Command Index

* , 3, 4

+ , 3, 4, 7

− , 3, 4

-Inf , 128

… , 361, 362, 364, 414–416

/ , 3, 4

: , 8

< , 13, 14

<- , 9

<= , 13

= , 5, 9, 13

== , 13, 66, 73

> , 13

>= , 13

? , 5, 19, 37

?? , 20

[[ ]] , 82

%*% , 365

%in% , 74

& , 13, 14

&& , 14, 374

{} , 111, 360, 374

abline , 27, 65, 121, 337, 348, 363

abs , 13, 14, 347, 371

add1 , 212

AIC , 213

all , 73

all.equal , 74, 103, 104

allEffects , 174, 180, 181

Anova , 186, 193, 194, 197, 223, 238, 239, 243, 244, 248, 253, 261, 272, 317

anova , 38, 192, 193, 195, 223, 238, 243, 415

aov , 38

apply , 377–380, 423

apropos , 20

args , 7, 110, 223

array , 76, 383

arrows , 339, 340

as , 101

as.character , 158, 393

as.list , 379

as.matrix , 76

as.numeric , 158

as.vector , 93, 395

attach , 24, 57–59, 61

avPlots , 34, 286, 292, 300, 307, 313, 317, 321, 329

axis , 123, 332, 334, 337, 342

basicPowerAxis , 137

bcPower , 132, 304

bcPowerAxis , 137

binom.test , 38

binomial , 236

bootCase , 187

box , 109, 332, 335

boxCox , 304, 305

boxcox , 304

boxCoxVariable , 306

Boxplot , 114, 137

boxplot , 38, 114

boxTidwell , 312, 313

break , 375, 388

browser , 399, 400, 402

bs , 178

bwplot , 168, 204, 353, 354

c , 7, 44, 45, 71

carWeb , xvii, xviii, 20, 49

cat , 388, 409

cbind , 26, 141, 155, 172, 389, 405

ceresPlots , 311, 317

character , 383

chisq.test , 38, 251

chol , 369

choose.dir , 50

class , 39, 40, 157, 407

cloud , 125

coef , 143, 155, 172, 187, 223, 306, 415

coeftest , 186 441

colMeans , 378

colors , 343

colSums , 378

compareCoefs , 199, 299

complete.cases , 65

complex , 383

confidenceEllipse , 189

confint , 153, 172, 188, 237

constrOptim , 390

contr.helmert , 196, 197, 215

contr.poly , 196, 216–218

contr.SAS , 215

contr.Sum , 216

contr.sum , 196, 215–217, 244

contr.Treatment , 216

contr.treatment , 159, 160, 196, 197, 214–216, 196

contrasts , 159, 214, 227

control , 282

cooks.distance , 298, 317, 320, 363

cor , 38, 218, 369

count.fields , 52

cov , 38

cov2cor , 182

crossprod , 368, 405

crPlots , 34, 310, 317

curve , 341, 341, 342, 349

cut , 70, 71

D , 201

data , 55, 225

data.frame , 67, 184, 259

dataEllipse , 189

dbinom , 38, 113

dchisq , 38, 112, 113

debug , 399, 402, 415

debugger , 399, 402

deltaMethod , 186, 200–202, 317

density , 111

det , 369

detach , 59

dev.cur , 358

dev.list , 358

dev.off , 357

dev.set , 358

deviance , 243

df , 38, 113

df.residual , 243

dfbeta , 301, 317

dfbetas , 301, 317

diag , 370, 401

dim , 76

dnorm , 38, 112, 113, 380

dt , 38, 113

dump.frames , 402

dunif , 113

edit , 47

effect , 164, 173, 174, 176, 181

eigen , 327, 369

else , 370, 372

eval.parent , 415

example , 6 example functions

abs1 , 371

convert2meters , 372

cuberoot , 420

fact1 , 373

fact2 , 374

fact3 , 374

fact4 , 375

fact5 , 375

fact6 , 376

fact7 , 376

fact8 , 376

Glmnet , 416, 417

grad , 391

inflPlot , 360–364, 386

lreg , 407, 408, 414, 415

lreg.default , 407, 408, 410, 414, 415

lreg.formula , 414, 415

lreg1 , 387–389, 399, 402–406

lreg2 , 390–392, 403

lreg3 , 399, 400, 402

lreg4 , 405, 406

lreg5 , 410

makeDigits , 393

makeNumber , 394

makePower , 419, 420

makeScale , 379

myMean , 15, 16, 21

myVar , 19, 21

negLogL , 391, 392

number2words , 394–396

numbers2words , 396, 397

print.lreg , 409, 415

print.summary.lreg , 409

sign1 , 372

sign2 , 372

squareit , 362

summary.lreg , 409

tc , 349

time1 , 383

