Intro to R

# Intro to R
### Applied Machine Learning with R <a href='https://therbootcamp.github.io'> The R Bootcamp @ AMLD </a> <a href='https://therbootcamp.github.io/AML_2020AMLD/'> </a>  <a href='https://therbootcamp.github.io'> </a>  <a href='mailto:therbootcamp@gmail.com'> </a>  <a href='https://www.linkedin.com/company/basel-r-bootcamp/'> </a>
### January 2020

---

<div class="my-footer">
 
 
 <img src="https://raw.githubusercontent.com/therbootcamp/therbootcamp.github.io/master/_sessions/_image/by-sa.png" height=14 style="vertical-align: middle"/>
 
 <a href="https://therbootcamp.github.io/">
 
 
 www.therbootcamp.com
 
 
 </a>
 <a href="https://therbootcamp.github.io/">
 
 Applied Machine Learning with R @ AMLD | January 2020
 
 </a>
 
 </div>

---

# Why R?

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.

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

]

.pull-right6[

 <img src="https://i0.wp.com/r4stats.com/wp-content/uploads/2017/02/Fig-1a-IndeedJobs-2017.png" height="450">

]

---

# R is great for ML

...because of high-performance R packages (extensions) downloaded and used millions of times.

---

# 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/)
]

[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. 
]

---

<div class="center_text">
 
 10 basic R lessons
 
</div>

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1">The assignment operator <mono><-</mono></li>
 <li class="m2"><mono><-</mono> creates/changes objects</li>
 <li class="m3">Everythings happens through functions</li>
 <li class="m4">Functions have (default) arguments</li>
 <li class="m5">Arguments expect classes</li>
 <li class="m6">Find help using <mono>?</mono></li>
</ul>

Analysis
<ul>
 <li class="m7">Functions exist in Packages</li>
 <li class="m8">Data lives in data frames</li> 
 <li class="m9">Three+ data types</li> 
 <li class="m10">Formulae</li> 
</ul>

]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1"><high>The assignment operator <mono><-</mono></high></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

Analysis
<ul>
 <li class="m7g">Functions exist in Packages</li>
 <li class="m8g">Data lives in data frames</li> 
 <li class="m9g">Three+ data types</li> 
 <li class="m10g">Formulae</li> 
</ul>

]

]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2"><high><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

```r
# An object called one_two_three
one_two_three <- c(1, 2, 3)

# Print the object
print(one_two_three)
```

```
## [1] 1 2 3
```

```r
# Print the object
one_two_three
```

```
## [1] 1 2 3
```
]

---

# 10 basic R lessons

]

```r
# An object called one_two_three
one_two_three <- c(1, 2, 3)

# Calculate arithmetic mean
mean(one_two_three)
```

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

]

---

# 10 basic R lessons

]

```r
# An object called one_two_three
one_two_three <- c(1, 2, 3)

# Calculate arithmetic mean
result <- mean(one_two_three)

# Use the result
result * 10
```

```
## [1] 20
```

]

---

# 10 basic R lessons

]

```r
# An object called one_two_three
one_two_three <- c(1, 2, 3)

# Print the object
one_two_three
```

```
## [1] 1 2 3
```

```r
# Add 100
one_two_three + 100
```

```
## [1] 101 102 103
```

```r
# Print the object
one_two_three
```

```
## [1] 1 2 3
```

]

---

# 10 basic R lessons

]

```r
# An object called one_two_three
one_two_three <- c(1, 2, 3)

# Print the object
one_two_three
```

```
## [1] 1 2 3
```

```r
# Add 100 and re-assign
one_two_three <- one_two_three + 100

# Print the object
one_two_three
```

```
## [1] 101 102 103
```

]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3"><high>Everythings happens through functions</high></li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

<img src="image/input_output.png" height="300">
]

---

# 10 basic R lessons

]

```r
# Function c()
one_two_three <- c(1, 2, 3)

# Function `+`()
one_two_three + 100
```

```
## [1] 101 102 103
```

```r
# Function print()
one_two_three
```

```
## [1] 1 2 3
```

```r
# Function mean()
mean(one_two_three)
```

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

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4"><high>Functions have (default) arguments</high></li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

```r
# No argument
mean()
```

```
## Error in mean.default(): argument "x" is missing, with no default
```

```r
# One (necessary) argument
mean(c(1, 2, 3))
```

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

```r
# Add a missing value
mean(c(1, 2, 3, NA))
```

```
## [1] NA
```
]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4"><high>Functions have (default) arguments</high></li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

```r
# No argument
mean()
```

```
## Error in mean.default(): argument "x" is missing, with no default
```

```r
# One (necessary) argument
mean(c(1, 2, 3))
```

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

```r
# Change the default to handle missing
mean(c(1, 2, 3, NA), na.rm = TRUE)
```

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

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4"><high>Functions have (default) arguments</high></li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

```r
# Mean of c(1, 2, 3)
mean(c(1, 2, 3))
```

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

```r
# Mean of c('1', '2', '3')
mean(c("1", "2", "3"))
```

```
## Warning in mean.default(c("1", "2", "3")): argument is not numeric or logical: returning NA
```

```
## [1] NA
```
]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5"><high>Arguments expect classes</high></li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

```r
# Class of c(1, 2, 3)
class(c(1, 2, 3))
```

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

```r
# Class of c('1', '2', '3')
class(c("1", "2", "3"))
```

```
## [1] "character"
```
]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6"><high>Find help using <mono>?</mono></high></li>
</ul>

