Introduction to R / RStudio

BMS

Karin Groothuis-Oudshoorn & Robert Marinescu-Muster

August 27th

1
Program today

• Introduction R / RStudio
• tables in R (with dplyr)
• Make table objects
• Select rows/columns
• Sort rows
• Add new columns
• Aggregate data
• Make graphs with ggplot2
• Simple regression models

2
R for Data Science

3
R for Data Science boek

book online: http://r4ds.had.co.nz/

4
R en RStudio

R: the engine RStudio: Dashboard

5
RStudio

6
R and R packages

R: a new phone R packages: Apps that you can

download

7
Installing and using packages

1. Install package: only once

2. Lading package: every session
3. Reinstall package: if you update R
4. List with default packages:
## which packages are default loaded?
search()

## [1] ".GlobalEnv" "package:stats" "package:graphics"

## [4] "package:grDevices" "package:utils" "package:datasets"
## [7] "package:methods" "Autoloads" "package:base"

8
Installing packages

The easy way: in the lower right

panel of RStudio:
a) Click on the ’Packages’ tab
b) Click on ’Install’
c) Type the name of the
package under ’Packages’
d) Click on ’Install’

9
Tidyverse

• Developer: Hadley Wickham (van RStudio)

• Collection of packages: dplyr, ggplot2, tibble, readr,

tidyr, purrr, stringr, forcats

• More consistent than standard R

• A good starting point to learn R

• Is not standard R!

• Webpage: http://www.tidyverse.org
install.packages(tidyverse)
library(tidyverse)
10
Base R
Variabels / Vectors: int, num

a <- 1L
class(a)

## [1] "integer"
vec1 <- c(1L,3L,5L,7L)
class(vec1)

## [1] "integer"
vec2 <- c(10.5,3.2,pi,4)
class(vec2)

## [1] "numeric"
vec1 + vec2

## [1] 11.500000 6.200000 8.141593 11.000000

11
Variabels / Vectors: chr, lgl, date

• vec3: character vector ("character")

• vec4: logical vector ("logical")
• vec5: date vector ("date")
vec3 <- c("low","low","high","medium")
vec4 <- c(TRUE,FALSE,TRUE,FALSE)
library(lubridate)
vec5 <- ymd(c("2000-9-14","2002-7-3",
"2004-4-14","2004-6-10"))

12
Tables: dataframe or tibble

• Columns of a dataframe / tibble are vectors

• Each column/vector has equal length and may have different
types of data
library(tibble)
table <- tibble(
col1 = vec1,
col2 = vec2,
col3 = vec3,
col4 = vec4,
col5 = vec5
)
table

## # A tibble: 4 x 5
## col1 col2 col3 col4 col5
## <int> <dbl> <chr> <lgl> <date>
## 1 1 10.5 low TRUE 2000-09-14
## 2 3 3.2 low FALSE 2002-07-03
## 3 5 3.14 high TRUE 2004-04-14
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## 4 7 4 medium FALSE 2004-06-10
Work with columns and vectors

• Use $ to work with columns

• Select elements or parts of a vector / table with the brackets: [
and ]
table$col1 # select the column vec1 from table
table[,1] # select the first column from the table
table[1,] # select the first row from the table
table[1:2,3:4] # select the first 2 row, 3 and 4e column
table[table$col3 == "low",] # select all rows with vec3 == "low"

14
Functions

• a function has a name and arguments

• the arguments are between parenthesis ().
• use no space between function name and the parenthesis!
• use the help() function for more info of a function
sum(c(3,5,7))

## [1] 15
mean(c(10,14,2000))

## [1] 674.6667
mean(c(10,14,NA), na.rm = T)

## [1] 12

15
Objects

• object contains the result of an assignment

• object can be used in a new assignment
• object you can make with <- (or with =)
• object will be save in global environment (so upper left panel)
• object global environment will be deleted if you quit
R/Rstudio (except if you save it)
a_row <- seq(from = 100, to = 200, by = 10)
a_row2 <- 2*a_row
a_row2

## [1] 200 220 240 260 280 300 320 340 360 380 400

16
Naming of objects

• the name of an object starts with a letter

• the name of an object contains only letters, numbers, _ and .
• small letters and capital letters are NOT the same
• don’s use spaces in names

17
R script

• Document with lines of assignments / code

• Extension of the file is .R
• Comments can be written in it starting with a hashtag (#)
• Run the code with the Run-button (in the middle/ above in
RStudio)
• Output will be shown in the Console
• Advances reproducibility

18
RStudio Project

• A directory on the hard disk

• Put scripts and data in a project directory
• A project directory is a working directory for R
• RStudio places some standard files in a project directory
• You can make a project directory with File > New Project
• You can open an existing project directory with File > Open
Project
• Data on a project will be saved in the file
<jouw_projectnaam>.Rproj.