time2 , 383

time3 , 383

time4 , 384

time5 , 384

tricube , 349

trim , 395, 396

tukeyTest , 421

exp , 128

expand.grid , 267

expression , 140, 349

f , 373

factor , 158, 159

factorial , 373

file.choose , 23, 50

fitted , 239

fix , 47, 400

for , 244, 336, 350, 373, 374

formula , 223

fractions , 367

friedman.test , 38

ftable , 203, 245, 259

function , 15, 26, 360

gamma , 233, 373

gamma.shape , 276

getAnywhere , 422

getwd , 50

ginv , 370

glm , 40, 92, 123, 208, 233, 236, 237, 240, 248, 259, 261, 281, 282, 359, 363, 386, 389, 392, 403, 406

glm.nb , 279, 280

glmnet , 415–417

gray , 343, 348

grep , 90

grid , 33, 337, 338

gsub , 89

hatvalues , 287, 297, 317, 363

hccm , 186, 201

head , 108, 151, 158, 160

help , 5, 19, 37

help.search , 20

help.start , 5, 19

hints , 19, 228

hist , 24, 25, 27, 31, 37, 38, 108–111, 207

hist.default , 110

I , 140, 219, 224, 313

identify , 29, 64, 145–148, 171, 189, 329, 360

if , 370–372, 388

ifelse , 70, 73, 74, 349, 371, 372, 389

influenceIndexPlot , 33, 297, 298, 320

influencePlot , 299, 360

integer , 383

integrate , 380, 381

interaction.plot , 170, 171, 241, 242

invTranPlot , 139, 145, 147

is , 101

is.character , 67

is.na , 66

jitter , 120, 171

kruskal.test , 38

lapply , 377, 379, 380

layout , 350

legend , 268, 329, 341, 342

length , 15, 76, 87

letters , 78

levels , 158

leveragePlots , 294

library , xvii, 31, 151

linearHypothesis , 186, 191, 200, 317

lines , 27, 111, 121, 123, 329, 334, 335, 336, 342

list , 77

lm , 27, 30, 31, 38, 39, 42, 65, 68, 92, 99, 121, 123, 150–152, 156, 161, 171, 192, 208, 216, 223, 233, 236, 281, 327, 359, 363, 368

load , 95

locator , 338, 339, 341

log , 4, 7, 64, 127, 128

log10 , 127

log2 , 127

logb , 128

logical , 383

logit , 134, 224

lowess , 27, 65, 66, 117, 121, 291, 310, 346

map , 355

mapplot , 355, 356

mapply , 377, 380, 381

marginalModelPlots , 291, 292, 317

match.arg , 372

match.call , 415

matrix , 75, 364, 383

max , 363

mean , xx, 14, 15, 37, 38, 59–61, 63, 380, 382

median , 38, 63

melt , 257

memory.limit , 93

memory.size , 93

menus

Change dir, 50

Change Working Directory, 50

Edit, xvi, 16, 17

Exit, xx File, xx, 17, 22, 50, 357

GUI preferences, xvi

Help, xviii, 16, 20

History, 358

Misc, 19, 50

New Document, 17

Open Document, 17

Packages, 1, 54

Packages & Data, 1

R, xvi

R console, 17, 25

Recording, 358

Run line or selection, 17

Save as, 17

Stop, 19, 29, 146, 189, 339

Stop locator, 29

methods , 40

missing , 361

mle , 390

model.matrix , 159, 164

ModelPlots , 292

mtext , 339, 351

multinom , 261

NA , 157, 226, 336

na.action , 226

na.exclude , 226, 290

na.fail , 226

na.omit , 65, 66, 191, 226, 347, 420

NaN , 128

nchar , 87

ncvTest , 36, 316

negative.binomial , 279, 281

new , 410

nlm , 390

nlminb , 390

ns , 178

NULL , 360, 370

numeric , 350, 383

objects , 21, 400

odbcConnectExcel , 54

offset , 227, 282

optim , 390–392

optimize , 390

options

error, 402

scipen, 393

options , 214, 333, 393

order , 347

outer , 366

outlierTest , 296, 317

p.arrows , 340

pairs , 25–27, 125

palette , 343, 344

par , 123, 128, 137, 241, 268, 332–334, 339, 347, 349–351

paste , 11, 87

pbinom , 38, 113

pchisq , 38, 113, 244

pdf , 357

persp , 125

pf , 38, 113

pi , 341

pie , 343, 344

plot , 27, 28, 33, 37, 38, 115, 116, 119, 123, 125, 129, 173, 174, 180, 247, 250, 290, 329–335, 337, 338, 347, 351, 356–358, 362–364

