Index of Functions

Numbers

.C, 384

.Call, 384, 388

.Fortran, 384

%dopar%, 284, 285

`:`, 33, 44–48, 57, 58, 65, 68, 70, 72, 74, 79, 114, 116, 118–120, 127, 130, 158, 180, 187, 188, 192, 193, 200, 216, 242, 244, 261, 262, 285, 323, 324, 350, 365, 366, 369, 370

`?`, 49

`[[`, 59, 66, 68, 145, 147, 164, 292, 294

`[`, 47, 56–60, 66, 70, 72, 96, 111, 114, 118, 125, 130–132, 134–138, 149, 158, 161–165, 188, 192, 193, 195, 197, 198, 200, 204, 216, 220–222, 242, 249, 261, 264, 288, 290, 306, 318, 323, 335, 336, 338, 346, 347, 350, 352

`$`, 56, 66, 74, 84, 85, 96, 125–127, 130, 131, 152, 158, 160–162, 175, 191, 192, 195, 200, 201, 203, 204, 207–209, 216, 220–222, 226, 228, 230, 232, 235, 239, 249, 257–259, 261, 265, 276, 278, 279, 282, 286, 288, 289, 298, 300, 302, 303, 306, 318, 320, 326, 329, 330, 333, 343, 346, 347, 349, 350, 352

A

a ply, 124

aaply, 124

abline, 279, 282, 289

acf, 318, 320

addBBands, 330

addMACD, 330

adply, 124

aes, 87–91, 93, 94, 96, 97, 152, 172, 175, 177, 180, 184, 185, 195, 201, 204, 205, 207, 209, 212, 216, 219–221, 223, 224, 235, 237, 250, 252, 253, 261, 265, 288, 290, 298, 300, 302, 304, 308, 317, 345, 351

aggregate, 120–123, 128, 135–137, 139, 152, 204

AIC, 255–257

all, 46, 47

all.equal, 176

alply, 124

anova, 254–257

ansari.test, 205

any, 46, 47, 125

aov, 208, 210, 215

apply, 117–120, 139

apropos, 49, 50

ar, 319, 324

arima, 319, 336

array, 72

as.character, 160, 349, 350

as.data.frame, 216, 300, 344

as.Date, 41, 49

as.factor, 48, 183

as.matrix, 290

as.numeric, 38, 41, 48, 105, 152, 160, 183, 252

as.POSIXct, 41

assign, 37, 142, 143

auto.arima, 319, 320

B

bartlett.test, 204

bayesglm, 271, 293–295

BIC, 255–257

binomial, 236, 292, 294, 310

boot, 263, 264

boot.ci, 264

bottomleft, 148

boxplot, 85

break, 115, 116

build, 383, 387, 390

build.x, 273, 274, 276, 313

build.y, 276, 313

buildModelCI, 379

by, 120

C

c, 43, 44, 46–48, 50, 51, 55, 57, 58, 61, 64, 70, 74, 110, 111, 114, 119, 132, 134, 135, 142, 144, 148, 149, 155–157, 161, 162, 168, 175, 188, 191–193, 195–198, 200, 201, 207, 219, 235, 244, 249, 262, 265, 279, 282, 289, 293, 305, 306, 316, 330, 335, 346, 347, 349, 350, 352

cbind, 122, 141, 142, 160, 196

chartSeries, 329, 330

check, 383, 384, 390

citation, 366

class, 38, 39, 41, 42, 56, 59, 60, 130, 276, 285, 326, 330

close, 162

clusGap, 343, 344

coef, 225, 226, 278, 279, 290, 300, 321, 377

coefficients, 226

coefplot, 33, 226, 228, 236, 238, 249, 326, 377–379

coefplot.default, 379

coefplot.glm, 379

coefplot.lm, 378, 379, 382

coefplot.rxGLM, 379

coefplot.rxGlm, 379

coefplot.rxLinMod, 379

coefplot.rxLogit, 379

collidev, 379

colnames, 70, 323, 324

colSums, 118

coord equal, 351

coord flip, 293

cor, 187, 191, 192, 195–200, 210

corner, 148

cov, 199, 200, 210

cox.zph, 244

coxph, 242–244

cv.glm, 257–259, 261, 262

cv.glmnet, 276, 282, 285, 288

D

d*ply, 135

d ply, 124

daisy, 352

daply, 124

data, 79, 80, 84, 121, 199, 215, 300, 363, 364

data.frame, 53, 54, 74, 79, 130, 142, 160, 175, 177, 180, 183, 201, 261, 262, 273, 286, 290, 302, 350

