IntroStats PDF

Prelim.
Data
Descriptive Statistics
Prob. Models
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Exercises
UCLA Department of Statistics

Statistical Consulting Center
Introductory Statistics with R

Mine C
etinkaya
mine@stat.ucla.edu
February 1, 2010
Mine C
etinkaya mine@stat.ucla.edu
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Outline
1
Preliminaries
Data sets
Probability Models
Hypothesis Testing and Confidence Intervals
Linear Regression
Online Resources for R
Upcoming Mini-Courses
Exercises
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Data
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Preliminaries
Software Installation
R Help
Data sets
Probability Models
Linear Regression
Exercises
Linear Reg.
Resources
Upcoming
Exercises
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Software Installation
Installing R on a Mac
Go to
http://cran.r-project.org/
and select MacOS X

2
Select to download the

latest version: 2.11.0
(2010-04-22)
Install and Open. The R

window should look like this:
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R Help
R Help
For help with any function in R,

put a question mark before the
function name to determine what
arguments to use, examples and
background information.
1
? plot
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Loading data into R
Viewing data sets in R
Probability Models
Linear Regression
Exercises
Linear Reg.
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Loading data into R
Loading data into R
Loading a data set into R:

1
survey = read . table ( " http : / / www . stat . ucla .

edu / ~ mine / students _ survey _ 2008. txt " ,
header = TRUE , sep = " \ t " )
Displaying the dimensions of the data set:

1
dim ( survey )
[1] 1325
29
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Displaying the first 3 rows and 5 columns of the data set:
1
survey [1:3 ,1:5]
gender hand eyecolor glasses california

1 female left
hazel
yes
yes
2
male right
brown
no
no
3 female right
brown
yes
yes
Displaying the variable names in the data set:

1
names ( survey )
[1] "gender"
[6] "birthmonth"
[11] "graduate"
...
"hand"
"birthday"
"oncampus"
"eyecolor"
"birthyear"
"time"
"glasses"
"california"
"ageinmonths" "height"
"walk"
"hsclass"
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Attaching / detaching data frames in R

Attaching the variables in a data set::
1
attach ( survey )
The following object(s) are masked from package:datasets :

sleep
The warning is telling us that we have attached a data frame

that contains a column, whose name is sleep. If you type:
1
sleep
the object with that name in the data frame will be seen
before another object with the same name that is lower in the
search() path. Thus, your object is masking the other.
To detach a data frame, i.e. remove from the search() path
of available R objects - but we wont do that now.
1
detach ( sleep )
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Variable classes
Displaying categorical data
Displaying quantitative data
Describing distributions numerically
Probability Models
Linear Regression
Exercises
Linear Reg.
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Variable classes
Displaying the class of a variable:

1
class ( instructor )
[1] "factor"
Changing the class of a variable:

1
2
instructor = as . character ( instructor )

class ( instructor )
[1] "character"
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Tables
Tables are useful for displaying the distribution of categorical

variables.
1
table ( gender )
gender
female
882
male
443
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Contingency tables
Contingency tables display two categorical variables at a time.

1
table ( gender , hand )
hand
gender
ambidextrous left right
female
9
67
806
male
11
45
387
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Frequency bar plots

Display counts of each category next to each other for easy
comparison.
1
barplot ( table ( gender ) , main = " Barplot of

Gender " )
0 200
600
Barplot of Gender
female
male
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Relative frequency bar plots

Display relative proportions of each category.
1
barplot ( table ( gender ) / length ( gender ) , main = "

Relative Frequency \ n Barplot of Gender " )
0.0
0.3
0.6
Relative Frequency
Barplot of Gender
female
male
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Segmented bar charts

Displays two categorical variables at a time.
1
barplot ( table ( gender , hand ) , col = c ( " skyblue "

