Index

[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][X][Y]

SYMBOL

! operator
!= operator
# symbol
%a symbol
%A symbol
%B symbol
%b symbol
%d symbol
%m symbol
%Y symbol
%y symbol
* operator, 2^nd
** operator
... option, 2^nd
. symbol
/ operator
: symbol
? function
?? function
Λ operator, 2^nd, 3^rd
~ symbol
+ operator, 2^nd
< operator
<<- operator
<= operator
== operator
> operator
>= operator
-1 symbol
brackets
3D pie charts
3D scatter plots

A

abline( ) function, 2^nd
abs( ) function
absolute widths
acos( ) function
acosh( ) function
AER package
aggr( ) function, VIM package
aggregate( ) function, 2^nd
aggregating data
AIC( ) function, 2^nd
all subsets regression, 2^nd
alpha option
alternative= option
Amelia package, 2^nd, 3^rd
analyses, excluding missing values from
analysis of variance (ANOVA), 18^th
  fitting models
    aov( ) function
    order of formula terms
  MANOVA
    assessing test assumptions
    robust
  one-way
    assessing test assumptions
    multiple comparisons
  one-way ANCOVA
    assessing test assumptions
    visualizing results
  as regression
  repeated measures
  terminology of
  two-way factorial
analytic packages, for large datasets
ANCOVA.
    See analysis of covariance.
ancova( ) function, HH package
AND operator
annotating datasets
annotations
ANOVA.
    See analysis of variance.
anova( ) function, 2^nd
Anova( ) function, car package, 2^nd
aov( ) function
append option
apply( ) function
apropos( ) function
aq.plot( ) function, mvoutlier package
arithmetic operators
arrayImpute package, 2^nd
arrayMissPattern package, 2^nd
arrays
Arthritis dataset
as.character( ) function
ASCII file
as.datatype( )function
as.Date( ) function, 2^nd
asin( ) function
asinh( ) function
aspect option
asypow package
at option
atan( ) function
atanh( ) function
attach( ) function, 2^nd, 3^rd
auto.key option
avPlots( ) function, 2^nd
axes, 2^nd
axes option
axis( ) function

B

background color (bg) option
backslash character, 2^nd
bar plots
  fitting labels in
  for mean values
  simple
  spinograms
  stacked and grouped
  tweaking
barplot( ) function, 2^nd
base package
batch processing
Beta distribution
bg option.
    See background color option.
bg parameter
biganalytics package
biglars package
bigmemory package
bigtabulate package
Binomial distribution
bitro.diameter variable
bivariate relationships
block comments
bmp( ) function
boot package
bootstrap package
bootstrapping, 2^nd
box plots
  parallel, comparing groups with
  violin variation of
box type (bty) option
boxplot( ) function, 2^nd
boxplots option
boxplot.stats( ) function
boxTidwell( ) function
Box-Tidwell transformations
breaks option
Brobdingnag package
bty option.
    See box type option.
bubble plots
by function
by option
byrow option
bzfile( ) function

