1 Introduction

First class, introduction to R and how to use it

1.1 General R usage

Set up your directory

setwd(".")

Install and load tidyverse

install.packages("tidyverse")
library(tidyverse)

1.2 Basics :

• R comments start with #
• Use text editor and beware of ”smart quotes”
• To get help about anything use ?: ?seq will show you the manual to use the function seq (a function which generates sequences of numbers)
• To assign a value to a variable use the assignment operator <-

1.3 Explore dataset:

We will use the mpg dataset which is load by default with tidyverse

To have more info about this dataset:

?mpg 

To see the first lines of a dataset:

 head(mpg) 
## # A tibble: 6 x 11
##   manufacturer model displ  year   cyl trans      drv     cty   hwy fl    class 
##   <chr>        <chr> <dbl> <int> <int> <chr>      <chr> <int> <int> <chr> <chr> 
## 1 audi         a4      1.8  1999     4 auto(l5)   f        18    29 p     compa…
## 2 audi         a4      1.8  1999     4 manual(m5) f        21    29 p     compa…
## 3 audi         a4      2    2008     4 manual(m6) f        20    31 p     compa…
## 4 audi         a4      2    2008     4 auto(av)   f        21    30 p     compa…
## 5 audi         a4      2.8  1999     6 auto(l5)   f        16    26 p     compa…
## 6 audi         a4      2.8  1999     6 manual(m5) f        18    26 p     compa…

To see the structure of the data:

 str(mpg)
## Classes 'tbl_df', 'tbl' and 'data.frame':    234 obs. of  11 variables:
##  $ manufacturer: chr  "audi" "audi" "audi" "audi" ...
##  $ model       : chr  "a4" "a4" "a4" "a4" ...
##  $ displ       : num  1.8 1.8 2 2 2.8 2.8 3.1 1.8 1.8 2 ...
##  $ year        : int  1999 1999 2008 2008 1999 1999 2008 1999 1999 2008 ...
##  $ cyl         : int  4 4 4 4 6 6 6 4 4 4 ...
##  $ trans       : chr  "auto(l5)" "manual(m5)" "manual(m6)" "auto(av)" ...
##  $ drv         : chr  "f" "f" "f" "f" ...
##  $ cty         : int  18 21 20 21 16 18 18 18 16 20 ...
##  $ hwy         : int  29 29 31 30 26 26 27 26 25 28 ...
##  $ fl          : chr  "p" "p" "p" "p" ...
##  $ class       : chr  "compact" "compact" "compact" "compact" ...

You can see from the output that this is a data.frame: a rectangular structure with column and lines (?data.frame if you want to learn more data.frame). As you can see each column may store data of different types: here int ie numbers and chrs ie string of characters.

To get the list of column names:

names(mpg)
##  [1] "manufacturer" "model"        "displ"        "year"         "cyl"         
##  [6] "trans"        "drv"          "cty"          "hwy"          "fl"          
## [11] "class"

To get some simple summary statistics of the dataset:

summary(mpg)
##  manufacturer          model               displ            year     
##  Length:234         Length:234         Min.   :1.600   Min.   :1999  
##  Class :character   Class :character   1st Qu.:2.400   1st Qu.:1999  
##  Mode  :character   Mode  :character   Median :3.300   Median :2004  
##                                        Mean   :3.472   Mean   :2004  
##                                        3rd Qu.:4.600   3rd Qu.:2008  
##                                        Max.   :7.000   Max.   :2008  
##       cyl           trans               drv                 cty       
##  Min.   :4.000   Length:234         Length:234         Min.   : 9.00  
##  1st Qu.:4.000   Class :character   Class :character   1st Qu.:14.00  
##  Median :6.000   Mode  :character   Mode  :character   Median :17.00  
##  Mean   :5.889                                         Mean   :16.86  
##  3rd Qu.:8.000                                         3rd Qu.:19.00  
##  Max.   :8.000                                         Max.   :35.00  
##       hwy             fl               class          
##  Min.   :12.00   Length:234         Length:234        
##  1st Qu.:18.00   Class :character   Class :character  
##  Median :24.00   Mode  :character   Mode  :character  
##  Mean   :23.44                                        
##  3rd Qu.:27.00                                        
##  Max.   :44.00

