Index

A note on the digital index

A link in an index entry is displayed as the section title in which that entry appears. Because some sections have multiple index markers, it is not unusual for an entry to have several links to the same section. Clicking on any link will take you directly to the place in the text in which the marker appears.

Symbols

! operator, Logical Vectors

# symbol, How to Get Help in R

$ operator, Indexing Lists

% operator, Formatting Numbers

%% operator, Mathematical Operations and Vectors

%*% operator, Array Arithmetic

%/% operator, Mathematical Operations and Vectors

%in% operator, Environments

%o% operator, Array Arithmetic

& operator, Logical Vectors

+ operator, Mathematical Operations and Vectors, Turning Strings into Code

: operator, Mathematical Operations and Vectors, Mathematical Operations and Vectors, Vectors

<- operator, Assigning Variables, Reference Classes

<<- operator, Assigning Variables, Reference Classes

== operator, Mathematical Operations and Vectors

? operator, How to Get Help in R

?? operator, How to Get Help in R, How to Get Help in R

[[]] indexing, Indexing Lists

[] indexing, Indexing Vectors, Indexing Lists

^ operator, Array Arithmetic

| operator, Logical Vectors

A

adding dates, Arithmetic with Dates and Times

adding vectors, Mathematical Operations and Vectors

aggregate function (stats), Split-Apply-Combine

alarm function (utils), Special Characters

all.equal function (base), Mathematical Operations and Vectors

anova function (stats), Comparing and Updating Models

apply function (base), Cleaning Strings

*apply function family, The plyr Package

apropos function (utils), How to Get Help in R

Architect, Eclipse/Architect, Eclipse/Architect (see Eclipse)

args function (base), Creating and Calling Functions

arguments, Your First Program, Pairlists, Creating and Calling Functions, Passing Functions to and from Other Functions

formal, Creating and Calling Functions

pass into functions, Pairlists

using functions as, Passing Functions to and from Other Functions

arithmetic, Array Arithmetic–Summary, List Dimensions and Arithmetic, Arithmetic with Dates and Times

date/time, Arithmetic with Dates and Times

lists, List Dimensions and Arithmetic

on arrays, Array Arithmetic–Summary

arrange function (plyr), Sorting

array function (base), Creating Arrays and Matrices

arrays, Other Common Classes, Matrices and Arrays–Summary, Creating Arrays and Matrices, Rows, Columns, and Dimensions–Indexing Arrays, Rows, Columns, and Dimensions–Indexing Arrays, Rows, Columns, and Dimensions–Indexing Arrays, Indexing Arrays, Array Arithmetic–Summary, Looping Over Arrays–Looping Over Arrays

arithmetic on, Array Arithmetic–Summary

columns of, Rows, Columns, and Dimensions–Indexing Arrays

creating, Creating Arrays and Matrices

dimensions of, Rows, Columns, and Dimensions–Indexing Arrays

indexing, Indexing Arrays

looping over, Looping Over Arrays–Looping Over Arrays

rows of, Rows, Columns, and Dimensions–Indexing Arrays

two-dimensional, Other Common Classes

as* functions (base, methods), Checking and Changing Classes

assertive package, Checking and Changing Classes

assign function (base), Assigning Variables, Environments, Turning Strings into Code

atomic variable types, Atomic and Recursive Variables, Properties of Variables

Autoloads, The Search Path

axis scales, Take 2: lattice Graphics

B

backslash characters, Special Characters

bar charts, Bar Charts–Bar Charts, Bar Charts–Bar Charts, Bar Charts–Bar Charts, Bar Charts–Bar Charts

in base graphics, Bar Charts–Bar Charts

in ggplot2 graphics, Bar Charts–Bar Charts

in lattice graphics, Bar Charts–Bar Charts

base environment, Environments, The Three Plotting Systems

limitations of, The Three Plotting Systems

base graphics package, Take 1: base Graphics–Take 1: base Graphics, Line Plots, Histograms–Histograms, Box Plots, Bar Charts–Bar Charts

bar charts in, Bar Charts–Bar Charts

box plots in, Box Plots

histograms in, Histograms–Histograms

line plots in, Line Plots

scatterplots in, Take 1: base Graphics–Take 1: base Graphics

basename function (base), File Paths

Bell Laboratories, What Is R?

bibmemory package, Other Things to Do in R

binary data files, Reading Binary Files–Reading Other File Types, Reading Excel Files

Excel files as, Reading Excel Files

binding matrices, Combining Matrices

Bitbucket, Installing Packages

box plots, Box Plots–Bar Charts, Box Plots, Box Plots, Box Plots

in base graphics, Box Plots

in ggplot2 graphics, Box Plots

in lattice graphics, Box Plots

breaks argument, Histograms

browseEnv function (utils), The Workspace

browseVignettes function (utils), How to Get Help in R

by function (base), Split-Apply-Combine

C

c function (base), Mathematical Operations and Vectors, Vectors, Combining Matrices, Combining Lists

call objects, Turning Strings into Code

cancor function (stats), Summary Statistics

casting, Checking and Changing Classes

cat function (base), Examining Variables, Constructing and Printing Strings

cbind function (base), Combining Matrices, Combining Lists

Chambers, John, What Is R?