C

c( ) function, 2^nd, 3^rd
ca package
car package, 2^nd, 3^rd, 4^th, 5^th
case identifiers, 2^nd
case-wise deletion
cast( ) function
casting, 2^nd
cat( ) function, 2^nd
cat package, 2^nd
categorical variables
Cauchy distribution
cbind( ) function, 2^nd, 3^rd, 4^th
ceiling( ) function
cex ( ) option
cex parameter, 2^nd
cex.axis parameter
cex.lab parameter
cex.main parameter
cex.names option
cex.sub parameter
CFA.
    See confirmatory factor analysis.
character functions
character variables, converting date values to
Chi-square tests
Chi-squared (noncentral) distribution
class( ) function
cld( ) function
CLI.
    See command-line interface.
close( ) function
cm.colors( ) function
cmdscale( ) function
code editors, list of
coefficients( ) function
coin package
col option, 2^nd, 3^rd, 4^th, 5^th, 6^th, 7^th
col.axis parameter
colClasses option, 2^nd
col.corrgram( ) function
colfill vector
col.lab parameter
col.main parameter
color option, 2^nd
colorRampPalett( ) function
colors, graphical parameters
colors( ) function
col.sub parameter
combine objects.
    See c( ) function.
combining graphs.
    See page arrangement of graphs.
command prompt
command-line interface (CLI)
command-line options
command-line prompt
comments, # symbol, 2^nd
common factors
comparisons, multiple
complete( ) function
complete-case analysis
complete.cases( ) function, 2^nd
comprehensive GUIs, for R
Comprehensive R Archive Network (CRAN), 2^nd
conditional execution
  if-else construct
  ifelse construct
  repetition and looping
  switch construct
conditioning variables, 2^nd
confint( ) function, 2^nd
confirmatory factor analysis (CFA)
constant residual variance
contrasts( ) function
contr.helmert function
control flow
contr.poly function
contr.SAS function
contr.sum function
contr.treatment function
conversions, type
Cook's distance, 2^nd, 3^rd, 4^th
cooks.distance( ) function
cor( ) function
corrective measures
  deleting observations
  variables
    adding or deleting
    transforming
correlograms, 2^nd
corrgram( ) function, corrgram package
corrgram package, 2^nd
corrperm package
cos( ) function
cosh( ) function
cov( ) function
cov2cor( ) function
Cox proportional hazards regression
cpairs( ) function
CRAN.
    See Comprehensive R Archive Network.
crimedat dataframe
cross-tabulations
crossval( ) function
cross-validation, 2^nd
crPlots( ) function, 2^nd
curly braces
cut( ) function, 2^nd, 3^rd

D

D plots, Cook.
    See Cook's distance.
D values, Cook.
    See Cook's distance.
data( ) function
data frames, 2^nd
  applying functions to
  attach( ), detach( ), and with( ) functions
  case identifiers
  using SQL statements to manipulate
data option, 2^nd, 3^rd, 4^th, 5^th, 6^th, 7^th, 8^th, 9^th, 10^th, 11^th
data storage, outside of RAM
data structures
  arrays
  data frames
    attach( ), detach( ), and with( ) functions
    case identifiers
  factors
  lists
  matrices
  vectors
data type, converting from one to another
database interface (DBI) related packages
database management systems (DBMSs), accessing
  DBI-related packages
  ODBC interface
data.frame( ) function
date( )function
date values
DBI related packages.
    See database interface related packages.
DBMSs, accessing.
    See database management systems, accessing.
deleting old versions of R
deletion, pairwise
demo( ) function
density( ) function
densityplot( ) function
dependent variable
detach( ) function, 2^nd
dev.new( ) function
dev.next( ) function
dev.off( ) function, 2^nd
dev.prev( ) function
dev.set( ) function
diagnostics, regression
  enhanced approach
  global validation of linear model assumption
  multicollinearity
  typical approach
diag.panel option
diff( ) function
difftime( )function
dim( ) function
dimensions
  of an array
  of graphs and margins
dimnames
dir.create( ) function
directory initialization file
distribution functions, normal
dmat.color( ) function, gclus package
doBy package
dollar sign character
dot plots, 2^nd
dotchart( ) function
Durbin-Watson test
durbinWatsonTest( ) function, 2^nd

E

echo option
edit( ) function
EFA.
    See exploratory factor analysis.
effect( ) function, 2^nd
  defined for ANOVA
  defined for chi-square tests
  defined for correlation
  defined for linear models, 2^nd
  defined for test of proportions
  defined for t-test
  effect size
  effect size benchmarks
effects library
effects package, 2^nd, 3^rd
environment, customizing startup
environment variables
errors, independence of
escape character, 2^nd
ES.w2( ) function
eval option
example( ) function
example.Rnw file
Excel, Microsoft
  accessing files with RODBC
  exporting data to spreadsheet
  importing data from
excluding
  missing values from analyses
  observations
  variables
exp( ) function
exploratory factor analysis (EFA), 2^nd
  deciding number of common factors to extract
  FactoMineR package
  factors
    extracting common
    rotating
    scores
  FAiR package
  GPArotation package
  nFactors package
  other latent variable models
exponential distribution, 2^nd
exponentiation operator
exporting data
  delimited text file
  Excel spreadsheet
  for statistical applications
expression( ) function
expression statement