, " blue " ) , main = " Segmented Bar Plot \ n
of Gender " )
legend ( " topleft " , c ( " females " ," males " ) , col =
c ( " skyblue " , " blue " ) , pch = 16 , inset =
0.05)
Segmented Bar Plot
of Gender
200 400 600 800
females
males
ambidextrous
left
right
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Pie charts
Pie charts display counts as percentages of individuals in each
category.
1
pct = round ( table ( gender ) / length ( gender ) *

100)
lbls = paste ( names ( table ( gender ) ) , " \ n " , " % " ,
pct )
pie ( table ( gender ) , labels = lbls )
female
% 67
male
% 33
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Histograms
Display the number of cases in each bin
1
hist ( ageinmonths , main = " Histogram of Age in

Months " )
300
200
0
100
Frequency
400
Histogram of Age in Months
200
250
300
350
ageinmonths
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Relative frequency histograms

Display the proportion of of cases in each bin.
1
hist ( ageinmonths , freq = FALSE , main = "

Relative Frequency \ n Histogram of Age in
Months " , xlab = " Age in Months " )
0.020
0.000
0.010
Density
0.030
Relative Frequency
200
250
300
350
Age in Months
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Stem-and-Leaf Plots
Preserve individual data values.
1
stem ( ageinmonths )
The decimal point is 1 digit(s) to the right of the |

20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
48
004444555566666666666666666777777777778888888888889999999999999999
00000000000000000000000000111111111111111122222222222222222222333333+258
00000000000000000000000000000000000000000000001111111111111111111111+379
00000000000000000000000000000000000000000000111111111111111111111111+170
00000000000001111111111111112222222222222222222223333333344444444445+24
000000000001111111111222222333334444444444556666778889
00111222222344566789
01334558888
0004569
267
02257
44
5
89
3
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Boxplots
1
boxplot ( ageinmonths , main = " Boxplot of Age in

Months " )
200
250
300
350
Boxplot of Age in Months
Five Number Summary (Min, Q1, Median, Q3, Max):

1
fivenum ( ageinmonths )
[1] 204 228 235 243 353
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Summary
Categorical variables:
1
summary ( hand )
ambidextrous
20
left
112
right
1193
Quantitative variables:
1
summary ( ageinmonths )
Min. 1st Qu.

204.0
228.0
Median
235.0
Mean 3rd Qu.

237.8
243.0
Max.
353.0
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Measures of center
Mean (arithmetic average):
1
mean ( ageinmonths )
[1] 237.8309
Median (value that divides the histogram into two equal

areas):
1
median ( ageinmonths )
[1] 235
Mode (the most frequent value): for discrete data

1
as . numeric ( names ( sort ( table ( ageinmonths ) ,

decreasing = TRUE ) ) [1])
[1] 228
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Mode (alternative)
To find the mode, you may also use the Mode function in the
prettyR package.
1
2
3
install . packages ( " prettyR " )

library ( prettyR )
Mode ( ageinmonths )
[1] "228"
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Adding measures to plots

Adding mean and median to a histogram.
1
2
3
4
hist ( ageinmonths , main = " Histogram of Age in

Months " )
abline ( v = mean ( ageinmonths ) , col = " blue " )
abline ( v = median ( ageinmonths ) , col = " green " )
legend ( " topright " , c ( " Mean " , " Median " ) , pch =
16 , col = c ( " blue " , " green " ) )
300
200
0
100
Frequency
400
Mean
Median
200
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Measures of spread
Range (Min, Max):
1
range ( ageinmonths )
[1] 204 353
IQR:
1
IQR ( ageinmonths )
[1] 15
Standard deviation:
1
sd ( ageinmonths )
[1] 16.03965
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Geometric
Binomial
Poisson
Normal
Linear Regression
Exercises
Linear Reg.
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Geometric
Geometric distribution
If the probability of success is 0.35, what is the probability that the
first success will be on the 5th trial?
1
dgeom (4 ,0.35)
[1] 0.06247719
Note: dgeom gives the density (or probability mass function for discrete
variables), pgeom gives the distribution function, qgeom gives the
quantile function, and rgeom generates random deviates. This is true for
the functions used for Binomial, Poisson and Normal calculations as well.
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Binomial
Binomial distribution
If the probability of success is 0.35, what is the probability of
3 successes in 5 trials?
1
dbinom (3 ,5 ,0.35)
[1] 0.1811469
at least 3 successes in 5 trials?

