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R
R :
1.7

R Development Core Team June 10, 2006

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Contents
1 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 1.11 2 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 3 3.1 3.2 3.3 3.4 4 4.1 4.2 4.3 5 5.1 5.2 5.3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . tapply() ragged . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (index vector); . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . R R R R . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1 1 2 2 2 3 3 3 4 4 4 5 5 5 6 7 7 7 8 9 10 10 11 11 11 12 12 12 13 14 14 14 15

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CONTENTS 5.4 5.5 5.6 5.7 array() . . . 5.4.1 . . . 5.7.1 5.7.2 5.7.3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . QR . . . . . . . . . . . . . cbind() rbind() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

ii 16 16 17 17 18 18 18 19 19 19 19 19 20 21 21 22 22 22 22 23 23 24 24 25 25 26 26 27 27 28 28 29 32 35 35 35 35 35 37 37 38 38 39 39 39

5.8 5.9 5.10 5.11 5.12 6 6.1 6.2 6.2.1 6.3 6.3.1 6.3.2 6.3.3 6.3.4 6.3.5 7 7.1 7.2 7.3 7.4 8 8.1 8.2 8.3 9 9.1 9.2 9.2.1 9.2.2 10 10.1 10.2 10.3 10.4 10.5 10.6 R—

c()

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . attach() detach() . . . . . . . . . .

read.table() . . scan() . . . . . . . 7.3.1 R . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . if . . . . . . . . . . . for repeat while . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . . ’...’ . . . . . . . . . . . . . . . . . .

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CONTENTS 10.6.1 10.6.2 10.6.3 . 10.7 (scope) . . . . . . . . 10.8 . . . . . . . . . 10.9 11 R 11.1 11.1.1 11.2 11.3 11.4 11.4.1 11.5 11.6 11.6.1 11.6.2 11.7 11.7.1 11.7.2 11.8 12 12.1 12.1.1 12.1.2 12.1.3 12.1.4 12.2 12.2.1 12.2.2 12.3 12.4 12.4.1 12.4.2 12.5 12.5.1 12.5.2 12.5.3 12.5.4 12.6 12.6.1 12.6.2 12.7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Hershey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (Permanent changes): . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (Figure margins) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . PostScript . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . plot() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . par() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (Efficiency factors) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

iii 39 40 41 41 43 44 45 45 48 48 48 49 49 50 50 51 51 53 53 54 55 56 56 56 57 58 58 59 61 61 61 62 62 63 63 63 64 65 65 67 67 67 68

. . . . . . . . (contrasts) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (ANOVA tables) . . . . . . . . . . . . . . . . . . . . . . . . (families) . . . . . . . . . glm() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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Chapter 1

1.1
R • • • • •

R

S ” ” environment R R

R

R

R

1.2
R Rick Becker,John Chambers AllanWilks Bell S-Plus S John Chambers R , The New S Language: A Programming Environment for Data Analysis and Graphics Richard A. Becker, John M. Chambers and Allan R. Wilks 1991 S (S version 3) Statistical Models in S edited by John M. Chambers and Trevor J. Hastie S-Plus R R S S

1

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CHAPTER 1.

2

1.3

R
R R R http://cran.r-project.org R

8 CRAN R S SAS R SPSS

S R R

1.4
R

R
R R X window UNIX Windows R

1.5
R

R
>, UNIX shell 1. work. $ mkdir work $ cd work $ UNIX . R , UNIX shell R

2. 3. 4.

R $ R R R > q() R ) R R $ cd work $ R 1. work R yes,no cancel( R

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CHAPTER 1. 2. R Windows R q() R ” ” R

3

1.6
R

1.7
UNIX man solve >help(solve) >?solve if,for > help("[[") ”It’s important” HTML > help.start() Web (UNIX netscape UNIX ’Search Engine and Keywords’ help.search ?help.search > example(topic) Windows R > ?help function R

) HTML R

1.8

R
R R R ) . ***note 1*** A a (

UNIX ( locale )

(;)

( { }) (#)