19
Exercise session 1
Tables in R
Tables

• A table object has a name

• A talbe has rows and columns
• Data in a column should have the same type
• Columns are all of equal size
• Columns have a name
• Rows sometimes have a name (possible for dataframes, not
for tibbles)

20
Example: Gapminder table

library(gapminder)
gapminder

## # A tibble: 1,704 x 6
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Afghanistan Asia 1952 28.8 8425333 779.
## 2 Afghanistan Asia 1957 30.3 9240934 821.
## 3 Afghanistan Asia 1962 32.0 10267083 853.
## 4 Afghanistan Asia 1967 34.0 11537966 836.
## 5 Afghanistan Asia 1972 36.1 13079460 740.
## 6 Afghanistan Asia 1977 38.4 14880372 786.
## 7 Afghanistan Asia 1982 39.9 12881816 978.
## 8 Afghanistan Asia 1987 40.8 13867957 852.
## 9 Afghanistan Asia 1992 41.7 16317921 649.
## 10 Afghanistan Asia 1997 41.8 22227415 635.
## # ... with 1,694 more rows

21
Base R versus tidyverse

# Base R
asia <- gapminder[gapminder$continent == "Asia",]
mean(asia$lifeExp)

## [1] 60.0649
library(dplyr) # Tidyverse
gapminder %>%
filter(continent == "Asia") %>%
summarise(mean_exp = mean(lifeExp))

## # A tibble: 1 x 1
## mean_exp
## <dbl>
## 1 60.1
22
The pipe operator

• A way of chaining commands next to each other

• You can read it as and then
• Part of package magittr (but is automatically loaded with
dplyr)
gapminder %>%
filter(continent == "Asia") %>%
summarise(mean_exp = mean(lifeExp))
# without pipe
temp <- filter(gapminder, continent == "Asia")
temp <- summarise(temp, mean_exp = mean(lifeExp))
23
Seven verbs for data wrangling (package dplyr)

• filter
• summarise
• group_by (and ungroup)
• mutate
• arrange
• rename
• select

24
filter()

• select rows from a table

• arguments are filters that you want to apply
• use == to compare values
gap_2007 <- gapminder %>%
filter(year == 2007)
head(gap_2007, n = 4)

## # A tibble: 4 x 6
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Afghanistan Asia 2007 43.8 31889923 975.
## 2 Albania Europe 2007 76.4 3600523 5937.
## 3 Algeria Africa 2007 72.3 33333216 6223.
## 4 Angola Africa 2007 42.7 12420476 4797.

25
filter(): more filters simultaneously (OR operator)

• use | to use more filters simultaneously

• checks if at least one filter is satisfied
gapminder %>%
filter(year == 2007 | continent == "Asia") %>%
sample_n(8)

## # A tibble: 8 x 6
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Djibouti Africa 2007 54.8 496374 2082.
## 2 Bahrain Asia 1977 65.6 297410 19340.
## 3 Thailand Asia 1997 67.5 60216677 5853.
## 4 Namibia Africa 2007 52.9 2055080 4811.
## 5 Singapore Asia 1982 71.8 2651869 15169.
## 6 Korea, Dem. Rep. Asia 2007 67.3 23301725 1593.
## 7 Nepal Asia 1997 59.4 23001113 1011.
## 8 Reunion Africa 2007 76.4 798094 7670.

26
filter(): more filters simultaneously (AND operator)

• use, of & or to use more filters

• checks whether all filters are satisfied
gapminder %>%
filter(year == 2002, continent == "Asia")

## # A tibble: 33 x 6
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Afghanistan Asia 2002 42.1 25268405 727.
## 2 Bahrain Asia 2002 74.8 656397 23404.
## 3 Bangladesh Asia 2002 62.0 135656790 1136.
## 4 Cambodia Asia 2002 56.8 12926707 896.
## 5 China Asia 2002 72.0 1280400000 3119.
## 6 Hong Kong, China Asia 2002 81.5 6762476 30209.
## 7 India Asia 2002 62.9 1034172547 1747.
## 8 Indonesia Asia 2002 68.6 211060000 2874.
## 9 Iran Asia 2002 69.5 66907826 9241.
## 10 Iraq Asia 2002 57.0 24001816 4391.
## # ... with 23 more rows
27
filter(): use of %in%

• repeatedly use of | with ==

gapminder %>%
filter(year %in% c(1987,1992,1997),
country %in% c("Netherlands","Belgium"))

## # A tibble: 6 x 6
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Belgium Europe 1987 75.4 9870200 22526.
## 2 Belgium Europe 1992 76.5 10045622 25576.
## 3 Belgium Europe 1997 77.5 10199787 27561.
## 4 Netherlands Europe 1987 76.8 14665278 23651.
## 5 Netherlands Europe 1992 77.4 15174244 26791.
## 6 Netherlands Europe 1997 78.0 15604464 30246.