data.table, 130, 149

dbeta, 185

dbinom, 180, 185

dcast, 152, 153, 288, 323

dcauchy, 185

dchisq, 185

ddply, 124, 126, 127, 139, 205, 209, 216

detach, 33

dexp, 185

df, 185

dgamma, 185

dgeom, 185

dhyper, 185

diff, 319, 324, 336

dim, 54, 68, 69, 148, 180, 276

dir, 142

dist, 352, 354

dlnorm, 185

dlogis, 185

dlply, 124, 129

dmultinom, 185

dnbinom, 185

dnorm, 172, 175, 185

do.call, 104

document, 381, 383, 390

dollar, 317

download.file, 142, 347

dpois, 182, 185

dt, 185

dunif, 185

dweibull, 185

E

each, 128

eapply, 120

element blank, 351

element text, 152, 261

else, 105–108, 112

else if, 107

eval, 145

extract.coef, 379

extract.coef.default, 379

extract.coef.glm, 379

extract.coef.lm, 379

extract.coef.rxGlm, 379

extract.coef.rxLinMod, 379

extract.coef.rxLogit, 379

F

facet grid, 89, 90, 308

facet wrap, 89, 90, 152, 180, 184, 220, 261, 288

factor, 40, 48, 61, 252, 273, 302, 346, 350

file.path, 143

FitKMeans, 341, 342

for, 110, 113–116, 142, 143, 261, 292, 294

foreach, 282, 284

forecast, 321

function, 107–109, 120, 261, 264, 286, 302, 371, 380, 381, 388

G

gam, 308, 310

gaussian, 258, 259

gc, 38

geom abline, 252

geom boxplot, 91

geom density, 87, 185, 201, 207, 235

geom errorbar, 345

geom errorbarh, 205, 209, 216

geom histogram, 87, 90, 177, 180, 184, 204, 219, 220, 237, 253, 265

geom hline, 250

geom jitter, 308

geom line, 87, 94, 96, 152, 175, 261, 288, 317, 345

geom point, 87, 88, 90, 94, 97, 172, 175, 205, 209, 212, 216, 221, 223, 224, 250, 288, 290, 298, 300, 304, 308, 345

geom polygon, 175

geom smooth, 212, 213, 250

geom tile, 195

geom violin, 93, 94

geom vline, 201, 207, 235, 265, 290

getSymbols, 328

getXKCD, 199

ggpairs, 192, 193, 198, 199

ggplot, 86–88, 90, 91, 93, 94, 96, 97, 152, 172, 175, 177, 180, 184, 185, 195, 201, 204, 205, 207, 209, 212, 216, 219–221, 223, 224, 235, 237, 252, 253, 261, 265, 288, 290, 293, 298, 300, 302, 304, 308, 317, 345, 351

ggtitle, 184, 185, 216

glm, 235–238, 240, 257–259, 271, 292, 294, 304, 308

glmnet, 271, 272, 274, 276, 279, 282, 289, 295

guide colorbar, 195

guides, 261

H

hclust, 352, 354, 357

head, 55, 56, 73, 74, 76, 78, 80, 84, 121, 125, 144, 147, 150, 151, 153, 158, 160, 163, 164, 167, 168, 175, 180, 191, 199, 200, 207, 212, 215, 219, 232, 235, 241, 249, 250, 263, 273, 274, 276, 291, 293, 298, 302, 303, 305, 306, 317, 323, 326, 330, 338, 349, 350, 363, 364