F

F distribution
fa( ) function, 2^nd, 3^rd
facets, ggplot2 package
facets option
factanal( ) function
FactoMineR package, 2^nd
factor( ) function, 2^nd
factor intercorrelation matrix
factor pattern matrix
factor structure matrix
factorial ANOVA design
factor.plot( ) function, 2^nd
fa.diagram( ) function, 2^nd
FAiR package, 2^nd
family parameter
fan plots
fan.plot( ) function
fa.parallel( ) function, 2^nd, 3^rd
fCalendar package, 2^nd
ff package
fg parameter
fgui package
fig graphical parameter
fig option, in Sweave
figures, creating with fine control
file( ) function
filehash package
fill option
fine control, creating figure arrangements with
First( ) function
fit lines
fitted( ) function
fitting ANOVA models
  aov( ) function
  order of formula terms
fitting regression models, with lm( ) function
fix( ) function, 2^nd, 3^rd
FlexMix package
floor( ) function
fmi, fraction of missing information
font families
  changing
  examples on Windows platform
font parameter
font.axis parameter
font.lab parameter
font.main parameter
font.sub parameter
for loop
foreign package, 2^nd, 3^rd
format( ) function
formulas, in R, 2^nd
frame.plot option
freq option
frequency tables
Friedman test

G

Gamma distribution
gap package
gclus package, 2^nd, 3^rd
gcolor option
generalizability
genome-wide association studies (GWAS)
geom option
geometric distribution
geostatistical data
getwd( ) function, 2^nd
GGobi program
ggplot2 package, 2^nd
Gibbs sampling
glht( ) function, multcomp package
glm( ) function
glmPerm package
global validation, of linear model assumption
gls( ) function, nlme package
gmodels package
GPArotation package
gplots package, 2^nd, 3^rd, 4^th
graph dimensions, 2^nd
graphic output
graphic user interfaces (GUIs), 2^nd
  IDEs for
  for R
graphical parameters
  colors
  graph and margin dimensions
  reference lines
  symbols and lines
  text characteristics
graphics
  four systems of
  ggplot2 package
  interactive graphs
    identifying points
    iplots package
    latticist package
    playwith package
    rggobi package
    lattice package
    graphic parameters
    page arrangement
    panel functions
    variables, 2nd
  parameters
gray( ) function
grep( ) function, 2^nd
grid function
grid package, 2^nd
grouped bar plots
grouping variables
groups option dot plots
  lattice package, 2^nd
gsub( ) function
GUIs.
    See graphic user interfaces gvlma( ) function.
gvlma package, 2^nd, 3^rd
GWAS.
    See genome-wide association studies gzfile( ) function.

H

hat statistic
HDF5 files.
    See Hierarchical Data Format files.
hdf5 package, 2^nd
head( ) function
header value
heat.colors( )function
height variable
height vector
heights option
help ( ) or ? function
help facilities, 2^nd
help.search( ) or ?? function
help.start( ) function
hexbin( ) function
hexbin package, 2^nd
HH package, 2^nd, 3^rd
Hierarchical Data Format (HDF5) files
high-density scatter plots
high-leverage observations
hist( ) command
hist( ) function
histograms
  of bootstrapped statistics
  in ggplot2 plots
  in iplots
  in lattice plots, 2^nd
  in scatterplot matrices
  of studentized residuals
history( ) function
Hmisc package, 2^nd, 3^rd, 4^th
horiz option
hsv( ) function
hypergeometric distribution
hypothesis testing