character arrays, Strings

character class, Other Common Classes

character vector, Other Common Classes, Lengths, Strings

characters, Special Characters, Changing Case

case, changing, Changing Case

special, Special Characters

check function (devtools), Checking and Building Packages

check* function family (RUnit), RUnit

class factory, Reference Classes

class function (base), Checking and Changing Classes, Arithmetic with Dates and Times

combining unclass and, Arithmetic with Dates and Times

class generator, Reference Classes

classes, Classes, Other Common Classes–Other Common Classes, Other Common Classes, Checking and Changing Classes–Checking and Changing Classes, Checking and Changing Classes–Checking and Changing Classes

changing, Checking and Changing Classes–Checking and Changing Classes

checking, Checking and Changing Classes–Checking and Changing Classes

of variables, Classes

vectors, Other Common Classes

cleaning data, Cleaning and Transforming–Summary, Cleaning Strings–Manipulating Data Frames, Functional Programming–Summary

functions for, Functional Programming–Summary

strings, Cleaning Strings–Manipulating Data Frames

cleaning datasets, Dropping Factor Levels

closure, Environments

colbycol package, CSV and Tab-Delimited Files

colClasses argument, Reading Excel Files

collaboration, Live-R and, Live-R

colMeans function (base), Basic Data Frame Manipulation

colnames function (base), Row, Column, and Dimension Names, Summary, Creating Data Frames

colon operator, Vectors (see : operator)

colSums function (base), Basic Data Frame Manipulation

column functions, List Dimensions and Arithmetic

columns, Rows, Columns, and Dimensions–Indexing Arrays, Row, Column, and Dimension Names, Manipulating Data Frames–Sorting, Adding and Replacing Columns

adding/replacing, Manipulating Data Frames–Sorting, Adding and Replacing Columns

naming, Row, Column, and Dimension Names

comma-separated value (CSV) files, CSV and Tab-Delimited Files–CSV and Tab-Delimited Files

comments, How to Get Help in R

comparing, Mathematical Operations and Vectors, Mathematical Operations and Vectors

integers, Mathematical Operations and Vectors

strings, Mathematical Operations and Vectors

complete.cases function (stats), Dealing with Missing Values

complex class, Different Types of Numbers

compulsary files, The Package Directory Structure

concatenating, Vectors, Combining Lists

values, Vectors

vectors, Combining Lists

conditional execution, if and else

coordinated universal time, Parsing Dates

cor function (stats), Summary Statistics

Core Team, What Is R?

CRAN package repository, Installing Packages

CRAN task views, Other Things to Do in R

CRANextra, Installing Packages

CSV files, Conversion to and from Strings, CSV and Tab-Delimited Files–CSV and Tab-Delimited Files

cummax function (base), Summary Statistics

cummin function (base), Summary Statistics

cumprod function (base), Summary Statistics

cumsum function (base), Summary Statistics

cumulative density function (CDF), Distributions

customizing Emacs, Emacs + ESS

cut function (base), Converting Continuous Variables to Categorical

D

data directory, The Package Directory Structure

data frames, Data Frames–Basic Data Frame Manipulation, Creating Data Frames–Creating Data Frames, Indexing Data Frames–Indexing Data Frames, Basic Data Frame Manipulation, Basic Data Frame Manipulation, Manipulating Data Frames–Sorting, Manipulating Data Frames–Sorting, Dealing with Missing Values, Converting Between Wide and Long Form, Using SQL–Sorting, Functional Programming–Summary

columns, adding/replacing, Manipulating Data Frames–Sorting

creating, Creating Data Frames–Creating Data Frames

indexing, Indexing Data Frames–Indexing Data Frames

manipulating, Basic Data Frame Manipulation, Manipulating Data Frames–Sorting

manipulating, functions for, Functional Programming–Summary

missing values in, Dealing with Missing Values

SQL, manipulating with, Using SQL–Sorting

transposing, Basic Data Frame Manipulation

wide/long forms, converting between, Converting Between Wide and Long Form

data function (utils), Built-in Datasets

data, cleaning, Cleaning and Transforming–Summary, Cleaning Strings–Manipulating Data Frames, Functional Programming–Summary

functions for, Functional Programming–Summary

strings, Cleaning Strings–Manipulating Data Frames

data, rectangular, CSV and Tab-Delimited Files

data, visualizing, Exploring and Visualizing–Summary, Summary Statistics–Summary Statistics, Scatterplots–Line Plots, Line Plots–Line Plots, Histograms–Histograms, Bar Charts–Bar Charts

bar charts, Bar Charts–Bar Charts

histograms, Histograms–Histograms

line plots, Line Plots–Line Plots

scatterplots, Scatterplots–Line Plots

summary statistics, Summary Statistics–Summary Statistics

data.frame function (base), Creating Data Frames

database management systems (DBMSs), Accessing Databases

databases, accessing, Accessing Databases–Accessing Databases

datasets, Dropping Factor Levels, Getting Data–Summary, Built-in Datasets, Reading Text Files–JSON and YAML Files, CSV and Tab-Delimited Files–CSV and Tab-Delimited Files, CSV and Tab-Delimited Files–CSV and Tab-Delimited Files, Unstructured Text Files, XML and HTML Files, XML and HTML Files, JSON and YAML Files–JSON and YAML Files, JSON and YAML Files–JSON and YAML Files, Reading Binary Files–Reading Other File Types, Reading Excel Files, Reading SAS, Stata, SPSS, and MATLAB Files, Reading Other File Types, Web Data–Scraping Web Pages, Sites with an API, Scraping Web Pages–Scraping Web Pages, Accessing Databases–Accessing Databases