hist, 84

I

I, 230

idata.frame, 128, 129

identical, 115, 128, 197, 200

if, 105–112, 116

ifelse, 105, 109–112

ignore.case, 162

infocriteria, 335, 336

install, 383

install.packages, 31

install bitbucket, 383

install git, 383

install github, 31, 383, 384

install version, 384

is.integer, 38, 39

is.logical, 42

is.na, 50, 110, 111, 125

is.null, 51, 109

is.numeric, 38, 39, 111

J

J, 134, 135

join, 142, 144, 148, 350

K

key, 134

kmeans, 338, 340, 357

knit, 362, 369–371

L

l ply, 124

labs, 96, 175, 212, 219, 220, 250, 290, 345, 351

laply, 128

laply, 124

lapply, 117–120, 127, 139, 286

ldply, 124, 286, 302

legend, 244, 252, 323, 324

length, 46, 49, 68, 114, 145, 189, 261

levels, 252

library, 32

limits, 235

list, 61, 63, 65, 104, 119, 120, 127, 128, 132, 136–138, 283, 299, 302, 330, 335

llply, 124, 128, 139

llpply, 127

lm, 213, 215, 216, 224, 225, 228, 230, 232, 235, 236, 249, 253, 269, 271, 274, 298, 308, 324, 363, 364, 384

load, 78, 79, 162, 291, 298

load all, 383

log, 223, 224, 279, 282, 336

ls, 99

M

ma, 319

makeCluster, 283, 285

mapply, 117, 119, 120

matrix, 69, 118–120, 127

max, 175, 189, 190, 261

mean, 49, 104, 121–123, 128, 136–138, 187–189, 192, 195, 201, 205, 209, 210, 216, 261, 298, 300

median, 128, 189, 190

melt, 150–152, 183, 195, 261, 288

merge, 142–144

min, 175, 189, 190

model.matrix, 60, 61, 272, 273

month, 96

multinom, 240

multiple.dollar, 235

multiple format, 152, 317

multiplot, 230, 240, 253, 292–294, 379

muted, 195

N

names, 48, 54, 55, 63–65, 68, 114, 115, 145, 160, 207, 219, 249, 292, 294, 316, 326, 338, 347, 350, 352

nchar, 40, 47, 49, 114, 115, 119

ncol, 54, 68, 69

ndiffs, 319, 324

next, 115, 116

nls, 298, 299

nonzeroCoef, 290

NROW, 120, 209, 216, 264

nrow, 54, 68, 69, 129, 192, 205, 207, 209, 261, 283, 345

ns, 302–304

O

odbcClose, 76

odbcConnect, 75, 76

odbcConnectExcel2007, 75

options, 371

order, 195

ordered, 273

P

pacf, 318, 320

pam, 345–347, 351, 357

parse, 145

paste, 155, 156, 169

pbeta, 185

pbinom, 180, 185

pcauchy, 185

pchisq, 185, 239

pexp, 185

pf, 185

pgamma, 185

pgeom, 185

phyper, 185

plnorm, 185

plogis, 185

plot, 85, 243, 244, 252, 278, 279, 282, 289, 310, 318, 319, 321, 323, 324, 329, 333, 335, 339, 343, 352, 354–356, 365, 366, 369, 370