1
sum ( dbinom (3:5 ,5 ,0.35) )
[1] 0.2351694
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Poisson
Poisson distribution
The number of traffic accidents per week in a small city has
Poisson distribution with mean equal to 3. What is the probability
of
two accidents in a week?
1
dpois (2 ,3)
[1] 0.2240418
at most one accident in a week?

1
sum ( dpois (0:1 ,3) )
[1] 0.1991483
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Normal
Normal distribution
Scores on an exam are distributed normally with a mean of 65 and
a standard deviation of 12. What percentage of the students have
scores
below 50?
1
pnorm (50 ,65 ,12)
[1] 0.1056498
between 50 and 70?

1
pnorm (70 ,65 ,12) - pnorm (50 ,65 ,12)
[1] 0.5558891
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Normal
Normal distribution (cont.)
What is the 90th percentile of the score distribution?

1
qnorm (.90 ,65 ,12)
[1] 80.37862
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One sample means
Two sample means
One sample proportions
Two sample proportions
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One sample means
Hypothesis testing for one sample means

Is there evidence to suggest that the average age in months for
Stats 10 students is more than 235 months? Use = 0.05.
1
2
3
sample100 = sample (1:1325 , 100 , replace =

FALSE )
survey . sub = survey [ sample100 ,]
t . test ( survey . sub $ ageinmonths , alternative = "
greater " , mu = 235 , conf . level = 0.95)
One Sample t-test

data: survey.sub$ageinmonths
t = 1.5922, df = 99, p-value = 0.05726
alternative hypothesis: true mean is greater than 235
95 percent confidence interval:
234.9118
Inf
sample estimates:
mean of x
237.06
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One sample means
Confidence intervals for one sample means

The t.test function prints out a confidence interval as well.
However this function returns a one-sided interval when the
alternative is "greater" or "less".
When alternative = "greater" is chosen the lower
confidence bound is calculated and the upper bound is given
as Inf by default.
When alternative = "less" is chosen the upper
confidence bound is calculated and the lower bound is given
as -Inf by default.
When alternative = "two.sided" is chosen both the
upper and the lower confidence bounds are calculated.
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One sample means
Confidence intervals for one sample means (cont.)

1
t . test ( survey . sub $ ageinmonths , alternative = "

two . sided " , mu = 235 , conf . level = 0.90)
One Sample t-test

data: survey.sub$ageinmonths
t = 1.5922, df = 99, p-value = 0.1145
alternative hypothesis: true mean is not equal to 235
234.9118 239.2082
sample estimates:
mean of x
237.06
Note that we changed the confidence level to 0.90 in order to

correspond to a one-sided hypothesis test with = 0.05.
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One sample means
Confidence intervals for one sample means (cont.)

Alternative calculation of confidence interval:
1
2
3
4
5
6
7
8
9
onesample . mean . ci = function (x , conf . level ) {

tstar = - qt ( p = ((1 - conf . level ) / 2) , df = (
length ( x ) - 1) )
xbar = mean ( x )
sexbar = sd ( x ) / sqrt ( length ( x ) )
cilower = xbar - tstar * sexbar
ciupper = xbar + tstar * sexbar
return ( list = c ( cilower , ciupper ) )
}
onesample . mean . ci ( survey . sub $ ageinmonths ,
0.90)
[1] 234.9118 239.2082

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Two sample means
Hypothesis testing and CI for two sample means

Is there a difference between the ages of females and males?
Construct a 95% confidence interval for the difference between the
average ages of females and males.
1
t . test ( survey . sub $ ageinmonths [ survey .