APIs, websites with, Sites with an API

from binary files, Reading Binary Files–Reading Other File Types

built-in, Built-in Datasets

cleaning, Dropping Factor Levels

CSV files as, CSV and Tab-Delimited Files–CSV and Tab-Delimited Files

databases as, Accessing Databases–Accessing Databases

HTML files as, XML and HTML Files

JSON files, JSON and YAML Files–JSON and YAML Files

packages for, Reading Other File Types

scraping web pages for, Scraping Web Pages–Scraping Web Pages

in spreadsheets, Reading Excel Files

from statistical packages, Reading SAS, Stata, SPSS, and MATLAB Files

tab-delimited files as, CSV and Tab-Delimited Files–CSV and Tab-Delimited Files

text files as, Reading Text Files–JSON and YAML Files

unstructured text files as, Unstructured Text Files

web data as, Web Data–Scraping Web Pages

XML files as, XML and HTML Files

YAML files as, JSON and YAML Files–JSON and YAML Files

datasets package, Built-in Datasets

Date class, The Date Class

date classes, add-on, Other Date Classes

dates, Dates and Times–Summary, POSIX Dates and Times, POSIX Dates and Times, The Date Class, Conversion to and from Strings, Parsing Dates, Formatting Dates, Arithmetic with Dates and Times, Arithmetic with Dates and Times, Lubridate–Lubridate

arithmetic with, Arithmetic with Dates and Times

Date class, The Date Class

formatting, Formatting Dates

lubridate package and, Lubridate–Lubridate

manipulating, Arithmetic with Dates and Times

parsing, Parsing Dates

POSIXct class, POSIX Dates and Times

POSIXlt class, POSIX Dates and Times

strings, converting to/from, Conversion to and from Strings

DBMSs, Accessing Databases

dcast function (reshape2), Converting Between Wide and Long Form

ddply function (plyr), The plyr Package

debugging, Eclipse/Architect, Environments, Debugging–Debugging

using Eclipse for, Eclipse/Architect

defineTestSuite function, RUnit

demo directory, The Package Directory Structure

demo function (utils), How to Get Help in R

deparse function (base), Creating and Calling Functions, Turning Code into Strings

deparsing, Turning Code into Strings

DESCRIPTION files, The Package Directory Structure

devtools package, Checking and Building Packages

difftime class, Arithmetic with Dates and Times

difftime function (base), Arithmetic with Dates and Times

dim argument, Creating Arrays and Matrices

dim function (base), Rows, Columns, and Dimensions

dimensions, of arrays/matrices, Rows, Columns, and Dimensions–Indexing Arrays, Row, Column, and Dimension Names

naming, Row, Column, and Dimension Names

dimnames function (base), Row, Column, and Dimension Names, Summary, Creating Data Frames

directories, The Package Directory Structure, The Package Directory Structure

optional, The Package Directory Structure

dirname function, File Paths

distributions, Sampling from Distributions, Distributions

random numbers and, Sampling from Distributions

do.call function (base), Passing Functions to and from Other Functions

doc directory, The Package Directory Structure

double quotes, Special Characters

E

ecdf function (stats), Passing Functions to and from Other Functions

Eclipse, Eclipse/Architect, Eclipse/Architect

debugger, Eclipse/Architect

edit function (utils), Examining Variables

elements of vectors, Names, Indexing Vectors–Indexing Vectors, Vector Recycling and Repetition, Vector Recycling and Repetition

indexing, Indexing Vectors–Indexing Vectors

naming, Names

recycling, Vector Recycling and Repetition

repetition of, Vector Recycling and Repetition

else statements, Multiple Selection

Emacs, Emacs + ESS, Emacs + ESS

customizing, Emacs + ESS

Emacs Speaks Statistics (ESS), Emacs + ESS

empty environments, Environments

empty variables, NULL

environments, Environments–Environments, Environments, Environments, Environments

converting to lists, Environments

empty, Environments

frames and, Environments

error argument, Error Handling

error handling, Error Handling–Error Handling

errors, Messages, Warnings, and Errors–Messages, Warnings, and Errors

ESRI ArcGIS spatial data files, Reading Other File Types

ESS (Emacs Speaks Statistics), Emacs + ESS

eval function (base), Turning Code into Strings, Turning Code into Strings

using substitute with, Turning Code into Strings

example function (utils), How to Get Help in R

Excel (Microsoft), Reading Excel Files

exists function (base), Environments, Variable Scope

expect* function family (testthat), testthat

expression objects, Turning Strings into Code

F

facets, Take 3: ggplot2 Graphics

factor function (base), Changing Factor Levels

factors, Other Common Classes, Factors–Combining Factors, Creating Factors, Changing Factor Levels, Dropping Factor Levels, Ordered Factors, Converting Continuous Variables to Categorical, Generating Factor Levels, Combining Factors

combining, Combining Factors

continuous vs. categorical variables and, Converting Continuous Variables to Categorical

creating, Creating Factors

levels of, Other Common Classes

levels, changing, Changing Factor Levels

levels, dropping, Dropping Factor Levels

levels, generating, Generating Factor Levels

ordered, Ordered Factors

factors class, Other Common Classes

FALSE, Logical Vectors

ff package, Other Things to Do in R

file formats, Conversion to and from Strings

file paths as strings, File Paths

file.path function (base), File Paths

filter function (stats), Functional Programming

Find function (base), Functional Programming

finding functions, How to Get Help in R

first-class objects, What Is R?