plot.kmeans, 339

plotcoef, 379

PlotHartigan, 342

pmultinom, 185

pnbinom, 185

pnorm, 172, 173, 175, 176, 185

poisson, 238

polr, 240

pos dodgev, 379

ppois, 182, 185

predict, 230–232, 261, 302, 321, 326, 327

print, 99–104, 106–108, 114–116, 377, 378

print.anova, 382

print.data.frame, 378

print.lm, 378

pt, 185

punif, 185

pweibull, 185

Q

qbeta, 185

qbinom, 181, 182, 185

qcauchy, 185

qchisq, 185

qexp, 185

qf, 185

qgamma, 185

qgeom, 185

qhyper, 185

qlnorm, 185

qlogis, 185

qmultinom, 185

qnbinom, 185

qnorm, 175, 176, 185

qpois, 182, 185

qt, 185, 209

quantile, 190, 191

quasipoisson, 240

qunif, 185

qweibull, 185

R

randomForest, 313

rapply, 120

rbeta, 185

rbind, 141, 142, 160, 175, 180, 286

rbinom, 176, 177, 180, 185

rcauchy, 185

rchisq, 185

Rcpp.package.skeleton, 388

read.csv, 73

read.csv2, 74

read.delim2, 74

read.dta, 77

read.mtp, 77

read.octave, 77

read.spss, 77

read.ssd, 77

read.systat, 77

read.table, 73, 74, 77, 81, 143, 218, 231, 233, 249, 272, 305, 338

readHTMLTable, 80, 81, 157

readShapeSpatial, 348, 349

rect.hclust, 355, 356

Reduce, 145, 147–149, 160, 286

registerDoParallel, 283, 285

remove, 37

remove.packages, 32

reorder, 290

rep, 114, 130, 273

require, 31–33, 80, 84, 97, 121, 125, 149, 151, 152, 157, 160, 172, 175, 183, 184, 191, 195, 199, 205, 207, 212, 216, 226, 235, 236, 241, 250, 258, 261, 263, 274, 276, 282, 288, 293, 298, 302, 303, 308, 310–313, 316, 317, 319, 323, 326, 328–330, 339, 344, 346, 347, 349, 350, 363, 364, 383, 386

return, 103, 104, 380, 381

revalue, 349

rexp, 185

rf, 185

rgamma, 185

rgeom, 185

rhyper, 185

rlnorm, 185

rlogis, 185

rm, 37, 38, 78, 79

rmultinom, 185

rnbinom, 185

rnorm, 171, 172, 185

round, 302

rownames, 55, 70, 216, 290, 346, 350

rowSums, 118, 346

rpart, 311

rpart.plot, 312

rpois, 182, 183, 185

rt, 185, 201

runif, 185

rweibull, 185

RxSasData, 77

S

s, 310

sample, 187, 188, 273, 283

sapply, 119, 120, 128, 164, 285

save, 78, 79

scale color discrete, 96, 185, 302

scale color gradient2, 298, 300

scale colour economist, 97

scale colour excel, 97

scale fill discrete, 185

scale fill gradient2, 195

scale x continuous, 152, 235, 308

scale y continuous, 96, 152, 317

sd, 189, 192, 200, 201, 205, 207, 209, 210, 216

seq, 152, 175, 283

set.seed, 288, 338, 340

setkey, 133, 134

shapiro.test, 204

shQuote, 371

smooth.spline, 300

sourceCpp, 386, 387

sprintf, 100–103, 155–157, 169, 262

sqlQuery, 75, 76

sqrt, 44, 189, 205, 207, 209, 216, 239, 265

stat qq, 252

stat smooth, 304

step, 265, 269

stopCluster, 283, 285

str detect, 161–163, 165, 169

str extract, 164–167, 169, 183, 288

str replace, 168, 169, 288

str replace all, 168

str split, 158, 160, 163, 164, 169

str sub, 143, 145, 152, 160, 161, 169

str trim, 164

strata, 243, 244

sum, 104, 118, 119, 127, 128, 137, 152, 162, 189, 192, 222, 239, 264

summarize, 205, 209

summary, 190, 208, 213–216, 225, 236, 238, 243, 244, 299, 310, 363, 364, 377

Surv, 241–244

survfit, 242–244

Sweave, 359

switch, 105, 108, 109, 111, 112

Sys.time, 285

system.time, 129

T

t, 70, 300

t.test, 187, 201, 203, 205–207, 210

table, 343

tables, 133, 134

tail, 56, 126, 158, 160, 180, 276

tapply, 117, 120

te, 310

theme, 152, 261, 308, 351

theme economist, 97

theme excel, 97

theme minimal, 195

theme tufte, 97

theme wsj, 97

topleft, 276

topright, 276

ts, 318, 322, 323

U

ugarchboot, 335

ugarchfit, 330, 335, 336

ugarchspec, 330, 335, 336

unique, 200, 292

unzip, 142, 348

url, 162

V

vapply, 120

VAR, 324, 326, 336

var, 187, 189, 195, 210, 265

var.test, 204

vector, 65, 145, 292, 294

W

WDI, 316, 346, 349

weighted.mean, 188

which, 96, 323, 338, 346, 347, 352

which.min, 288

while, 113, 115, 116

with, 126, 127, 216, 235, 242, 276

within, 216

X

xlab, 308

Y

year, 96