Microbes on Earth - ES2304 & ES7027

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# Microbes on Earth

---

## R session 01 - Introduction to R

2021-10-12

---

## R sessions

1 - Introduction to R   
2 - Data wrangling  
3 - Data visualisation  
4 - Analysis of metabarcoding data 
]

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# Outline

.font150[
* What is R and why use R ?
* Resources
* Get started
* Fundamentals of R
    - Data objects
    - Vectors
    - Operators
    - [Functions](#functions)
    - Packages
]
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# Wooclap - Past experience

https://www.wooclap.com/MICROR
]

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# Introduction

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- .font150[For those who are experts in R]

--
    * please refrain to answer during this session...
    * help your neighbor (once COVID is gone...)

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## Computer languages

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## History of R

* **Mid 1970s** - S Language for Statistical Computing conceived by John Chambers, Rick Becker, Trevor Hastie, Allan Wilks and others at Bell Labs

* **Early 1990's** - R was first implemented in the early 1990’s by Robert Gentleman and Ross Ihaka, both faculty members at the University of Auckland.

* **1995** - Open Source Project

* **1997** - Managed by the R Core Group

* **2000** -  First release of R

* **2011** - First release of R studio

* [Historical notes - Paper from 1998](https://www.stat.auckland.ac.nz/~ihaka/downloads/Interface98.pdf)

---
## Why use R ?

- **Script vs. Menu driven software (e.g. Excel)**
     + Can be re-rerun with new data
     + Reproducible workflow
--
- **Open source**
    + Huge number of libraries
    + Tidy "universe" : tidyverse and ggplot2
        + Very easy to manipulate tables (select columns, create new variables)
        - High quality graphics
--
- **Work environment**
    - R studio
--
-  **Document your data processing**
    - R markdown
    - Create HTML, pdf, presentations
--
- **Share your data and workflow**
    - GitHub

---
## What can you do with R ?

- **Science**
    * Statistics of course...
    * Data processing
    * Graphics
    * Time series analyses
    * Maps
    * Bioinformatics
]

- **But also**
    * Teach
    * Do a presentation
    * Write your CV
    * Build a web site
    * Write a book
    * Much more...
]

--
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# Resources

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## Books and Manuals

* [Applied Statistics with R](https://daviddalpiaz.github.io/appliedstats/index.html) : Quite simple introduction with emphasis on Stats
* [R intro](https://cran.r-project.org/doc/manuals/r-release/R-intro.pdf) : Very good introduction to R, short and clear
* [R in a nutshell](http://rbasicsworkshop.weebly.com/uploads/1/8/6/0/18603232/adler_2009_r-inanutshell.pdf) : Many many receipes to solve all your questions
* R graphics cook book : very good for graphics

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## On line courses and web sites

* [Coursera](https://www.coursera.org/learn/r-programming)
*	[Pluralsight](https://www.pluralsight.com/courses/r-programming-fundamentals) - Not free
* [Quick-R, very simple](http://www.statmethods.net/)

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## Cheat sheets

* [R basics](http://github.com/rstudio/cheatsheets/raw/master/base-r.pdf)
* [ggplot2](https://github.com/rstudio/cheatsheets/raw/master/data-visualization-2.1.pdf)
* [dplyr](https://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf)

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## Forum

* https://stackoverflow.com/
*	http://r-statistics.co/
*	https://www.r-bloggers.com/

---

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## Setup

* Install [R](https://cran.r-project.org/index.html)

* Install [R studio](https://www.rstudio.com/products/rstudio/download/#download)

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## The R studio interface

- **Bottom left**
    - Console
- **Top left**
    - File editor for .R and .Rmd files
    - Data frame visualization
- **Top right**
    - Environment (i.e. R objects)
    - History
- **Bottom right**
    - Files
    - Plots
    - Packages
    - Help
]

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## Create a new project

* Open R studio
* Create new project for the course in a new directory
    - e.g. `Microbes course`

---

## Your first script

```r
print("Hello world")
```

```
[1] "Hello world"
```

### Two ways to proceed

1. Type directly in command window

2. Create a new script

---

---
## **variables** are abstracting your data

```r
> greeting = "Hello world"
> print(greeting)
```

```
[1] "Hello world"
```

```r
> greeting = "Bonjour"
> print(greeting)
```

```
[1] "Bonjour"
```

---
## variables are **objects**

* Assignement done with **<-**

```r
> x <- 1
> y <- 2
> x + y
```

```
[1] 3
```
--

```r
> z <- x + y
> z
```

```
[1] 3
```

---

**=** can be used instead of **<-** but refrain from it (not good style)

```r
>  z = x + y
```

You can view the values of the objects in R-studio environment window (top-right)