fivenum function (stats), Summary Statistics

fix function (utils), Examining Variables

fixed function (stringr), Cleaning Strings

flow control, Flow Control–Multiple Selection, if and else, Vectorized if, Vectorized if, Multiple Selection–Multiple Selection

if/else statements, if and else

switch, Multiple Selection–Multiple Selection

vectorized, Vectorized if

vectorized if, Vectorized if

for, Turning Strings into Code

for loops, for Loops–for Loops

foreign package, Reading SAS, Stata, SPSS, and MATLAB Files

formal arguments, Creating and Calling Functions

formalArgs function (methods), Creating and Calling Functions

formals function (base), Pairlists, Creating and Calling Functions

format function, Formatting Numbers

formatC function (base), Formatting Numbers

formatting numbers, Formatting Numbers–Special Characters, Formatting Numbers, Formatting Numbers, Formatting Numbers, Formatting Numbers

with format function, Formatting Numbers

with formatC, Formatting Numbers

with prettyNum function, Formatting Numbers

with sprintf function, Formatting Numbers

formula interface, Take 2: lattice Graphics

formulae, Formulae–Formulae

frames, Environments, Environments

environments and, Environments

freq argument, Histograms

Frogger, Split-Apply-Combine

functional programming, Functional Programming–Summary

functions, Your First Program, How to Get Help in R, How to Get Help in R, Examining Variables, Pairlists, Pairlists, Environments, Functions–Variable Scope, Creating and Calling Functions–Creating and Calling Functions, Creating and Calling Functions–Creating and Calling Functions, Creating and Calling Functions, Passing Functions to and from Other Functions–Variable Scope, Passing Functions to and from Other Functions, Variable Scope–Variable Scope, Converting Categorical Variables to Continuous, Lubridate, S3 Classes

calling, Creating and Calling Functions–Creating and Calling Functions

creating, Creating and Calling Functions–Creating and Calling Functions, Creating and Calling Functions

creating durations, Lubridate

finding, How to Get Help in R

help with, How to Get Help in R

importing, Converting Categorical Variables to Continuous

methods vs., Examining Variables

overloading, S3 Classes

pass arguments into, Pairlists

passing, to/from other functions, Passing Functions to and from Other Functions–Variable Scope

shortcuts, Environments

standard deviation, Pairlists

using as arguments, Passing Functions to and from Other Functions

variable scope and, Variable Scope–Variable Scope

G

Gentleman, Robert, What Is R?

get function (base), Environments, Variable Scope

getwd function (base), File Paths

ggplot function (ggplot2), Take 3: ggplot2 Graphics

ggplot2 graphics package, Take 3: ggplot2 Graphics–Line Plots, Line Plots–Line Plots, Histograms–Histograms, Box Plots, Bar Charts–Bar Charts

bar charts in, Bar Charts–Bar Charts

box plots in, Box Plots

histograms in, Histograms–Histograms

line plots in, Line Plots–Line Plots

scatterplots in, Take 3: ggplot2 Graphics–Line Plots

GitHub, Installing Packages

glm, Other Model Types

global assignment, Assigning Variables, Reference Classes

global environment, Environments, Environments

global error option, Debugging

global variables, Variable Scope

gnumeric package, Reading Excel Files

Gnumeric spreadsheets, Reading Excel Files

Google Code, Installing Packages

graphical representations, Exploring and Visualizing–Summary, Summary Statistics–Summary Statistics, Scatterplots–Line Plots, Line Plots–Line Plots, Histograms–Histograms, Bar Charts–Bar Charts

bar charts, Bar Charts–Bar Charts

histograms, Histograms–Histograms

line plots, Line Plots–Line Plots

scatterplots, Scatterplots–Line Plots

summary statistics, Summary Statistics–Summary Statistics

grep function (base), Cleaning Strings

grepl function (base), Cleaning Strings

GROUP BY operations (SQL), Split-Apply-Combine

gWidgets framework, Other Things to Do in R

H

HDF5 files, Reading Other File Types

head function (utils), Examining Variables, XML and HTML Files

internal nodes and, XML and HTML Files

help function (utils), How to Get Help in R

help search operator, How to Get Help in R

help, sources for, How to Get Help in R–How to Get Help in R

help.search function (utils), How to Get Help in R

hist function (graphics), Histograms

histograms, Histograms–Histograms, Histograms–Histograms, Histograms–Histograms, Histograms–Histograms

in base graphics, Histograms–Histograms

in ggplot2 graphics, Histograms–Histograms

in lattice graphics, Histograms–Histograms

HTML files, XML and HTML Files

htmlParse function (XML), Scraping Web Pages

I

IDEs, Choosing an IDE–Other IDEs and Editors, Choosing an IDE, Emacs + ESS, Emacs + ESS, Emacs + ESS, Eclipse/Architect, Eclipse/Architect, RStudio, Revolution-R, Live-R