I

I( ) operator, 2^nd
ibar( ) function
ibox( ) function
identify( ) function
id.method option, 2^nd
IDPmisc package
if-else construct
ifelse construct
if-else control structure
ihist( ) function
imap( ) function
imosaic( ) function
imputation
  multiple
  simple
incomplete data.
    See missing data.
independence, of errors, 2^nd, 3^rd
index.cond option
indices in R
infile
influencePlot( ) function, 2^nd
influential observations, 2^nd, 3^rd
input, 2^nd
installations, updating
installed.packages( ) function, 2^nd, 3^rd
install.packages( ) function, 2^nd, 3^rd
integrated development environments (IDEs)
interaction2wt( ) function, HH package
interaction.plot( ) function, 2^nd
interactions, multiple linear regression with
interactive graphs
  identifying points
  iplots package
  latticist package
  playwith package
  rggobi package
intermediate graphs
  bubble plots
  correlograms
  line charts
  mosaic plots
  scatter plots
    3D
    high-density
    matrices
ipairs( ) function, IDPmisc package
ipcp( ) function
iplot( ) function, 2^nd
iplots package, 2^nd
is.datatype( ) function
is.infinite( ) function
is.na( ) function, 2^nd
is.nan( ) function
isoMDS( ) function
isTRUE( ) operator

J

JGR/Deducer GUI
jpeg( ) function

K

kernel density estimation
kernel density plots, 2^nd
key (or auto.key) option
keyboards, entering data from
k-fold cross-validation
kmi package, 2^nd
Kruskal-Wallis test

L

labels, fitting in bar plots
labels option, 2^nd, 3^rd
lapply( ) function
las option
Last( ) function
latent variable models, 2^nd
LaTeX documents, R code + (Sweave package)
lattice package, 2^nd, 4^th, 11^th
  graphic parameters
  graphs types
  page arrangement
  panel functions
  variables
    conditioning
    grouping
latticist package, 2^nd
lavaan package, 2^nd
layout( ) function
layout option
lcda package, 2^nd
lcm( ) function
lcmm package
leadership data frame
leaps package, 2^nd
legend( ) function, 2^nd
legend option
legend.plot option
legends
  in bar plots
  in kernel density plots
  in lattice plots
  in line plots
  in mosaic plots
  in scatter plots, 2^nd
legend.text parameter
length( ) function, 2^nd, 3^rd, 4^th
level option, cld( ) function
leverage value, of observations
.libPaths( ) function, 2^nd
library( ) function
line( ) function
line charts
lines
  graphical parameters
  reference
lines( ) function, 2^nd, 3^rd
link function
list( ) function
lists
list-wise deletion
listwise deletion
lm( ) function, 2^nd
lme4 package
lmer( ) function, lme4 package
lmfit list object
lmPerm package
load( ) function, 2^nd
loadhistory( ) function
location option, 2^nd
locator() function
loess( ) function
log( ) function
log10( ) function
logical operators
logistic regression, 2^nd, 3^rd, 4^th
  extensions
  fitting
  interpreting parameters
  overdispersion
lognormal distribution
logregperm package
long data format
longitudinalData package, 2^nd
looping, repetition and
lower.panel option
lowess( ) function
ls( ) function, 2^nd
lsa package, 2^nd
.ls.objects( ) function
ltm package
lty option, 2^nd
lty parameter
lty.smooth option, 2^nd
lubridate package, 2^nd
lwd option
lwd parameter