---

## R is **case sensitive**

```r
>  Z
```

```
Error in eval(expr, envir, enclos): objet 'Z' introuvable
```

---

## Rules for naming objects
* Use
    * letters
    * numbers
    * the dot
    * the underscore (not the minus sign !)
    
    
* Start always with a letter
    * `Myvariable`, `Myvariable1`, `Myvariable.1`,`Myvariable-01` are OK
    * `1Myvariable`, `My-variable`, `Myvariable@` are **not** OK

---
exclude: true

## Use consistent naming
Five conventions

* alllowercase: e.g. adjustcolor
* period.separated: e.g. plot.new
* **underscore_separated**: e.g. numeric_version
* lowerCamelCase: e.g. addTaskCallback
* UpperCamelCase: e.g. SignatureMethod

Prefer third one, much more easy to read
* Use **names** for objects : **last_name**
* Use **verbs** for function : **build_name**
* Think about best order
    - e.g. prefer maybe **name_last** because then you can have name_first, name_full... 
    - and you identify that all these objects are related to a name...

---
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# R objects

---

## Data types

* **character**: "Daniel", "This is a course in R", 'Joe Biden'

* **numeric**: 2, 15.5, 10e-3

* **integer**: 2L (the L tells R to store this as an integer)

* **date**: 2018-02-25

* **logical**: TRUE, FALSE

* **complex**: 1+4i (complex numbers with real and imaginary parts)

* **No data** "NA"

* **Not a number** "NaN" (e.g. division by zero)

---

## Data structures

* **Vector**

* **List**

* **Matrix**

* **Data frames**

* **Function**

---
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# Vectors

---

The basic R structure is a vector (think as a column in Excel): 
`$$\begin{bmatrix}10 \\ 20 \\ 30 \end{bmatrix}$$`

A vector can contain only a single element
`$$\begin{bmatrix}10 \end{bmatrix}$$`

--
## Assign a value to a vector

```r
 x <- 10
 x
```

```
[1] 10
```

---

## Assign several elements

```r
 x <- c(10,20,30)
 x
```

```
[1] 10 20 30
```
--

## Assign range

```r
 x <- 10:30
 x
```

```
 [1] 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
```

---

## Assign characters

```r
 PoTU <- c("Jo", "Biden")
 PoTU
```

```
[1] "Jo"    "Biden"
```

## Assign logical

```r
 flags <- c(TRUE, FALSE, TRUE)
 flags
```

```
[1]  TRUE FALSE  TRUE
```

---

## Access specific elements of a vector

### First

```r
 x[1] 
```

```
[1] 10
```

### Range

```r
 x[1:5] 
```

```
[1] 10 11 12 13 14
```

### Remove one element

```r
 x[-1] 
```

```
 [1] 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
```

---
exclude: true   
## Determine object properties

Apply functions (we will come back to functions latter)

* **typeof()** - what is the object’s data type (low-level)?
* **length()** - how long is it? What about two dimensional objects?

```r
 typeof(x)
 length(x)
```
--
exclude: true

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

```
[1] 21
```

--
exclude: true

---
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# Operators

---

## Arithmetic Operators

| Operator |	Description | 
|---|---|---|
| +	| addition|   
| -	| subtraction |  
| *	| multiplication| 
| /	| division | 
| ^ or ** | 	exponentiation | 
| x %% y | 	modulus (x mod y) 5%%2 is 1 | 
| x %/% y	| integer division 5%/%2 is 2 |

---

## Arithmetic Operators

We are performing vector operations !

`$$\begin{bmatrix} 1\\2\\3\\..\end{bmatrix}+\begin{bmatrix}1\\2\\3\\..\end{bmatrix}=\begin{bmatrix}2\\4\\6\\..\end{bmatrix}$$`

---
## Arithmetic Operators

Vector one element

```r
 x <- 1
 y <- 2
 z <- x + y
 z
```

```
[1] 3
```

---
## Arithmetic Operators

Vector several elements

```r
# Two instructions on the same line
 x <- 1:9; y <- 1:9
 z <- x + y
 z
```

```
[1]  2  4  6  8 10 12 14 16 18
```
--

.warning[
* Several instructions on same line separate by **;**
* The hastag **#** indicate a comment -> Use heavily to document your code
* However, it is even better to use R markdown (look it up for next class)
]
--
.student[
Use the other operators
]

---
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## Arithmetic Operators

What happens when the vectors have different number of elements ?

```r
 x <- 1:9
 y <- 1
 z <- x + y
 z
```

--
exclude: true

```
[1]  2  3  4  5  6  7  8  9 10
```

--
exclude: true

Equivalent to

```r
 y <- c(1,1,1,1,1,1,1,1,1)
```

The recycling rule...