Architect, Eclipse/Architect

Eclipse, Eclipse/Architect

Emacs, Emacs + ESS

ESS, Emacs + ESS

Live-R, Live-R

popular choices, Choosing an IDE

Revolution-R, Revolution-R

RStudio, RStudio

XEmacs, Emacs + ESS

if, Turning Strings into Code

if/else statements, if and else, Vectorized if

vectorized, Vectorized if

ifelse function (base), if and else, Vectorized if

Ihaka, Ross, What Is R?

importing, XML and HTML Files, JSON and YAML Files

XML files, XML and HTML Files

YAML files, JSON and YAML Files

%in% operator, Environments

INDEX files, The Package Directory Structure

indexing, Indexing Vectors–Indexing Vectors, Indexing Vectors, Indexing Arrays, Indexing Lists–Indexing Lists, Indexing Data Frames–Indexing Data Frames

arrays, Indexing Arrays

data frames, Indexing Data Frames–Indexing Data Frames

elements (vectors), Indexing Vectors–Indexing Vectors

lists, Indexing Lists–Indexing Lists

infinite values, Special Numbers

initialize method, Reference Classes

inst directory, The Package Directory Structure

install.packages function (utils), Installing Packages

install.Rtools function (installr), Prerequisites

installed.packages function (utils), Libraries and Installed Packages

installr package, Installing Extra Related Software, Prerequisites

install_github function (devtools), Installing Packages

integer class, Different Types of Numbers

Integrated Development Environment, Choosing an IDE (see IDEs)

integration testing, Testing

interpreter, Magic–Turning Code into Strings

intervals, Lubridate

inverse CDF, Distributions

is.* function family (base, methods), Checking and Changing Classes

J

JDBC API, Accessing Databases

JGR, Other IDEs and Editors

JSON files, JSON and YAML Files–JSON and YAML Files

K

knitr package, The Package Directory Structure

L

labelling elements, Names

language objects, Properties of Variables

language variable types, Magic

lapply function (base), Looping Over Lists

lattice graphics package, Loading Packages, Take 2: lattice Graphics–Take 3: ggplot2 Graphics, Take 2: lattice Graphics, Line Plots, Histograms–Histograms, Box Plots, Bar Charts–Bar Charts

bar charts in, Bar Charts–Bar Charts

box plots in, Box Plots

histograms in, Histograms–Histograms

line plots in, Line Plots

plots, benefits of, Take 2: lattice Graphics

scatterplots in, Take 2: lattice Graphics–Take 3: ggplot2 Graphics

layout function (graphics), Take 1: base Graphics, Plotting and Inspecting Models

learningr package, Debugging

length function (base), Lengths, Rows, Columns, and Dimensions

levels argument, Changing Factor Levels

levels function (base), Creating Factors

libraries, Loading Packages, Libraries and Installed Packages

problems with, Libraries and Installed Packages

library function (base), Loading Packages

LICENSE files, The Package Directory Structure

line plots, Line Plots–Line Plots, Line Plots, Line Plots, Line Plots–Line Plots

in base graphics, Line Plots

in ggplot2 graphics, Line Plots–Line Plots

in lattice graphics, Line Plots

linear regression models, A First Model: Linear Regressions–Comparing and Updating Models

list function (base), Vectors, Creating Lists

list2env function (base), Environments

listing elements, Creating Lists

lists, Lists–Pairlists, Creating Lists–Creating Lists, Atomic and Recursive Variables, List Dimensions and Arithmetic, List Dimensions and Arithmetic, Indexing Lists–Indexing Lists, Indexing Lists, Converting Between Vectors and Lists, Combining Lists, NULL–Pairlists, Pairlists, Environments, Looping Over Lists–Looping Over Lists

accessing elements of, Indexing Lists

arithmetic, List Dimensions and Arithmetic

combining, Combining Lists

converting environments to, Environments

creating, Creating Lists–Creating Lists

dimensions of, List Dimensions and Arithmetic

indexing, Indexing Lists–Indexing Lists

looping over, Looping Over Lists–Looping Over Lists

NULL value and, NULL–Pairlists

pairlists, Pairlists

as recursive variables, Atomic and Recursive Variables

vectors, converting to/from, Converting Between Vectors and Lists

Live-R, Live-R, Live-R, Live-R

collaborating with, Live-R

downsides, Live-R

lm function (stats), A First Model: Linear Regressions

local assignment operator, Reference Classes

local variables, Assigning Variables

log scales, Take 3: ggplot2 Graphics

logical class, Classes

logical operators, vectorized, Logical Vectors

logical vectors, Logical Vectors–Logical Vectors, Other Common Classes

looping, Loops–for Loops, repeat Loops–while Loops, while Loops, for Loops–for Loops, Advanced Looping–Summary, Replication, Looping Over Lists–Looping Over Lists, Looping Over Arrays–Looping Over Arrays, Multiple-Input Apply, Multiple-Input Apply, Instant Vectorization, Split-Apply-Combine, The plyr Package–Summary