M

mad( ) function
mai parameter
main option, 2^nd
Mallows Cp statistic
MANCOVA.
    See multivariate analysis of covariance Mann-Whitney U test.
MANOVA.
    See multivariate analysis of variance.
manova( ) function
MAR.
    See missing at random.
mar parameter
margin dimensions
marginplot( ) function, VIM package
MASS package, 2^nd, 3^rd, 4^th
math annotations
mathematical functions
matrices
  applying functions to
  matrix algebra with R
  of scatter plots
matrix function
matrixplot( ) function, VIM package
max( ) function
MCAR.
    See missing completely at random.
md.pattern( ) function, mice package
MDS.
    See multidimensional scaling.
mean( ) function, 2^nd, 3^rd, 4^th
mean substitution
mean values, bar plots for
median( ) function
melt( ) function
melting
merging datasets
  adding columns
  adding rows
metafile format, Windows
method option
mfrow parameter
MI.
    See multiple imputation mi package.
mice( ) function
mice package, 2^nd, 3^rd, 4^th
Microsoft Excel, importing data from
min( ) function
minor.tick( ) function
minus sign
missing at random (MAR)
missing completely at random (MCAR)
missing data
  approaches for dealing with incomplete data
  complete-case analysis
  exploring patterns
    exploring missing data visually
    missing values, 2nd
  identifying
  multiple imputation
  pairwise deletion
  rational approaches for correcting
  simple imputation
  steps in dealing with
  understanding sources and impact of
missing values
  excluding from analyses
  recoding values to missing
mix package
mixed-model ANOVA design
mlogit package
mode( ) function
MODULUS operator
mosaic( ) function, vcd library
mosaic plots
mosaicplot( ) function
mtcars data frame, 2^nd, 3^rd
mtext( ) function, 2^nd
multcomp package, 2^nd, 3^rd
multicollinearity
multidimensional scaling (MDS)
multiline comments
multiple comparisons
  nonparametric
  parametric
    one-way ANCOVA
    one-way ANOVA
multiple graphs per page.
    See page arrangement of graphs.
multiple imputation (MI), 2^nd
multiple linear regression, 2^nd, 3^rd
multiple regression
multivariate analysis of covariance (MANCOVA)
multivariate analysis of variance (MANOVA), 2^nd
  assessing test assumptions
  robust
multivariate normal data, generating
multivariate regression
mvnmle package, 2^nd
mvoutlier package, 2^nd
mvrnorm( ) function

N

NA.
    See not available.
names( ) function, 2^nd
names.arg argument
NaN.
    See not a number.
na.omit( ) function, 2^nd
na.rm option
ncdf package, 2^nd, 3^rd
ncdf4 package, 2^nd, 3^rd
nchar( ) function
ncvTest( ) function, 2^nd
netCDF files.
    See network Common Data Form files netCDF library, Unidata.
network Common Data Form (netCDF) files
new option
nFactors package, 2^nd
NHST.
    See null hypothesis significance testing.
nlme package
NMAR.
    See not missing at random.
nonlinear model, versus linear model
nonlinear regression
nonparametric regression
nonparametric tests
nonstochastic imputation
no.readonly option
normal data, generating multivariate
normal distribution functions
normal Q-Q plot
not a number (NaN), 2^nd
not available (NA), 2^nd
not missing at random (NMAR)
notched box plots
noweb file, 2^nd
npmc package
nrows option
null hypothesis significance testing (NHST)

O

obcConnectExcel( ) function
objects
oblique rotation, 2^nd
ODBC interface.
    See Open.
  Database Connectivity
  interface
odbcConnect( ) function
ODF.
    See Open Documents Format odfTable( ) function.
odfWeave package
OLS regression.
    See ordinary least squares regression.
one-way analysis of covariance (ANCOVA)
  assessing test assumptions
  visualizing results
one-way between-groups ANOVA design
one-way within-groups ANOVA design
Open Database Connectivity (ODBC) interface
Open Documents Format (ODF)
openMx package, 2^nd
OpenOffice documents, creating reports with odfWeave package
OpenOffice ODT file
options( ) function, 2^nd
OR operator
order( ) function, 2^nd
order of formula terms, 2^nd
order.clusters( ) function
ordered factor
order.single( ) function, gclus package
ordinary least squares (OLS) regression
  cross-validation
  fitting regression models with lm( ) function
  multiple linear regression
  multiple linear regression with interactions
  polynomial regression
  regression diagnostics
  simple linear regression
  variable (model) selection
  variable importance
orthogonal rotation, 2^nd
outlier observation
outliers
outlierTest( ) function, 2^nd, 3^rd
output
  graphic
  text
  using as input