28
summarise()

• function to calculate aggregate statistics

stats_2007 <- gapminder %>%
filter(year == 2007) %>%
summarise(max_exp = max(lifeExp),
mean_exp = mean(lifeExp),
sd_exp = sd(lifeExp))
stats_2007

## # A tibble: 1 x 3
## max_exp mean_exp sd_exp
## <dbl> <dbl> <dbl>
## 1 82.6 67.0 12.1

29
combination of group_by() and summarise()

• calculate a numerical summary per group using a

categorical variable
stats_2007 <- gapminder %>%
filter(year == 2007) %>%
group_by(continent) %>%
summarise(max_exp = max(lifeExp),
mean_exp = mean(lifeExp),
sd_exp = sd(lifeExp),
aantal = n())
stats_2007

## # A tibble: 5 x 5
## continent max_exp mean_exp sd_exp aantal
## <fct> <dbl> <dbl> <dbl> <int>
## 1 Africa 76.4 54.8 9.63 52
## 2 Americas 80.7 73.6 4.44 25
## 3 Asia 82.6 70.7 7.96 33
## 4 Europe 81.8 77.6 2.98 30
## 5 Oceania 81.2 80.7 0.729 2
30
mutate()

• create a new column with a fixed value

gap_plus <- gapminder %>%
mutate(just_one = 1)
head(gap_plus, n=4)

## # A tibble: 4 x 7
## country continent year lifeExp pop gdpPercap just_one
## <fct> <fct> <int> <dbl> <int> <dbl> <dbl>
## 1 Afghanistan Asia 1952 28.8 8425333 779. 1
## 2 Afghanistan Asia 1957 30.3 9240934 821. 1
## 3 Afghanistan Asia 1962 32.0 10267083 853. 1
## 4 Afghanistan Asia 1967 34.0 11537966 836. 1

31
mutate()

• create a new column with other variables/columns

gap_gdp <- gapminder %>%
mutate(gdp = pop * gdpPercap)
head(gap_gdp, n=4)

## # A tibble: 4 x 7
## country continent year lifeExp pop gdpPercap gdp
## <fct> <fct> <int> <dbl> <int> <dbl> <dbl>
## 1 Afghanistan Asia 1952 28.8 8425333 779. 6567086330.
## 2 Afghanistan Asia 1957 30.3 9240934 821. 7585448670.
## 3 Afghanistan Asia 1962 32.0 10267083 853. 8758855797.
## 4 Afghanistan Asia 1967 34.0 11537966 836. 9648014150.

32
mutate()

• adapt existing columns

• also if you have made a column in the same mutate statement
gap_gdp <- gap_gdp %>%
mutate(gdp = gdp/1000000)
head(gap_gdp, n=4)

## # A tibble: 4 x 7
## country continent year lifeExp pop gdpPercap gdp
## <fct> <fct> <int> <dbl> <int> <dbl> <dbl>
## 1 Afghanistan Asia 1952 28.8 8425333 779. 6567.
## 2 Afghanistan Asia 1957 30.3 9240934 821. 7585.
## 3 Afghanistan Asia 1962 32.0 10267083 853. 8759.
## 4 Afghanistan Asia 1967 34.0 11537966 836. 9648.

33
combination of mutate() and group_by

• mutate colums by subcategory

gapminder %>%
filter(year == 2007) %>%
group_by(continent) %>%
mutate(rank = rank(desc(lifeExp))) %>% arrange(rank)

## # A tibble: 142 x 7
## # Groups: continent [5]
## country continent year lifeExp pop gdpPercap rank
## <fct> <fct> <int> <dbl> <int> <dbl> <dbl>
## 1 Australia Oceania 2007 81.2 20434176 34435. 1
## 2 Canada Americas 2007 80.7 33390141 36319. 1
## 3 Iceland Europe 2007 81.8 301931 36181. 1
## 4 Japan Asia 2007 82.6 127467972 31656. 1
## 5 Reunion Africa 2007 76.4 798094 7670. 1
## 6 Costa Rica Americas 2007 78.8 4133884 9645. 2
## 7 Hong Kong, China Asia 2007 82.2 6980412 39725. 2
## 8 Libya Africa 2007 74.0 6036914 12057. 2
## 9 New Zealand Oceania 2007 80.2 4115771 25185. 2
## 10 Switzerland Europe 2007 81.7 7554661 37506. 2 34
## # ... with 132 more rows
arrange()