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CHAPTER 1. R + R

4

1.9
UNIX Windows R

( readline R

UNIX

) Emacs ( ESS Emacs Speaks Statistics) R Emacs

1.10 work R > source("commands.R") Windows Source File > sink("record.lis") > sink() commands.R

sink record.lis

1.11
R R ( ( > objects() ls() ) workspace rm > rm(x, y, z, ink, junk, temp, foo, bar) R R R R x y R .RData workspace ) R

R

***Note3***

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Chapter 2

2.1
R R (10.4, 5.6, 3.1, 6.4 21.7) > x assign("x", c(10.4, 5.6, 3.1, 6.4, 21.7)) ¡assign()

> c(10.4, 5.6, 3.1, 6.4, 21.7) -> x

> 1/x ( > y v s3 s3 c(-5.0, -4.8, -4.6, ..., 4.6, 4.8, 5.0) > s4 s5 temp 13 temp x =, c1 c2 c1 & c2 (”or”) !c1 c1 FALSE

==

TRUE FALSE != (”and”) c1 | c2 1

0 TRUE

2.5
” NA is.na(x) x TRUE FALSE > z Inf - Inf NaN TRUE

is.nan(xx)

is.na(xx) NA NaN NaN TRUE

2.6
R e.g. "x-values" "New iteration results" (’) (”) ( backslash \\ \". \n, , c()

) R C \\, ” \t, tab \b, paste()

sep=string > labs y (x+1)[(!is.na(x)) & x>0] -> z

x[6] > x[1:10] x 10 ( x

x 10) 16 "x", "y", "y", "x" 4

> c("x","y")[rep(c(1,2,2,1), times=4)]

3. > y fruit names(fruit) lunch x[is.na(x)] y[y < 0] y z digits d e e[3] alpha attr(z,"dim") winter > unclass(winter) winter

sec10.9

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Chapter 4

1

R

4.1
30 > state statef statef [1] tas sa qld nsw nsw nt wa wa qld vic nsw vic qld qld sa [16] tas sa nt wa vic qld nsw nsw wa sa act nsw vic vic act Levels: act nsw nt qld sa tas vic wa levels()

4.2
> incomes incmeans stderr incster incster act nsw nt qld sa tas vic wa 1.5 4.3102 4.5 4.1061 2.7386 0.5 5.244 2.6575 95% tapply() t tapply() length() qt()

ragged array

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Chapter 5

5.1
R 2 1 dim z 1500 > dim(z) x x [,1] [,2] [,3] [,4] [,5] [1,] 1 5 9 13 17 [2,] 2 6 10 14 18 [3,] 3 7 11 15 19 [4,] 4 8 12 16 20 > i i [,1] [,2] [1,] 1 3 [2,] 2 2 [3,] 3 1 > x[i] [1] 9 6 3 > x[i] x [,1] [,2] [,3] [,4] [,5] [1,] 1 5 0 13 17 [2,] 2 0 10 14 18 [3,] 0 7 11 15 19 [4,] 4 8 12 16 20 > blocks(b levels) (v levels) n plot varieties

> Xb Xv > > > > ib eigen(Sm)

Sm

5.8
1

5.9 lsfit() > ans > > > X qr() Xplus search() [1] ".GlobalEnv" "Autoloads" "package:base" .GlobalEnv lentils workspace
1

> search() [1] ".GlobalEnv" "lentils" "Autoloads" "package:base" > ls(2) [1] "u" "v" "w" ls objects

> detach("lentils") > search() [1] ".GlobalEnv" "Autoloads" "package:base"

1

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Chapter 7

R R Perl R read.table() R R data Import/Export scan()
1

R

7.1
• •

read.table()

01 02 03 04 05 ...

Price 52.00 54.75 57.50 57.50 59.75

Floor 111.0 128.0 101.0 131.0 93.0

Area 830 710 1000 690 900

Rooms 5 5 5 6 5

Age 6.2 7.5 4.2 8.8 1.9

Cent.heat no no no no yes

Cent.heat read.table()
1

Unix

Sed

Awk

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CHAPTER 7. > HousePrice HousePrice inp label