P

packages
  analytic, for large datasets
  description of
  function of
  installing
  list of
  loading
  updating
page arrangement of graphs
  with base graphics
  with lattice graphs
pairs( ) function
pairwise deletion
pamm package
pan package
panel functions, 2^nd
panel option, 2^nd
panel.abline( ) function
panel.ellipse option
panel.grid( ) function
panel.lmline( ) function
panel.loess( ) function
panel.minmax option
panel.pie option
panel.pts option
panel.rug( ) function
panel.shade option
panel.txt option
panel.xyplot( ) function, 2^nd
par( ) function, 2^nd, 3^rd, 4^th, 5^th, 6^th
parallel analysis approach
parallel box plots, comparing groups with
parameters, graphic
paste( ) function, 2^nd
pastecs package
PCA.
    See principal components analysis.
pch parameter
pdf( ) function
pedantics package
period character
PHYS variable
pie charts
pie3D( ) function
piface package, 2^nd
pin parameter
playwith package, 2^nd
plot( ) function, 2^nd, 3^rd, 4^th
plot3d( ) function, rgl package
plotmath( ) function
plotmeans( ) function, gplots package, 2^nd
plot.new( ) function
plotrix package
plots, power analysis
plotting symbols, with pch parameter
pmm.
    See predictive mean matching.
png( ) function
points, identifying
poisson regression, 2^nd
  fitting
  interpreting parameters
  overdispersion
  robust
  with varying time periods
  zero-inflated
poLC package
poLCA package
polygon( ) function
polynomial regression, 2^nd, 3^rd, 4^th
pool( ) function
pos option, 2^nd
position option
postscript( ) function
power analysis, 13^th
  hypothesis testing
  implementing with pwr package
    ANOVA
    Chi-square tests
    correlations
    effect size benchmarks
    linear models
    tests of proportions
    t-tests
  plots
  specialized packages
powerGWASinteraction package
powerpkg package
powerSurvEpi package
predict( ) function
predictive mean matching (pmm)
pretty() function
primary variables, in lattice functions
principal( ) function, 2^nd, 3^rd
principal components analysis (PCA)
  other latent variable models
  principal components
    extracting
    obtaining scores
    rotating
  selecting number of
    components to extract
princomp( ) function
print( ) statement
probability functions
  generating multivariate normal data
  setting seed for random number generation
profr package
prooftools package
proportions, tests of
ps parameter
pseudo-random numbers
  multivariate normal
  probability distributions
  setting the seed
psych package, 2^nd
pundat dataframe
pwr package, implementing power analysis with
  ANOVA
  Chi-square tests
  correlations
  effect size benchmarks
  linear models
  tests of proportions
  t-tests
pwr.2p2n.test function
pwr.2p.test( ) function, 2^nd
pwr.anova.test( ) function, 2^nd, 3^rd
pwr.chisq.test( ) function, 2^nd
pwr.f2.test( ) function, 2^nd
PwrGSD package
pwr.p.test function
pwr.r.test( ) function, 2^nd, 3^rd
pwr.t2n.test function, 2^nd
pwr.t.test( ) function

Q

q( ) function, 2^nd
qcc package
qplot( ) function
qqPlot( ) function
quadratic regression
quantile( ) function, 2^nd
quartzFonts( )function

