quotes are used to define strings
"a" == 'a'

# Expression and calls
my_fun(x,y){ x  + y }

# two expression in one line
2 + 2 ; 3 + 3

# are these equal/different
2 == 2 ; 2 != 2
```

]

---

# Help

.pull-left5[

R provides extremely helpful **help files** and **vignettes**. 
>**Help files** are required documentations for every R function and package published on [**CRAN**](https://cran.r-project.org/). 
>**Vignettes** are long tutorials sometimes provided by the authors of a package.

```r
# To access help files
help("name_of_function")
?name_of_function

# find help files
??name_of_function

# To list and access vignettes
vignette(package="name_of_package")
vignette(package="name_of_vignette")
```

]
.pull-right45[
<img src="https://raw.githubusercontent.com/therbootcamp/therbootcamp.github.io/master/_sessions/_image/mean_help.png" width="500">

]

<!---
## The workflow of R
<img src="https://raw.githubusercontent.com/therbootcamp/therbootcamp.github.io/master/_sessions/_image/rstudio_workings.png" height="500" align="center">

--->

---

# Datasets Day 1

<a href="https://github.com/therbootcamp/BaselRBootcamp_2018April/blob/master/_sessions/_data/data_BaselRBoocamp_Day1.zip?raw=true">download link</a>

---

# Interactive session

Open up **Rstudio**...

<a href="https://therbootcamp.github.io/BaselRBootcamp_2018April/_sessions/D1S1_WhatIsR/What_is_R_practical.html">Link to practical</a>