• Order rows on the basis of other columns

• Default is ascending or alphabetical order
• NAs will be placed in the end
gapminder %>% arrange(year,country) %>% head(5)

## # A tibble: 5 x 6
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Afghanistan Asia 1952 28.8 8425333 779.
## 2 Albania Europe 1952 55.2 1282697 1601.
## 3 Algeria Africa 1952 43.1 9279525 2449.
## 4 Angola Africa 1952 30.0 4232095 3521.
## 5 Argentina Americas 1952 62.5 17876956 5911.

35
arrange() : descending order

• use the function desc()

gapminder %>% filter(year == 2007) %>%
arrange(desc(lifeExp)) %>% head(n = 5)

## # A tibble: 5 x 6
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Japan Asia 2007 82.6 127467972 31656.
## 2 Hong Kong, China Asia 2007 82.2 6980412 39725.
## 3 Iceland Europe 2007 81.8 301931 36181.
## 4 Switzerland Europe 2007 81.7 7554661 37506.
## 5 Australia Oceania 2007 81.2 20434176 34435.

36
group_by and ungroup()

• Split the categories with group_by() and unsplit with

ungroup()
temp <- gapminder %>%
group_by(continent, country)
head(temp, n = 1)

## # A tibble: 1 x 6
## # Groups: continent, country [1]
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Afghanistan Asia 1952 28.8 8425333 779.
temp <- temp %>% ungroup()
head(temp, n = 1)

## # A tibble: 1 x 6
## country continent year lifeExp pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Afghanistan Asia 1952 28.8 8425333 779.

37
select(): select columns

• select columns from a table

## select continent and country
gapminder %>% select(continent, country)

## select all column except gdpPercap

gapminder %>% select(-gpdPercap)

## select all columns continent untill pop

gapminder %>% select(continent:pop)

## select all columns except for continent untill pop

gapminder %>% select(-(continent:pop))

38
rename(): change column name

• change name of column

• left from = new name
• right from = old name
gapminder_NL <- gapminder %>%
rename(land = country,
jaar = year,
levensverwachting = lifeExp)

head(gapminder_NL, n = 2)

## # A tibble: 2 x 6
## land continent jaar levensverwachting pop gdpPercap
## <fct> <fct> <int> <dbl> <int> <dbl>
## 1 Afghanistan Asia 1952 28.8 8425333 779.
## 2 Afghanistan Asia 1957 30.3 9240934 821.

39
Some usefull functions for tables

nrow(gapminder) # number rows table

ncol(gapminder) # number columns table
names(gapminder) # columns names table
str(gapminder) # structure table
head(gapminder) # head of table (first rows)
tail(gapminder) # tail of table (last rows)

40
Difference with and without pipe

## select continent en country

temp <- gapminder %>% select(continent, country) ## with pipe
temp <- select(gapminder, continent, country) ## without pipe

## Add column with gpd

gap_gdp <- gapminder %>%
mutate(gdp = pop * gdpPercap) ## with pipe
gap_gdp <- mutate(gapminder, gdp = pop * gdpPercap) ## without pipe

## calculate maximale life expectacy

stats_2007 <- gapminder %>%
filter(year == 2007) %>%
summarise(max_exp = max(lifeExp)) ## with pipe

temp <- filter(gapminder, year == 2007) ## without pipe

stats_2007 <- summarise(temp, max_exp = max(lifeExp))

41
Import datasets

• package readr
• via menu (in Environment button )
library(readr)
lbw <- read_csv("data/lbw_data.csv")

42
Make categorical variables

• package forcats
library(forcats)
lbw <- lbw %>%
mutate(low = factor(low),
low = fct_recode(low,"No" = "0", "Yes" = "1"),
race = factor(race),
race = fct_recode(race,"White" = "1","Black" = "2",
"Other" = "3"),
smoke = factor(smoke),
smoke = fct_recode(smoke,"No" = "0", "Yes" = "1"),
ht = factor(ht),
ht = fct_recode(ht,"No" = "0", "Yes" = "1"),
ui = factor(ui),
ui = fct_recode(ui,"No" = "0", "Yes" = "1"))