---
exclude: true   
## Can we add logical ?

```r
 x <- TRUE
 y <- FALSE
 z <- x + y
 z
```

--
exclude: true

```
[1] 1
```

---
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## Can we add logical ?

No error but...

The resulting variable is transformed to a **numeric**

--
exclude: true

```r
 typeof(x)
```

```
[1] "logical"
```

```r
 typeof(z) 
```

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

---

## Logical Operators
| Operator |	Description | 
|---|---|---|
| <	| less than	|
| <=	| less than or equal to	|
| >	| greater than	|
| >=	| greater than or equal to	|
| ==	| exactly equal to	|
| !=	| not equal to	|
| !x	| Not x	|
| x &#124; y	| x OR y	|
| x & y	| x AND y	|
| isTRUE(x)	| test if X is TRUE	|

---

## Logical Operators

```r
 x <- TRUE
 y <- FALSE
 z1 <- x | y
 z2 <- x == y
```

```
[1] TRUE
```

```
[1] FALSE
```

---
exclude: true   
## Can we add characters ?

```r
 first <- "Jo"
 last <- "Biden"
 full <- first + last
```

--
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Generates an error

```
Error in first + last: argument non numérique pour un opérateur binaire
```

--
exclude: true

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# Functions

---
name: functions

Functions perform specific task on objects

* e.g. to concatanate strings we use **paste()**

```r
  paste(first,last)
```

```
[1] "Jo Biden"
```
--

* Functions take **arguments** and return an object called **result**

* To know the arguments use ?

```r
  ? paste()  # Do not forget the parenthesis
```
--

* Can go directly to Help panel and type function name

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## Help

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## Help

---
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## Getting what you want

Let's apply paste :

```r
  paste(first,last)
```

```
[1] "Jo Biden"
```

.student[
* We would like to get "Jo_Biden"
* Can you read the help and suggest a change in the way we call the function ?
* https://app.wooclap.com/R01
]

--
exclude: true

```r
  paste(first,last, sep="_")
```

```
[1] "Jo_Biden"
```

---
## Write your own function

```r
 my_sum <- function(a, b) {
 c <-a + b
 return (c)
 }
```
* __my_sum__ : function name
* __first_number, second_number__ : arguments
* instructions are enclosed by braces ({})
* return() : the value(s) returned

--
exclude: true

#### More compact way

```r
 my_sum <- function(a, b) {a + b}
```

---
## Call your function

```r
 my_sum(10, 20)
```

```
[1] 30
```

--
* better

```r
 my_sum(a = 10, b = 20)
```

```
[1] 30
```

---
exclude: true   
## Write a function to compute a product

* https://app.wooclap.com/R01

---
## Examples of functions

Most of the time you do not have to write functions because someone has already written one for what you want to do...

* Sum

```r
 x <- 1:100
 sum(x)
```

```
[1] 5050
```

* Normal distribution

```r
 y <- rnorm(10, mean = 0, sd = 1)
 y
```

```
 [1]  0.18698515 -1.90285690  1.06906481 -0.55548326  0.59540370 -0.04581134  0.38981055  0.92785608 -0.81038363 -0.08401824
```

---

## Statistics

```r
 mean(y)
```

```
[1] -0.02294331
```

```r
 sd(y)
```

```
[1] 0.8903981
```

Sample more points... 10,000 instead of 100

```r
 y <- rnorm(10000, mean = 0, sd = 1)
 mean(y)
```

```
[1] 0.003199685
```

```r
 sd(y)
```

```
[1] 1.003417
```

---

## Plot

```r
  library(graphics)
  hist(y)
```
]

<img src="R-session-01-intro_files/figure-html/unnamed-chunk-48-1.png" style="display: block; margin: auto;" />
]

---

---
Packages are set of functions that have a common goal

They are really the strength of R

And these are only the "official"" packages. You can find more on GitHub

---

## Installing a package

Download on your computer the package you need

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<img src="img/R_studio_package_01.png" width="45%" /><img src="img/R_studio_package_02.png" width="35%" />
]

---

## Using a package

To use functions from the package

- use the syntax `package::function`

```r
 stringr::str_c(first,last, sep= " ")
```

```
[1] "Jo Biden"
```

- load the package with the library function

```r
 library(stringr)
 str_c(first,last, sep= " ")
```

```
[1] "Jo Biden"
```

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## List installed packages

---

# Recap

.font150[
- R is case sensitive: Z !=  z
- Objects: data types vs data structures
- Vectors: think in vector operations
- Operators: arithmetic vs. logical
- Functions: try to practice
]

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# Next: 02 - Data wrangling

.font150[
* Data frames
* Concept of tidy data
* Reading data
* Manipulating data
    * Selecting columns
    * Selecting ows
]