1. Stat405
Statistical computing & graphics
Hadley Wickham
Monday, 23 August 2010

2. 1. Introductions
2. Syllabus
3. Introduction to linux
4. Introduction to R
5. Basic graphics
Monday, 23 August 2010

3. HE LLO
my name is
Hadley
Monday, 23 August 2010

4. had.co.nz/stat405
(if you can’t remember just google stat405)
hadley@rice.edu
Monday, 23 August 2010

5. About me
From New Zealand
Divisional advisor for McMurtry
Major advisor for statistics
Monday, 23 August 2010

6. Syllabus
Monday, 23 August 2010

7. Computing
environment
Lab computers: linux
Your computers: mac and windows
Essential tools: R, text editor, latex
Use of command line strongly
encouraged.
Will show basic set up for mac, windows
and linux.
Monday, 23 August 2010

8. Lab access
Once registrations are finalised, I’ll get
everyone lab access. (But can use R on
any computer on campus - including your
own)
Monday, 23 August 2010

9. Setup
Find the instructions related to your
operating system on the class website.
Follow them to get R and running
I’ll circulate and make sure everyone gets
set up right.
Monday, 23 August 2010

10. Introduction to R
Monday, 23 August 2010

11. Learning a new
language is hard!
Monday, 23 August 2010

12. Scatterplot basics
install.packages("ggplot2")
library(ggplot2)
?mpg
head(mpg)
str(mpg)
summary(mpg)
qplot(displ, hwy, data = mpg)
Monday, 23 August 2010

13. Scatterplot basics
install.packages("ggplot2")
library(ggplot2)
?mpg
head(mpg)
str(mpg)
Always explicitly
summary(mpg) specify the data
qplot(displ, hwy, data = mpg)
Monday, 23 August 2010

14. ●
●
40
●
●
35 ●
●
● ●
● ●
● ●●
30 ● ● ●
● ● ● ● ●● ●
hwy
● ● ● ● ●
● ● ●● ● ● ● ●
● ● ● ●● ● ●● ●● ● ● ● ●
25 ● ● ● ●● ● ● ● ●
●● ●● ● ● ● ●
● ● ● ● ● ● ●
● ● ● ● ●
● ●
20 ● ● ●●
● ● ● ●● ●
● ● ● ● ● ●●
●● ●● ● ●● ● ● ● ● ● ●
●● ● ●
15 ● ●● ●●● ● ●
● ●
●
2 3 4 5 6 7
qplot(displ, hwy, data = mpg)
displ
Monday, 23 August 2010

15. Additional variables
Can display additional variables with
aesthetics (like shape, colour, size) or
facetting (small multiples displaying
different subsets)
Monday, 23 August 2010

16. ●
●
40
●
●
35 ●
●
● ● class
● ●
● ●●
● 2seater
30 ● ● ● ● compact
● ● ● ● ●● ●
● midsize
hwy
● ● ● ● ●
● ● ●● ● ● ● ● ● minivan
● ● ● ●● ● ●● ●● ● ● ● ●
25 ● ● ● ●● ● ● ● ● ● pickup
●● ●● ● ● ● ●
● ● ● ● ● ● ●
● subcompact
● ● ● ● ● ● suv
● ●
20 ● ● ●●
● ● ● ●● ●
● ● ● ● ● ●●
●● ●● ● ●● ● ● ● ● ● ●
●● ● ●
15 ● ●● ●●● ● ●
● ●
●
2 3 4 5 6 7
qplot(displ, hwy, colour = class, data = mpg)
displ
Monday, 23 August 2010

17. ●
●
40
●
●
35 ●
●
● ● class
● ●
● ●●
● 2seater
30 ● ● ● ● compact
● ● ● ● ●● ●
● midsize
hwy
● ● ● ● ●
● ● ●● ● ● ● ● ● minivan
● ● ● ●● ● ●● ●● ● ● ● ●
25 ● ● ● ●● ● ● ● ● ● pickup
●● ●● ● ● ● ●
● ● ● ● ● ● ●
● subcompact
● ● ● ● ● ● suv
● ●
20 ● ● ●●
● ● ● ●● ●
● ● ● ● ● ●● Legend chosen and
displayed automatically.
●● ●● ● ●● ● ● ● ● ● ●
●● ● ●
15 ● ●● ●●● ● ●
● ●
●
2 3 4 5 6 7
qplot(displ, hwy, colour = class, data = mpg)
displ
Monday, 23 August 2010

18. Your turn
Experiment with colour, size, and shape
aesthetics.
What’s the difference between discrete or
continuous variables?
What happens when you combine
multiple aesthetics?
Monday, 23 August 2010

19. Discrete Continuous
Rainbow of Gradient from
Colour
colours red to blue
Linear mapping
Discrete size
Size between radius
steps
and value
Different shape
Shape Doesn’t work
for each
Monday, 23 August 2010