for, for Loops–for Loops

mapply function, Multiple-Input Apply

over arrays, Looping Over Arrays–Looping Over Arrays

over lists, Looping Over Lists–Looping Over Lists

over multiple vectors, Multiple-Input Apply

plyr package for, The plyr Package–Summary

repeat, repeat Loops–while Loops

replicate function, Replication

tapply function, Split-Apply-Combine

Vectorize function, Instant Vectorization

while, while Loops

ls function (base), The Workspace, Environments

ls.str function (utils), The Workspace, Environments

lubridate package, Lubridate–Lubridate

M

magic function (matlib), Looping Over Arrays

magic squares, Looping Over Arrays

man directory, The Package Directory Structure

manipulating dates, Arithmetic with Dates and Times

manual offsets, Time Zones

Map function, Functional Programming

mapply function (base), Multiple-Input Apply, Instant Vectorization

Vectorize function and, Instant Vectorization

mathematical functions, Mathematical Operations and Vectors

mathematical operations, Mathematical Operations and Vectors–Mathematical Operations and Vectors

MATLAB files, Reading SAS, Stata, SPSS, and MATLAB Files

matlab package, Looping Over Arrays

matrices, Matrices and Arrays–Summary, Creating Arrays and Matrices, Creating Arrays and Matrices, Rows, Columns, and Dimensions–Indexing Arrays, Rows, Columns, and Dimensions–Indexing Arrays, Rows, Columns, and Dimensions–Indexing Arrays, Combining Matrices, Combining Matrices, Combining Matrices, Array Arithmetic

binding, Combining Matrices

columns of, Rows, Columns, and Dimensions–Indexing Arrays

combining, Combining Matrices

converting to vectors, Combining Matrices

creating, Creating Arrays and Matrices

creating with array function, Creating Arrays and Matrices

dimensions of, Rows, Columns, and Dimensions–Indexing Arrays

rows of, Rows, Columns, and Dimensions–Indexing Arrays

transposing, Array Arithmetic

matrix class, Other Common Classes

max function, Summary Statistics

mean function, Arithmetic with Dates and Times, Summary Statistics

median function, Summary Statistics

median function (base), Mathematical Operations and Vectors

merge function, Basic Data Frame Manipulation

messages, Messages, Warnings, and Errors–Messages, Warnings, and Errors

methods, Examining Variables, Reference Classes

functions vs., Examining Variables

static, Reference Classes

methods function, S3 Classes

min function, Summary Statistics

models, Formulae–Formulae, A First Model: Linear Regressions–Other Model Types, A First Model: Linear Regressions–Comparing and Updating Models, Comparing and Updating Models–Comparing and Updating Models, Comparing and Updating Models–Comparing and Updating Models, Plotting and Inspecting Models–Plotting and Inspecting Models, Plotting and Inspecting Models–Plotting and Inspecting Models, Other Model Types

comparing, Comparing and Updating Models–Comparing and Updating Models

formulae for, Formulae–Formulae

inspecting, Plotting and Inspecting Models–Plotting and Inspecting Models

linear regression, A First Model: Linear Regressions–Comparing and Updating Models

plotting, Plotting and Inspecting Models–Plotting and Inspecting Models

types of, Other Model Types

updating, Comparing and Updating Models–Comparing and Updating Models

multidimensional objects, Examining Variables

multiple expressions, for Loops

multiword search terms, How to Get Help in R

N

NA value, NULL

na.fail function, Dealing with Missing Values

na.omit function, Dealing with Missing Values

names function, Names, Creating Lists

NAMESPACE files, The Package Directory Structure

naming elements, Creating Lists

ncol function, Rows, Columns, and Dimensions

Negate function, Functional Programming

nested elements, Indexing Lists

NetCDF files, Reading Other File Types

new method, Reference Classes

new.env function, Environments

NEWS files, The Package Directory Structure

nlevels function (base), Creating Factors

nlme package, Other Model Types

normalize function, Creating and Calling Functions

NppToR, Other IDEs and Editors

nrow argument (read), CSV and Tab-Delimited Files

nrow function, Rows, Columns, and Dimensions, List Dimensions and Arithmetic

null characters in strings, Special Characters

NULL value, NULL–Pairlists, NULL

lists and, NULL–Pairlists

NA vs., NULL

numbers, Special Numbers, Different Types of Numbers, Checking and Changing Classes, Formatting Numbers–Special Characters

converting strings to, Checking and Changing Classes

formatting, Formatting Numbers–Special Characters

special, Special Numbers

types of, Different Types of Numbers

numeric class, Classes, Different Types of Numbers

numeric types, Formatting Numbers

O

object-oriented programming (OOP), Object-Oriented Programming–Reference Classes, Object-Oriented Programming, S3 Classes, Reference Classes–Reference Classes

reference classes, Reference Classes–Reference Classes

S3 classes, S3 Classes

S4 classes, Object-Oriented Programming

ODBC database connections, Accessing Databases

operations, vectorized, for Loops

optional directories, The Package Directory Structure

optional files, The Package Directory Structure

order function, Sorting

P

package.skeleton function, Your First Package

packages, How to Get Help in R, Packages–Summary, Loading Packages–Libraries and Installed Packages, The Search Path, Libraries and Installed Packages–Libraries and Installed Packages, Libraries and Installed Packages–Libraries and Installed Packages, Installing Packages–Installing Packages, Maintaining Packages, Maintaining Packages, Making Packages–Summary, Prerequisites, The Package Directory Structure, Your First Package–Your First Package, Your First Package–Your First Package, Documenting Packages–Documenting Packages, Checking and Building Packages, Checking and Building Packages, Maintaining Packages