sub $ gender == " female " ] , survey .
sub $ ageinmonths [ survey . sub $ gender == " male
" ] , alternative = " two . sided " , conf . level
= 0.95)
Welch Two Sample t-test

data: survey.sub$ageinmonths[survey.sub$gender == "female"] and
survey.sub$ageinmonths[survey.sub$gender == "male"]
t = 1.25, df = 95.736, p-value = 0.2143
alternative hypothesis: true difference in means is not equal to 0
-1.765100 7.768572
sample estimates:
mean of x mean of y
238.1406 235.1389
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Hypothesis testing for one sample proportions

64 out of 100 students in a random sample are females. Is there
evidence to suggest that the population proportion of females is
less than 65%? Use a 90% confidence level.
1
prop . test (64 , 100 , p = 0.65 , alternative = "

less " , conf . level = 0.90)
1-sample proportions test with continuity correction

data: 64 out of 100, null probability 0.65
X-squared = 0.011, df = 1, p-value = 0.4583
alternative hypothesis: true p is less than 0.65
0.0000000 0.7035286
sample estimates:
p
0.64
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Confidence intervals for one sample proportions

Just like the t.test, the prop.test function will calculate both
the upper and the lower bounds of the confidence interval only
when alternative = "two.sided" is chosen. Otherwise a lower
bound of 0 or an upper bound of 1 is produced.
1
prop . test (64 , 100 , p = 0.65 , alternative = "

two . sided " , conf . level = 0.80)
1-sample proportions test with continuity correction

data: 64 out of 100, null probability 0.65
alternative hypothesis: true p is not equal to 0.65
0.5715825 0.7035286
sample estimates:
p
0.64
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Two sample proportions
Hypothesis testing and CI for two sample proportions

54 out of 64 females and 32 out of 36 males are right handed. Is
there evidence to suggest that proportions of males and females
who are right handed are different?
1
prop . test ( c (54 ,32) , c (64 ,36) )
2-sample test for equality of proportions with continuity correction

data: c(54, 32) out of c(64, 36)
alternative hypothesis: two.sided
-0.2026789 0.1124012
sample estimates:
prop 1
prop 2
0.8437500 0.8888889
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Scatterplots
Is there an association between amount of alcohol consumed and
maximum speed?
1
plot ( speed ~ alcohol , main = " Scatterplot of

Speed vs . Alcohol " , pch = 20 , cex = 0.5)
100
0
50
speed
150
Scatterplot of Speed vs. Alcohol
20
40
60
80
alcohol
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Correlation
cor ( alcohol , speed , use = " pairwise . complete .

obs " )
[1] 0.2309745
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Build a linear regression model predicting speed from alcohol.
1
summary ( lm ( speed ~ alcohol ) )
Call:
lm(formula = speed ~ alcohol)
Residuals:
Min
1Q
-90.769 -8.725
Median
1.275
3Q
11.275
Max
91.541
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 88.7248
0.6511 136.261
<2e-16 ***
alcohol
0.9469
0.1108
8.549
<2e-16 ***
--Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
Residual standard error: 21.83 on 1297 degrees of freedom
(26 observations deleted due to missingness)
Multiple R-squared: 0.05335, Adjusted R-squared: 0.05262
F-statistic: 73.09 on 1 and 1297 DF, p-value: < 2.2e-16
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Download R: http:// cran.stat.ucla.edu/
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Search Engine for R: rseek.org
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R Reference Card:
http:// cran.r-project.org/ doc/ contrib/ Short-refcard.pdf
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R Reference Card:
UCLA Statistics Information Portal: http:// info.stat.ucla.edu/ grad/
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R Reference Card:
UCLA Statistics Information Portal: http:// info.stat.ucla.edu/ grad/

UCLA Statistical Consulting Center: http:// scc.stat.ucla.edu
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May 5, R Stats II: Linear Regression