R

R AnalyticFlow GUI
R CMD BATCH statement
R code + LaTeX documents (Sweave package), typesetting with
R Commander GUI
R Data Import/Export manual
.R extension
R GUI Generator (RGG)
R GUI Projects page
R icon
R programming, common mistakes in
R statements
R_HOME value
R_HOME/etc directory
R2HTML package
rainbow( ) function, 2^nd
Random Access Memory (RAM), storing data outside of
random number generation, setting seed for
random samples
randomized block design
randomLCA package, 2^nd
range( ) function
Rattle (for data mining) GUI
rbind( ) function, 2^nd, 3^rd
Rcmdr package, 2^nd
Rcpp package
RCurl package
.RData file
readLines( ) function
read.spss( ) function
read.ssd( ) function
read.table( ) function, 2^nd
read.xlsx( ) function
recode( ) function
recodevar( ) function
recoding, values to missing
Red R GUI
reference lines
regression
  ANOVA as
  corrective measures
    deleting observations
    variables
  diagnostics
    enhanced approach
    global validation of linear model assumption
    multicollinearity
    typical approach
  measuring performance
    cross-validation
    relative importance
  OLS
    fitting regression models with lm( ) function
    multiple linear regression
    polynomial regression
    simple linear regression
  selecting model
    comparing models
    variable selection
  unusual observations
    high leverage
    influential
    outliers
  varieties of
regression diagnostics
regsubsets( ) function
relaimpo package
relative importance, of variables
relative weights
relative widths
relweights( ) function
rename( ) function
rep( ) function
repeated measures, ANOVA, 2^nd
repetition, and looping
resampling statistics, 2^nd
reshape package, 2^nd, 5^th
  casting
  melting
residplot( ) function
residual versus leverage plot
residuals( ) function
results option, Sweave
RGG.
    See R GUI Generator rggobi package.
rgl package, 2^nd
.Rhistory file
RJDBC package
Rkward GUI
rm( ) function, 2^nd, 3^rd
rms package
RMySQL package, 2^nd
robust MANOVA
robust package
Robust regression
RODBC package, 2^nd
ROracle package, 2^nd
rotating
  3D scatter plots
  factors
  principal components
round( ) function
.Rout extension
rownames
row.names option, 2^nd
rows, adding
RPostgreSQL package, 2^nd
Rprof( ) function
.Rprofile file
Rprofile.site file, 2^nd
rrcov package, 2^nd
RSiteSearch( ) function
RSQLite package, 2^nd
R-square statistic
rug plots, 2^nd
runif( ) function

S

sample( ) function
sample size quantity
samples, random
sampling package
sapply( ) function, 2^nd
sas.get( ) function
save( ) function
savehistory( ) function
save.image( ) function
scalar values
scale( ) function, 2^nd, 3^rd
scales option
scan( ) function
scatter plots
  3D
  high-density
  matrices
scatter3d( ) function, Rcmdr package
scatterplot( ) function, 2^nd, 3^rd
scatterplot3d( ) function, scatterplot3d package
scatterplot3d package, 2^nd
scatterplotMatrix( ) function, 2^nd, 3^rd, 4^th
scores option
scree( ) function
sd( ) function
search( ) command
seed, setting for random number generation
SELECT statements, 2^nd
SEM.
    See structural equation modeling sem package.
seq( ) function
SeqKnn package, 2^nd
sequence, in for statements
set.seed( ) function
setwd( ) function
Sexpr statement
shadow matrix
shape option
show.settings( ) function
shrinkage( ) function
side option, 2^nd
signif( ) function
significance levels
simple imputation
simple linear regression, 2^nd, 3^rd
simulate option
sin( ) function
singer dataset
sinh( ) function
sink( ) function, 2^nd
site initialization file
size option, in ggplot2
sm packages, 2^nd
sm.density.compare( ) function, 2^nd
smoothScatter( ) function, base package, 2^nd
software, updating
sorting, data management
source( ) function
speedglm package
sphericity
spine( ) function
spinning 3D scatter plots
spinograms
split( ) function, in bigtabulate package
split option, in lattice plots, 2^nd
splitting output
spread option, 2^nd
spreadLevelPlot( ) function, 2^nd, 3^rd
SPSS datasets.
    See Statistical Package for the Social Sciences datasets, importing data from spss. get( ) function.
SQL.
    See Structured Query Language sqldf( ) function.
sqldf package
sqlDrop( ) function
sqlFetch( ) function
sqlQuery( ) function
sqlSave( ) function
sqrt( ) function
ssize.fdr package
stacked bar plots
standardizing data
startup environment customizing
statements, in R
state.x77 dataset
Statistical Analysis System (SAS) datasets, importing data from
statistical applications, exporting data for
statistical functions
Statistical Package for the Social Sciences (SPSS) datasets, importing data from
Stat/Transfer application, importing data via
stepAIC( ) function
stepwise regression
stop( ) function
storage, outside of RAM
str( ) function, 2^nd
stringsAsFactors option
strip option
strsplit( ) function, 2^nd
structural equation modeling (SEM)
Structured Query Language (SQL)
sub( ) function
sub option
subset( ) function
subsets( ) function
subsetting datasets
  selecting observations
  selecting variables
  subset( ) function
substr( ) function
sum( ) function, 2^nd, 3^rd
sum of squares
  Type I (sequential)
  Type II (hierarchical)
  Type III (marginal)
summary( ) function, 2^nd, 3^rd
summary.aov( ) function
summaryRprof( ) function
Sweave( ) function, 2^nd
Sweave package (R code + LaTeX documents), typesetting with
switch construct
symbols
  graphical parameters
  plotting with pch parameter
  in R formulas
symbols( ) function
Sys.Date( ) function
Sys.getenv( ) function
system.time( ) function