20. Faceting
Small multiples displaying different
subsets of the data.
Useful for exploring conditional
relationships. Useful for large data.
Monday, 23 August 2010

21. Your turn
qplot(displ, hwy, data = mpg) +
facet_grid(. ~ cyl)
qplot(displ, hwy, data = mpg) +
facet_grid(drv ~ .)
qplot(displ, hwy, data = mpg) +
facet_grid(drv ~ cyl)
qplot(displ, hwy, data = mpg) +
facet_wrap(~ class)
Monday, 23 August 2010

22. Summary
facet_grid(): 2d grid, rows ~ cols, . for
no split
facet_wrap(): 1d ribbon wrapped into 2d
Monday, 23 August 2010

23. Aside: workflow
Keep a copy of the slides open so that
you can copy and paste the code.
For complicated commands, write them
in gedit and then copy and paste.
Monday, 23 August 2010

24. What’s the ● ●
40 problem with ●
this plot? ● ●
●
35 ●
●
● ●
● ● ●
● ● ● ●
30 ● ● ●
● ● ● ● ● ●
hwy
● ● ●
● ● ● ● ●
● ● ● ● ● ●
25 ● ● ● ● ● ●
● ● ● ●
● ● ●
● ● ●
●
20 ● ● ●
● ● ●
● ● ● ●
● ● ● ● ●
● ● ●
15 ●
●
●
10 15 20 25 30 35
qplot(cty, hwy, data = mpg)
cty
Monday, 23 August 2010

25. ● ●
●
40
●
●
●
●●
35
●
● ●
● ● ●
●
● ●
●● ● ●
●
●
30 ●
●
●
●
●● ●● ● ●
●●
●
●●
● ● ●● ●● ●
● ●● ●
hwy
●
●● ●
● ●● ●● ● ● ●
● ● ● ●
● ● ●
● ● ●● ●● ●
● ●
● ● ●
●● ● ●● ●
●● ● ● ●
● ● ●
● ● ● ●● ●●
●
25 ● ●● ● ● ● ●
● ● ●
● ●● ●
●
● ●
●● ●
●● ●
●
● ●
● ●●
● ●
●
● ●
●
●
●
20 ●● ● ● ●●
●
● ● ●
●● ● ●●
●
● ●● ● ● ●
●
● ● ●● ● ●
● ●
●
● ● ● ● ●● ● ●
●
●● ●●●●●● ●
●
●● ●
● ● ● ●●●
●
● ● ●●● ●
●
15 ●●
●●
●●
●
●
●
●
●
●●
●●
10 15 20 25 30 35
qplot(cty, hwy, data = mpg, geom = "jitter")
cty
Monday, 23 August 2010

26. ● ●
●
40
●
●
●
●●
35
●
● ●
● ● ●
●
● ●
●● ● ●
●
●
30 ●
●
●
●
●● ●● ● ●
●●
●
●●
● ● ●● ●● ●
● ●● ●
hwy
●
●● ●
● ●● ●● ● ● ●
● ● ● ●
● ● ●
● ● ●● ●● ●
● ●
● ● ●
●● ● ●● ●
●● ● ● ●
● ● ●
● ● ● ●● ●●
●
25 ● ●● ● ● ● ●
● ● ●
● ●● ●
●
● ●
●● ●
●● ●
●
● ●
● ●●
● ●
●
● ●
●
●
●
20 ●● ● ● ●●
●
● ● ●
●● ● ●●
●
● ●● ● ● ●
●
● ● ●● ● ●
● ●
●
● ● ● ● ●● ● ●
●
●● ●●●●●● ●
●
●● ●
● ● ● ●●●
●
● ● ●●● ●
●
15 ●●
●●
●●
●
●
●
●
●
●●
geom controls
●●
“type” of plot
10 15 20 25 30 35
qplot(cty, hwy, data = mpg, geom = "jitter")
cty
Monday, 23 August 2010

27. ● ●
●
40
●
●
35 ●
●
● ●
● ●
● ●
30 ● ●
● ● ●
hwy
● ● ●
● ● ● ●
● ● ● ● ●
25 ● ● ● ● ●
● ● ● ● ● ●
● ● ● ● ● ●
● ● ● ●
● ●
20 ● ● ●
● ●
● ●
● ● ●
● ●
15 ● ●
●
● ●
2seater compact midsize minivan pickup subcompact suv
qplot(class, hwy, data = mpg)
class
Monday, 23 August 2010

28. How could ● ●
we improve
●
40
this plot? ●
●
35 ●
●
Brainstorm ●
●
●
●
●
●
30
for 1 minute.
● ●
● ● ●
hwy
● ● ●
● ● ● ●
● ● ● ● ●
25 ● ● ● ● ●
● ● ● ● ● ●
● ● ● ● ● ●
● ● ● ●
● ●
20 ● ● ●
● ●
● ●
● ● ●
● ●
15 ● ●
●
● ●
2seater compact midsize minivan pickup subcompact suv
qplot(class, hwy, data = mpg)
class
Monday, 23 August 2010