## 2-tailed 2*pt(-2.43, ## upper 1% qf(0.99, 2,

8.2 summary fivenum stem ”stem and leaf” plot

> data(faithful) > attach(faithful) > summary(eruptions) Min. 1st Qu. Median Mean 3rd Qu. Max. 1.600 2.163 4.000 3.488 4.454 5.100 > fivenum(eruptions) [1] 1.6000 2.1585 4.0000 4.4585 5.1000 > stem(eruptions) The decimal point is 1 digit(s) to the left of the | 16 | 070355555588 18 | 000022233333335577777777888822335777888 20 | 00002223378800035778 22 | 0002335578023578 24 | 00228 26 | 23 28 | 080 30 | 7 32 | 2337 34 | 250077 36 | 0000823577 38 | 2333335582225577 40 | 0000003357788888002233555577778 42 | 03335555778800233333555577778 44 | 02222335557780000000023333357778888 46 | 0000233357700000023578 48 | 00000022335800333 50 | 0370 R > hist(eruptions) ## make the bins smaller, make a plot of density > hist(eruptions, seq(1.6, 5.2, 0.2), prob=TRUE) > lines(density(eruptions, bw=0.1)) > rug(eruptions) # show the actual data points hist

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CHAPTER 8. density density
1

30

bw

(trial-and-error)

MASS KernSmooth

Histogram of eruptions
0.7

Density

0.0

0.1

0.2

0.3

0.4

0.5

0.6

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

eruptions

stepfun

ecdf

> library(stepfun) > plot(ecdf(eruptions), do.points=FALSE, verticals=TRUE) eruption > > > > 3 CDF

long 3] plot(ecdf(long), do.points=FALSE, verticals=TRUE) x shapiro.test(long) Shapiro-Wilk normality test data: long W = 0.9793, p-value = 0.01052 Kolmogorov-Smirnov > ks.test(long, "pnorm", mean=mean(long), sd=sqrt(var(long))) One-sample Kolmogorov-Smirnov test data: long D = 0.0661, p-value = 0.4284 alternative hypothesis: two.sided

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CHAPTER 8.

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8.3
R ctest library(ctest) (cal/gm) Rice(1995,P.490) Method A: 79.98 80.04 80.02 80.04 80.03 80.03 80.04 79.97 80.05 80.03 80.02 80.00 80.02 Method B: 80.02 79.94 79.98 79.97 79.97 80.03 79.95 79.97 box-plot A var.test(A, B) F test to compare two variances t.test

33

data: A and B F = 0.5837, num df = 12, denom df = 7, p-value = 0.3938 alternative hypothesis: true ratio of variances is not equal to 1 95 percent confidence interval: 0.1251097 2.1052687 sample estimates: ratio of variances 0.5837405

t> t.test(A, B, var.equal=TRUE) Two Sample t-test data: A and B t = 3.4722, df = 19, p-value = 0.002551 alternative hypothesis: true difference in means is not equal to 0 95 percent confidence interval: 0.01669058 0.06734788 sample estimates: mean of x mean of y 80.02077 79.97875 Wilcoxon Whitney > wilcox.test(A, B) Wilcoxon rank sum test with continuity correction data: A and B W = 89, p-value = 0.007497 alternative hypothesis: true mu is not equal to 0 (null hypothesis) Mann-

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CHAPTER 8.

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Warning message: Cannot compute exact p-value with ties in: wilcox.test.default(A, B)

> library(stepfun) > plot(ecdf(A), do.points=FALSE, verticals=TRUE, xlim=range(A, B)) > plot(ecdf(B), do.points=FALSE, verticals=TRUE, add=TRUE) CDF Kolmogorov-Smirnov > ks.test(A, B) Two-sample Kolmogorov-Smirnov test data: A and B D = 0.5962, p-value = 0.05919 alternative hypothesis: two.sided Warning message: cannot compute correct p-values with ties in: ks.test(A, B) qqplot Q-Q ecdf

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Chapter 9

9.1
R

expr 1; . . . ; expr m

9.2
9.2.1
R > if (expr_1) expr_2 else expr_3 expr 1 && || & | && || if/else b[i] if & | ifelse condition[i] a,b && || ifelse (condition,a,b) a[i]

if

9.2.2

for

repeat

while

loop > for (name in expr_1) expr_2 name expr 1 expr 2 dummy name expr 1

1:20 expr 2 name

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CHAPTER 9. ind y x coplot() x

36

> xc yc for (i in 1:length(yc)) { plot(xc[[i]], yc[[i]]); abline(lsfit(xc[[i]], yc[[i]])) } split() help R for() ’ R ’ whole object

> repeat (expr )

> while (condition) expr break repeat next chapter 10

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Chapter 10

R R R R R var(),postscript() R

function

mean(),

> name twosam