plot.default , 330, 331

plot.formula , 331

plot.lm , 330

plotCI , 122, 356

pnorm , 38, 113, 381

points , 27, 171, 247, 329, 334, 335, 342, 348, 355

poisson , 246

polr , 271

poly , 131, 181, 217, 218, 311, 312

polygon , 340

powerTransform , 140–144, 304–306, 309

prcomp , 327, 369

predict , 205, 239, 267

princomp , 327, 369

print , 37, 401, 407, 409, 411

printCoefmat , 409

probabilityAxis , 137, 242

prod , 373

prop.table , 203

prop.test , 38

pt , 38, 113, 191

punif , 113

q , 22

qbinom , 38, 113

qchisq , 38, 112, 113

qf , 38, 113

qnorm , 38, 112, 113

qplot , 356

qqnorm , 112

qqPlot , 31, 32, 112, 295

qr , 369

qt , 38, 113

quantile , 38, 63, 70

quartz , 358

quasi , 233, 276

quasibinomial , 233, 276

quasipoisson , 233, 276, 278

quit , 22

qunif , 113

R window

Quartz, 17

R Commander, 1

R Console, xvi, xx

R.app, 1, 17

RGui, 1, 2, 17

rainbow , 343, 344

range , 38

rbinom , 38, 113, 403

rchisq , 38, 113

read.csv , 48

read.table , 94

read.fwf , 53

read.spss , 53

read.table , 23, 24, 42, 47–50, 53, 54, 56, 67, 94–96, 157–159

readLines , 86

Recall , 376, 396

recode , 70, 71, 73, 264

recover , 402

regsubsets , 213

relevel , 162, 202, 214

remove , 21, 376

rep , 46, 47, 241

repeat , 373, 375

representation , 410

residualPlots , 288–290, 292, 311, 314, 317, 319, 329, 420

residuals , 287, 415

return , 360, 373

rf , 38, 113

rnorm , 10, 38, 113

round , 218

rowMeans , 378

rownames , 389

rowSums , 378

Rprof , 404

RSiteSearch , 20

rstandard , 287

rstudent , 31, 287, 317, 318, 363

rt , 38, 113

rug , 111

runif , 113

sample , 38, 72, 206

sapply , 377, 379, 380, 396

save , 95

scale , 184

scan , 45, 46

scatmat , 28

scatter3d , 124, 125, 145, 147, 148, 357

scatterplot , 116–118, 121, 124–126, 145, 147, 148, 154, 290, 329, 345

scatterplotMatrix , 28, 125, 126, 143, 145, 147, 329

sd , 38, 63

search , 57

segments , 339, 340

seq , 8

set.seed , 72, 403

setClass , 410

setIs , 413

setMethod , 411, 412

setwd , 50

show , 411

showLabels , 147

sign , 372

sin , 384

singular.ok , 227

slotNames , 410

solve , 366, 367

some , 160

sort , 72, 90, 347

splom , 125

spreadLevelPlot , 35, 136, 315

sqrt , 10

start , 282

stem , 38, 110

stemleaf , 110

step , 208–212

stop , 374

str , 100, 379, 401, 415

strip.custom , 354

strsplit , 87, 88, 393

strwrap , 87

sub , 89

subset , 85

subsets , 213

substring , 87

sum , 15, 19, 377, 378

summary , 10, 24, 30, 37, 39, 40, 51, 68, 70, 99, 100, 152, 153, 182, 188, 236, 239, 262, 272, 407, 409, 413

summary.lm , 39, 40

summary.loess , 40

summaryRprof , 404

svd , 327, 369

switch , 372

symbox , 132

system.time , 94, 383, 403

t , 366

t.test , 38

table , 23, 38, 48, 67, 90

tail , 396

tapply , 122, 161, 167, 377, 381, 382

tempfile , 404

testTransform , 143, 144

text , 148, 334, 338, 339, 348, 349

title , 332, 351, 355

tolower , 89

trace , 376

traceback , 18, 19, 399, 401

transform , 69, 143

treatment , 196

ts.plot , 38

tukeyNonaddTest , 421, 422

unique , 90

unlink , 404

untrace , 376

update , 36, 154, 155, 163, 421

UseMethod , 39

useOuterStrips , 353

var , 18, 38, 63

vcov , 181, 191, 415

vector , 101, 383, 395

Vectorize , 377, 381

vglm , 271

View , 47

vif , 325, 327

weighted.mean , 344, 349

weights , 226, 281, 282

while , 373–375, 388

wilcox.test , 38

windows , 358

wireframe , 125

with , 62, 85, 108, 111, 369

womenlf , 271

write.csv , 56

write.table , 56, 94, 95

xtabs , 38, 161, 167, 203, 245, 247, 259

xyplot , 203, 354

yjPower , 132, 304

yjPowerAxis , 137