May 10, R Stats III: Nonlinear Regression
May 12, LaTeX V: Creating Vector Graphics in LaTeX
For a schedule of all mini-courses offered please visit
http:// scc.stat.ucla.edu/ mini-courses .
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Thank you
Any questions?
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Exercises
1
Construct side-by-side box plots for the distribution of amount

of time it takes students to get to class (time) by their means
of transportation (walk).
Usually younger students live on campus and older students

live off campus. Is there evidence to suggest this trend in this
data set? (Use a random sample of 100 students and
= 0.05.)
Calculate a 90% confidence interval for the difference between

the average ages of students who live on campus and off
campus.
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Solution to Exercise 1
1
boxplot ( time ~ walk , main = " Time to get to

class \ n by type of transportation " )
50
Minutes
100
150
Time to get to class

by type of transportation
bicycle
bus
car (by yourself) carpool
motorcycle
other
segway
skateboard
walk
Mine C
UCLA SCC
Prelim.
Data
Prob. Models
Hyp. Test & CI
Linear Reg.
Resources
Upcoming
Exercises
1

sub $ oncampus == " yes " ] , survey .
sub $ ageinmonths [ survey . sub $ oncampus == " no
" ] , alternative = " less " , conf . level =
0.95)

data: survey.sub$ageinmonths[survey.sub$oncampus == "yes"] and
survey.sub$ageinmonths[survey.sub$oncampus == "no"]
t = -5.3322, df = 34.867, p-value = 2.964e-06
alternative hypothesis: true difference in means is less than 0
-Inf -10.85376
sample estimates:
mean of x mean of y
232.6111 248.5000
Mine C
UCLA SCC
Prelim.
Data
Prob. Models
Hyp. Test & CI
Linear Reg.
Resources
Upcoming
Exercises
1

sub $ oncampus == " yes " ] , survey .
sub $ ageinmonths [ survey . sub $ oncampus == " no
" ] , alternative = " two . sided " , conf . level
= 0.90)

data: survey.sub$ageinmonths[survey.sub$oncampus == "yes"] and
survey.sub$ageinmonths[survey.sub$oncampus == "no"]
t = -5.3322, df = 34.867, p-value = 5.929e-06
alternative hypothesis: true difference in means is not equal to 0
-20.92402 -10.85376
sample estimates:
mean of x mean of y
232.6111 248.5000
Mine C
UCLA SCC

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Prelim.

Hyp. Test & CI

UCLA Department of Statistics

Introductory Statistics with R

Hyp. Test & CI

Hypothesis Testing and Confidence Intervals

Online Resources for R

Hyp. Test & CI

Hypothesis Testing and Confidence Intervals

Online Resources for R

Hyp. Test & CI

and select MacOS X

Select to download the

Install and Open. The R

Hyp. Test & CI

For help with any function in R,

Hyp. Test & CI

Hypothesis Testing and Confidence Intervals

Online Resources for R

Hyp. Test & CI

Loading data into R

Loading data into R

Loading a data set into R:

survey = read . table ( " http : / / www . stat . ucla .

Displaying the dimensions of the data set:

Hyp. Test & CI

Viewing data sets in R

Viewing data sets in R

survey [1:3 ,1:5]

gender hand eyecolor glasses california

Displaying the variable names in the data set:

Hyp. Test & CI

Viewing data sets in R

Attaching / detaching data frames in R

The following object(s) are masked from package:datasets :

The warning is telling us that we have attached a data frame

Hyp. Test & CI

Hypothesis Testing and Confidence Intervals

Online Resources for R

Hyp. Test & CI

Displaying the class of a variable:

Changing the class of a variable:

instructor = as . character ( instructor )

Hyp. Test & CI

Displaying categorical data

Tables are useful for displaying the distribution of categorical

Hyp. Test & CI

Displaying categorical data

Contingency tables display two categorical variables at a time.

table ( gender , hand )

Hyp. Test & CI

Displaying categorical data

Frequency bar plots

barplot ( table ( gender ) , main = " Barplot of

Hyp. Test & CI

Displaying categorical data

Relative frequency bar plots

barplot ( table ( gender ) / length ( gender ) , main = "

Hyp. Test & CI

Displaying categorical data

Segmented bar charts

barplot ( table ( gender , hand ) , col = c ( " skyblue "

200 400 600 800