43
Exercise session 2
Make graphs with ggplot2
Package ggplot2

• Not standard R
• Based on Grammar of Graphics
• Graph = Data + Layout + Coordinate system
• Graph can have more layers
• A layer has aesthetic (aes) properties coupled with properties of
data
• Handy cheatsheet: https://www.rstudio.com/wp-
content/uploads/2015/03/ggplot2-cheatsheet.pdf

44
Scatterplot example code

library(ggplot2)

ggplot(lbw, aes(x = age, y = bwt)) +

geom_point() +
geom_smooth(method = "lm", se = FALSE) +
coord_cartesian(xlim = c(15,46), ylim = c(0, 5500)) +
labs(title = "Birthweigth and age mother",
x = "Age mother",
y = "Birth weight")

45
Scatterplot example
Birthweigth and age mother

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0 46
Scatterplot example code: split according to smoking

• aes(): col, shape, size

library(ggplot2)

ggplot(lbw, aes(x = age, y = bwt)) +

geom_point(aes(col = smoke)) +
geom_smooth(method = "lm", se = FALSE) +
labs( x = "Age mother",
y = "Birth weight",
color = "Smoking")

47
Scatterplot split according to smoking

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48
Histogram

library(ggplot2)

ggplot(data = lbw) +
geom_histogram(aes(x = age, y = ..count.., fill = race)) +
labs(x = "Age mother",
y = "Number",
fill = "Race")

49
Histogram

20

Race
Number

White
Black
Other

10

0 50
Boxplot

library(ggplot2)

ggplot(data = lbw) +
geom_boxplot(aes(x = race, y = age, fill = smoke)) +
labs(x = "Race mother",
y = "Age mother",
fill = "Smoking")

51
Boxplot

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No
Yes

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52
Subplots

library(ggplot2)

ggplot(data = lbw) +
geom_histogram(aes(x = age, y = ..count..)) +
labs(x = "Age mother",
y = "Number") +
facet_wrap( ~ race, nrow = 1)

53
Histogram split with smoking
White Black Other

6
Number

20 30 40 20 30 40 20 30 40
Age mother

54
Exercise session 3
Simple models
Example: relation between FEV and age
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age

55
Linear regression

• function lm()
• formula model: response ~ x1 + x2 + etcetera
• intercept will be estimated automatically
• rows with missings (NA’s) will be discarded.
library(modelr)

fevDat <- read_csv(file = "data/fev.csv")

model <- lm(fev ~ age, data = fevDat)

summary(model) # Summary model

coefficients(model) # Beta's
nobs(model) # number of observations without NA's

56
Output lm

##
## Call:
## lm(formula = fev ~ age, data = fevDat)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.57539 -0.34567 -0.04989 0.32124 2.12786
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.431648 0.077895 5.541 4.36e-08 ***
## age 0.222041 0.007518 29.533 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.5675 on 652 degrees of freedom
## Multiple R-squared: 0.5722, Adjusted R-squared: 0.5716
## F-statistic: 872.2 on 1 and 652 DF, p-value: < 2.2e-16

57
Predictions

fevDat <- add_predictions(fevDat, model)

temp2 <- tibble(age = c(25,35,45,55,65))
temp2 <- add_predictions(temp2, model)
temp2

## # A tibble: 5 x 2
## age pred
## <dbl> <dbl>
## 1 25 5.98
## 2 35 8.20
## 3 45 10.4
## 4 55 12.6
## 5 65 14.9

58
Residuals

• add_residuals adds column resid with residual i

fevDat <- add_residuals(fevDat, model)

## histogram residuals
ggplot(fevDat) + geom_histogram(aes(x = resid))
## residualplot
ggplot(fevDat) + geom_point(aes(x = pred, y = resid))

59
Logistic regression

model <- glm(low ~ race + smoke + ht + ui + age + lwt,

data = lbw, family = "binomial")

summary(model)$coefficients # Beta's

## Estimate Std. Error z value Pr(>|z|)

## (Intercept) 0.43724022 1.191931228 0.3668334 0.713743272
## raceBlack 1.28064059 0.526694968 2.4314654 0.015037885
## raceOther 0.90188006 0.434362303 2.0763313 0.037863316
## smokeYes 1.02757057 0.393930669 2.6085061 0.009093838
## htYes 1.85761692 0.688848290 2.6966996 0.007003041
## uiYes 0.89538678 0.448493792 1.9964307 0.045887062
## age -0.01825600 0.035354134 -0.5163752 0.605592417
## lwt -0.01628503 0.006858566 -2.3744076 0.017577136

60
Exercise session 4
Information on the web

• www.stackoverflow.com
• www.r-project.org
• www.rweekly.org
• www.r-bloggers.com
• cheatsheets (zie ook Help > Cheatsheets)

61
End