building, Checking and Building Packages

checking, Checking and Building Packages

creating, Your First Package–Your First Package

directory structure for, The Package Directory Structure

documenting, Documenting Packages–Documenting Packages

finding, Libraries and Installed Packages–Libraries and Installed Packages

format of, Your First Package–Your First Package

installing, Installing Packages–Installing Packages

libraries, Libraries and Installed Packages–Libraries and Installed Packages

loading, Loading Packages–Libraries and Installed Packages

maintaining, Maintaining Packages, Maintaining Packages

search function, The Search Path

tools for, Prerequisites

updating, Maintaining Packages

pairlists, Pairlists

parentheses, Assigning Variables

parse function, Turning Strings into Code

parsing strings, Turning Strings into Code

paste function, Constructing and Printing Strings, Splitting Strings

periods, Lubridate, Lubridate

creating, Lubridate

plot function (base), Take 1: base Graphics

plyr package, Converting Continuous Variables to Categorical, The plyr Package–Summary

pmax function, Summary Statistics

pmin function, Summary Statistics

Position function, Functional Programming

POSIXct class, POSIX Dates and Times

POSIXlt class, POSIX Dates and Times

prettyNum function, Formatting Numbers

print function, Messages, Warnings, and Errors

print method, Examining Variables

probability density function, Distributions

Q

quantile function, Summary Statistics

R

R, Introduction–Summary, What Is R?, What Is R?, What Is R?, What Is R?, Installing R, Choosing an IDE–Other IDEs and Editors, Your First Program, How to Get Help in R–How to Get Help in R, Installing Extra Related Software, A Scientific Calculator–Summary, Mathematical Operations and Vectors–Mathematical Operations and Vectors, Mathematical Operations and Vectors, Assigning Variables–Assigning Variables, Special Numbers, Different Types of Numbers, The Three Plotting Systems, Programming, Messages, Warnings, and Errors–Messages, Warnings, and Errors, Messages, Warnings, and Errors–Messages, Warnings, and Errors, Messages, Warnings, and Errors–Messages, Warnings, and Errors, Error Handling–Error Handling, Debugging–Debugging, Testing–testthat, Magic–Turning Code into Strings, Turning Code into Strings, Object-Oriented Programming–Reference Classes

classes of numeric variable, Different Types of Numbers

code, deparsing, Turning Code into Strings

Core Team, What Is R?

debugging, Debugging–Debugging

error handling, Error Handling–Error Handling

errors, Messages, Warnings, and Errors–Messages, Warnings, and Errors

extensions, Installing Extra Related Software

help, sources for, How to Get Help in R–How to Get Help in R

history, What Is R?

IDEs for, Choosing an IDE–Other IDEs and Editors

installing, Installing R

interpreter, Magic–Turning Code into Strings

as language, What Is R?

mathematical functions, Mathematical Operations and Vectors

mathematical operations, Mathematical Operations and Vectors–Mathematical Operations and Vectors

messages, Messages, Warnings, and Errors–Messages, Warnings, and Errors

object-oriented programming in, Object-Oriented Programming–Reference Classes

plotting systems for, The Three Plotting Systems

programming language, Programming

programming paradigms, What Is R?

as scientific calculator, A Scientific Calculator–Summary

simple program in, Your First Program

special numbers, Special Numbers

testing, Testing–testthat

variables, assigning, Assigning Variables–Assigning Variables

warnings, Messages, Warnings, and Errors–Messages, Warnings, and Errors

R directory, The Package Directory Structure

R-bloggers, How to Get Help in R

random numbers, Random Numbers–Sampling from Distributions, Sampling from Distributions

distributions and, Sampling from Distributions

range function (base), Summary Statistics

rank function (base), Sorting

raply function (plyr), The plyr Package

raw class, Other Common Classes, Other Common Classes

rbind function (base), Combining Matrices, Combining Lists

rbinom function (stats), Vectorized if

Rcpp package, The Package Directory Structure

read.csv function (utils), CSV and Tab-Delimited Files

read.table function (utils), CSV and Tab-Delimited Files, CSV and Tab-Delimited Files, Scraping Web Pages

readLines function (base), Unstructured Text Files

recover function (utils), Debugging

rectangular data, CSV and Tab-Delimited Files

recursive variable types, Atomic and Recursive Variables, Properties of Variables