T

t( ) function
tab-delimited files
table( ) function, 2^nd
tabulating missing values
tail( ) function
tan( ) function
tanh( ) function
tapply( ) function
tck option
terrain.colors( )function
Test of proportions
TeX file
text( ) function
text characteristics, graphical parameters
text output
text.col ( ) option
text.panel option
tick marks
tick.ratio
tiff( ) function
time-series regression
time-stamping data
title( ) function, 2^nd, 3^rd
title option
titles
tolower( ) function
topo.colors( )function
toupper( ) function
transform( ) function
transformations, of variables
transmission disequilibrium test (TDT)
transpose
trellis.par.get( ) function
trellis.par.set( ) function
trt2times variable
trunc( ) function
twiddler package
two-way ANOVA design
two-way factorial ANOVA, 2^nd
type conversions
Type I (sequential) approach
Type II (hierarchical) approach
Type III (marginal) approach
type option

U

unbalanced design
Unidata netCDF library
uniquenesses
unz( ) function
update( ) function
update.packages( ) function, 2^nd
updating installations
upper.panel option
url( ) function
user-written functions, 2^nd

V

validation, of linear model assumption
value labels
var( ) function
variable <- expression statement
variable labels
variable[condition] <- expression statement
variance inflation factor (VIF)
varimax rotation
varwidth option
vcd package, 2^nd, 3^rd, 4^th, 5^th
vcov( ) function
vectors
vegan package
VIF.
    See variance inflation factor.
vif( ) function, 2^nd
vignette( ) function
VIM package, 2^nd, 3^rd
violin plots
vioplot( ) function
vioplot package

W

warning( ) function
webscraping
which( )function
while loop
widths option
Wilcoxon rank sum test
Wilks.test( ) function, rrcov package
Windows metafile format
windowsFont( ) function
win.metafile( ) function
with( ) function, 2^nd, 3^rd, 4^th
within( ) function
workspace, 2^nd
write.foreign( ) function
write.table( ) function
write.xlsx( ) function

X

xaxt option
xfig( ) function
xlab option, 2^nd, 3^rd
xlim option, 2^nd
xlsx package, 2^nd, 3^rd
XML files, importing data from
XML package, 2^nd
xtable( ) function, 2^nd
xtable package
xyplot( ) function
xzfile( ) function

Y

yaxt option
ylab option, 2^nd, 3^rd
ylim option, 2^nd