]

```r
?mean
```
<img src="image/help_mean.png" width="500">
]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6"><high>Find help using <mono>?</mono></high></li>
</ul>

]

```r
?mean
```
<img src="image/help_usage.png" width="500">
]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6"><high>Find help using <mono>?</mono></high></li>
</ul>

]

```r
# Mean of c(1, 2, 3)
mean(c(1, 2, 3))
```

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

```r
# Mean of c(TRUE, FALSE, TRUE)
mean(c(TRUE, FALSE, TRUE))
```

```
## [1] 0.6667
```

```r
# Mean of c("1", "2", "3")
mean(c("1", "2", "3"))
```

```
## Warning in mean.default(c("1", "2", "3")): argument is not numeric or logical: returning NA
```

```
## [1] NA
```

]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

Analysis
<ul>
 <li class="m7"><high>Functions exist in Packages</high></li>
 <li class="m8g">Data lives in data frames</li> 
 <li class="m9g">Three+ data types</li> 
 <li class="m10g">Formulae</li> 
</ul>

]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

<high>Install</high> packages <high>once</high> using `install.packages()`

```r
install.packages("tidyverse")
```
<br2>
<high>Attach</high> existing packages <high>every time</high> using `library()`

```r
library(tidyverse)
```

<img src="image/tidyverse.png" height="180">
]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

Analysis
<ul>
 <li class="m7g">Functions exist in Packages</li>
 <li class="m8"><high>Data lives in data frames</high></li> 
 <li class="m9g">Three+ data types</li> 
 <li class="m10g">Formulae</li> 
</ul>

]

.pull-right55[
<img src="https://raw.githubusercontent.com/therbootcamp/therbootcamp.github.io/master/_sessions/_image/main_objects.png"></img>
]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

Analysis
<ul>
 <li class="m7g">Functions exist in Packages</li>
 <li class="m8g">Data lives in data frames</li> 
 <li class="m9"><high>Three+ data types</high></li> 
 <li class="m10g">Formulae</li> 
</ul>

]

.pull-right5[
<img src="https://raw.githubusercontent.com/therbootcamp/therbootcamp.github.io/master/_sessions/_image/vector_types.png"></img>
]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

```r
print(baselers)
```

```
## # A tibble: 10,000 x 20
## id sex age height weight income
## <dbl> <chr> <dbl> <dbl> <dbl> <dbl>
## 1 1 male 44 174. 113. 6300
## 2 2 male 65 180. 75.2 10900
## 3 3 fema… 31 168. 55.5 5100
## 4 4 male 27 209 93.8 4200
## 5 5 male 24 177. NA 4000
## 6 6 male 63 187. 67.4 11400
## 7 7 male 71 152. 83.3 12000
## 8 8 fema… 41 156. 67.8 7600
## 9 9 male 43 176. 69.3 8500
## 10 10 fema… 31 166. 66.3 6100
## # … with 9,990 more rows, and 14 more variables
```
]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

```r
# select sex veriable using $
baselers$sex
```

```
## [1] "male"   "male"   "female" "male"  
## [5] "male"   "male"   "male"   "female"
##  [ reached getOption("max.print") -- omitted 9992 entries ]
```

```r
# select sex veriable using %>% select
baselers %>% select(sex) %>% pull()
```

```
## [1] "male"   "male"   "female" "male"  
## [5] "male"   "male"   "male"   "female"
##  [ reached getOption("max.print") -- omitted 9992 entries ]
```

```r
# Possible, but less pretty...
baselers[['sex']]
baselers[[2]]
```

]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

```r
# original sex vector
baselers$sex
```

```
## [1] "male"   "male"   "female" "male"   "male"  
##  [ reached getOption("max.print") -- omitted 9995 entries ]
```

```r
as.factor(baselers$sex)
```

```
## [1] male   male   female male   male  
##  [ reached getOption("max.print") -- omitted 9995 entries ]
## Levels: female male
```

```r
as.factor(baselers$weight)
```

```
## [1] 113.4 75.2 55.5 93.8 <NA> 
## [ reached getOption("max.print") -- omitted 9995 entries ]
## 719 Levels: 37.9 38.3 39.2 39.6 40.3 ... 125.4
```

]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

```r
# Run a regression and store result in my_lm
my_lm <- lm(formula = income ~ age + height,
 data = baselers)
```
 
<img src="https://raw.githubusercontent.com/therbootcamp/Erfurt_2018June/master/_sessions/_image/formula_description.png"></img>
]

---

# 10 basic R lessons

Syntax
<ul>
 <li class="m1g">The assignment operator <mono><-</mono></li>
 <li class="m2g"><mono><-</mono> creates/changes objects</high></li>
 <li class="m3g">Everythings happens through functions</li>
 <li class="m4g">Functions have (default) arguments</li>
 <li class="m5g">Arguments expect classes</li>
 <li class="m6g">Find help using <mono>?</mono></li>
</ul>

]

```r
# Include multiple terms with +
my_lm <- lm(formula = income ~ age + height,
 data = baselers)
```

<high>Include all variables</high> using `formula = y ~ .`

```r
# Use y ~ . to include ALL variables
my_lm <- lm(formula = income ~ .,
 data = baselers)
```

<high>Subtract variables</high> using `-`

```r
# Remove variables with -
my_lm <- lm(formula = income ~ . - id,
 data = baselers)
```

]

---

<h1><a>Interactive</a></h1>