1.4 Vectors

to create a vector use c() ### Exemple: * Numeric Vector

a <- c(1,2,3.5,6,-3,2)
b <- c("one","two","three","seven")
c <- c(TRUE,FALSE,FALSE,TRUE)

To select the ith element of a vector a use the notation a[i]. You can also select multiple values from the same vector by using the notation a[c(i,j)].

a[c(2,4)]
## [1] 2 6
b[c(2,4)]
## [1] "two"   "seven"
c[c(2,4)]
## [1] FALSE  TRUE

As you may have noticed this means you use a second vector to store the indices of the elements you want so the notation a[c(2,4)] could be rewritten as:

ind <- c(2,4)
a[ind]
## [1] 2 6
b[ind]
## [1] "two"   "seven"
c[ind]
## [1] FALSE  TRUE

1.5 Matrices and arrays

All columns must be the same type (numeric, character, etc.) and the same length. Arrays are similar than matrices but can have more than two dimensions

entries  <-  c(1,2,3,5)
rowNames  <- c("Burial 1","Burial 2")
columnNames  <- c("pots","bangles")
cementery  <-  matrix(entries,nrow=2,ncol=2,byrow=TRUE,dimnames=list(rowNames,columnNames))
cementery
##          pots bangles
## Burial 1    1       2
## Burial 2    3       5

1.6 Working directory

setwd("~/projects/bg4ss/") #adapt this command with a directory that exists in your computer 

To know the actual working directory:

getwd()
## [1] "/builds/sc/bd4ss"

1.7 Data Frame

1.8 Plots

x  <- rnorm(100,mean=20,sd=2)
y  <- rnorm(100,mean=60,sd=10)
plot(x,y)

We can use this simple plot function to visualise the mpg dataset:

plot(mpg$cty,mpg$hwy)

## ggplots

How can we do

1.8.1 The mpg data frame

We will reuse the mpg data set

mpg
## # A tibble: 234 x 11
##    manufacturer model    displ  year   cyl trans   drv     cty   hwy fl    class
##    <chr>        <chr>    <dbl> <int> <int> <chr>   <chr> <int> <int> <chr> <chr>
##  1 audi         a4         1.8  1999     4 auto(l… f        18    29 p     comp…
##  2 audi         a4         1.8  1999     4 manual… f        21    29 p     comp…
##  3 audi         a4         2    2008     4 manual… f        20    31 p     comp…
##  4 audi         a4         2    2008     4 auto(a… f        21    30 p     comp…
##  5 audi         a4         2.8  1999     6 auto(l… f        16    26 p     comp…
##  6 audi         a4         2.8  1999     6 manual… f        18    26 p     comp…
##  7 audi         a4         3.1  2008     6 auto(a… f        18    27 p     comp…
##  8 audi         a4 quat…   1.8  1999     4 manual… 4        18    26 p     comp…
##  9 audi         a4 quat…   1.8  1999     4 auto(l… 4        16    25 p     comp…
## 10 audi         a4 quat…   2    2008     4 manual… 4        20    28 p     comp…
## # … with 224 more rows

1.8.2 Creating a ggplot

To plot mpg

ggplot(data = mpg)+
    geom_point(mapping = aes(x = displ, y =hwy))

1.8.3 adding colors:

ggplot(data = mpg)+
    geom_point(mapping = aes(x = displ, y =hwy,color=class))

1.8.4 Facets

ggplot(data = mpg)+
    geom_point(mapping = aes(x = displ, y =hwy,color=class))+
facet_wrap(~ class,nrow=2)

ggplot(data = mpg)+
    geom_point(mapping = aes(x = displ, y =hwy,color=class))+
facet_wrap( drv ~ class,nrow=2)

1.9 For those who finished all

Can you reproduce the following plots? You will need some of the libraries listed below.

library(ggplot2)
library(ggthemes)

PLOT 1:

PLOT 2:

PLOT 3:

PLOT 4: (hint you will need to use theme_economist_white() from ggthemes)