29. ● ●
●
40
●
●
35 ●
●
● ●
● ●
● ●
30 ● ●
● ● ●
hwy
● ● ●
● ● ● ●
● ● ● ● ●
25 ● ● ● ● ●
● ● ● ● ● ●
● ● ● ● ● ●
● ● ● ●
● ●
20 ● ● ●
● ●
● ●
● ● ●
● ●
15 ● ●
●
● ●
pickup suv minivan 2seater midsize subcompact compact
reorder(class, hwy)
Monday, 23 August 2010

30. ● ●
●
40
●
●
35 ●
●
● ●
● ●
● ●
30 ● ●
● ● ●
hwy
● ● ●
● ● ● ●
● ● ● ● ●
25 ● ● ● ● ●
● ● ● ● ● ●
● ● ● ● ● ●
● ● ● ●
● ●
20 ● ● ●
● ●
● ●
● ● ●
● ●
15 ● ●
Incredibly useful
●
technique!
● ●
pickup suv minivan 2seater midsize subcompact compact
qplot(reorder(class, hwy), hwy, data = mpg)
reorder(class, hwy)
Monday, 23 August 2010

31. ● ●
●
40
●
●
●
● ●
35
●
●
●
● ● ●
● ●
● ● ●
● ● ●
●
30 ● ● ●
● ● ● ●● ● ●● ● ● ● ●
●
● ●●
●
● ● ●● ●
● ● ●
● ● ● ●
hwy
● ● ● ●
● ●
● ● ● ●● ● ●
● ● ●● ●
● ●
● ●● ●● ● ●
● ● ●
● ●
● ●●● ● ● ● ● ●●
● ● ●
● ● ●
25 ● ● ● ● ●●
●●
●
●
●
● ● ● ● ● ● ●
● ●
●● ● ●
● ●
● ● ● ●
●
● ● ● ●
● ● ●
●
●
● ●
20 ●
● ●
● ● ●● ● ●
● ●● ●●
●● ● ● ●●
● ●
● ●
● ●● ● ●●●
● ●
● ● ● ● ● ●●
● ● ● ●●● ● ● ● ●
● ● ●
● ●● ● ● ●
●● ● ● ● ●
●
● ● ●
15 ● ● ● ● ● ● ●
●
●
● ● ● ● ●
pickup suv minivan 2seater midsize subcompact compact
qplot(reorder(class, hwy),reorder(class, hwy) = mpg, geom = "jitter")
hwy, data
Monday, 23 August 2010

32. ● ●
●
40
●
35 ●
30
hwy
●
●
25 ●
●
●
●
20
●
15
● ●
pickup suv minivan 2seater midsize subcompact compact
qplot(reorder(class, hwy), hwy, data hwy)mpg, geom = "boxplot")
reorder(class, =
Monday, 23 August 2010

33. ●
● ●
●
● ●
40
● ●
● ●
35 ● ● ●
●
●
●
● ● ● ●
● ● ●
● ●● ●
30 ● ● ● ●
●●
●●
●
● ● ● ●●
● ●●● ●● ●● ● ●●
●
● ● ● ●
hwy
●
● ●
● ● ● ●● ●●
● ● ● ●
● ● ● ●
● ● ●
● ● ● ● ●●● ● ●●
● ● ●● ●
●● ● ●●
●
● ● ●
● ● ● ●● ●
●
25 ● ● ● ● ● ● ●● ●
●
● ● ● ●
● ● ● ● ●
● ●●
● ● ● ● ●
● ●
● ● ● ● ●
● ●
● ●
● ● ●
● ● ●
●
●
● ●
20 ● ● ●● ●
● ●
● ●
●● ● ●●
● ●● ● ● ● ● ●
●
● ● ● ● ●
●
● ●
● ● ● ●
● ●●
● ● ●● ●●●●● ● ● ●
●
● ●● ● ● ● ●
● ●
● ● ● ●
● ●
● ●
● ●
● ● ●
15 ● ● ● ● ●● ●
●
●
● ●
● ● ●
●
●
qplot(reorder(class,minivan
pickup suv
hwy), 2seater data = subcompact
hwy, midsize mpg, compact
geom = c("jitter", "boxplot"))
reorder(class, hwy)
Monday, 23 August 2010

34. Your turn
Read the help for reorder. Redraw the
previously plots with class ordered by
median hwy.
How would you put the jittered points on
top of the boxplots?
Monday, 23 August 2010

35. Aside: coding strategy
At the end of each interactive session, you
want a summary of everything you did. Two
options:
1. Save everything you did with savehistory()
then remove the unimportant bits.
2. Build up the important bits as you go.
(this is how I work)
Monday, 23 August 2010