Reduce function (base), Functional Programming

reference classes, Reference Classes–Reference Classes

regexpr function (base), Cleaning Strings

regular expressions, How to Get Help in R

release function (devtools), Checking and Building Packages

relevel function (stats), Comparing and Updating Models

removing variables, The Workspace

reorder function (stats), Box Plots

rep function (base), Vector Recycling and Repetition

rep.int function (base), Vector Recycling and Repetition

repeat loops, repeat Loops–while Loops

replicate function (base), Replication

require function (base), Loading Packages

reserved words, How to Get Help in R

reshape function (reshape2), Converting Between Wide and Long Form

Revolution-R, Revolution-R, Revolution-R, Revolution-R

community edition, Revolution-R

enterprise edition, Revolution-R

rjson package, JSON and YAML Files

RJSONIO package, JSON and YAML Files

rlnorm function (stats), Assigning Variables

rm function (base), The Workspace

RNGkind function, Sampling from Distributions

rnorm function (stats), Assigning Variables, Sampling from Distributions

RODBC package, Accessing Databases

rowMeans function (base), Basic Data Frame Manipulation

rows, Rows, Columns, and Dimensions–Indexing Arrays, Row, Column, and Dimension Names

naming, Row, Column, and Dimension Names

rowSums function (base), Basic Data Frame Manipulation, Looping Over Arrays

roxygen2 package, Documenting Packages

roxygenize function (roxygen2), Documenting Packages

RSeek, How to Get Help in R

RSiteSearch function, How to Get Help in R

RSS, XML and HTML Files

RStudio, RStudio

runif, Sampling from Distributions

RUnit, RUnit–RUnit, RUnit

checkWarning function and, RUnit

runTestSuite function (RUnit), RUnit

S

S3 classes, S3 Classes

S4 classes, Object-Oriented Programming

sample function (base), Other Common Classes, Random Numbers

sapply function (base), Looping Over Lists

SAS files, Reading SAS, Stata, SPSS, and MATLAB Files

scales argument, Take 2: lattice Graphics

scaling vectors, Creating and Calling Functions

scan function (base), CSV and Tab-Delimited Files

scatterplots, Scatterplots–Line Plots, Take 1: base Graphics–Take 1: base Graphics, Take 2: lattice Graphics–Take 3: ggplot2 Graphics, Take 3: ggplot2 Graphics–Line Plots

base graphics, Take 1: base Graphics–Take 1: base Graphics

ggplot2 graphics, Take 3: ggplot2 Graphics–Line Plots

lattice graphics, Take 2: lattice Graphics–Take 3: ggplot2 Graphics

Sci-Views-K, Other IDEs and Editors

scope, of variables, Variable Scope–Variable Scope

sd function (stats)”, Pairlists

search function (base), The Search Path

finding installed packages with, The Search Path

sep argument (read), CSV and Tab-Delimited Files

seq function (base), Sequences, Arithmetic with Dates and Times

seq.int function (base), Sequences

sequences, Sequences, Sequences, Sequences, Sequences

creating, Sequences

functions for, Sequences

specifying, Sequences

seq_along function (base), Sequences

seq_len function (base), Sequences

set.seed function (base), Sampling from Distributions

setRefClass function (methods), Reference Classes

setRepositories function (utils), Installing Packages

setwd function (base), File Paths

shorten vectors, Lengths

show method, Reference Classes

simpleError class, Error Handling

skip argument (read), CSV and Tab-Delimited Files

slicing, Indexing Vectors

SOAP, XML and HTML Files

solve function (base), Array Arithmetic

sort function (base), Sorting

source function (base), Looping Over Lists

special characters, How to Get Help in R, Special Characters

special numbers, Special Numbers, Special Numbers, Special Numbers, Special Numbers

infinity, Special Numbers

missing values, Special Numbers

not-a-number, Special Numbers

split argument, Splitting Strings

split-apply-combine, Split-Apply-Combine

sprintf function (base), Formatting Numbers

SPSS files, Reading SAS, Stata, SPSS, and MATLAB Files

SQL, data frames and, Using SQL–Sorting

sqldf package, CSV and Tab-Delimited Files, Using SQL

src directory, The Package Directory Structure

Stack Overflow, How to Get Help in R

stamp function (lubridate), Lubridate

standard deviation function, Pairlists

Stata files, Reading SAS, Stata, SPSS, and MATLAB Files

static methods, Reference Classes

stats package, The Search Path

stopifnot function (base), Messages, Warnings, and Errors

storing variables, Environments

str function (utils), The Workspace, XML and HTML Files

internal nodes and, XML and HTML Files

strftime function (base), Formatting Dates

strings, Mathematical Operations and Vectors, Checking and Changing Classes, Strings–File Paths, Constructing and Printing Strings, Constructing and Printing Strings, Formatting Numbers–Special Characters, Special Characters, Changing Case, Extracting Substrings, Splitting Strings, File Paths, Conversion to and from Strings, Conversion to and from Strings, Formatting Dates, Cleaning Strings–Manipulating Data Frames, Cleaning Strings, Turning Strings into Code

case, changing, Changing Case

cleaning, Cleaning Strings–Manipulating Data Frames

comparing, Mathematical Operations and Vectors

constructing, Constructing and Printing Strings

converting to numbers, Checking and Changing Classes

dates, converting to/from, Conversion to and from Strings

file paths as, File Paths

formatting date/time in, Formatting Dates

of numbers, formatting, Formatting Numbers–Special Characters

parsing, Turning Strings into Code

printing, Constructing and Printing Strings

replacing one with another, Cleaning Strings

special characters for, Special Characters

splitting, Splitting Strings

substrings, extracting, Extracting Substrings

times, converting to/from, Conversion to and from Strings

strptime function (base), Parsing Dates

strsplit function (base), Splitting Strings

subscripting, Indexing Vectors

subset function (base), Indexing Data Frames, Manipulating Data Frames

subsetting, Indexing Vectors

substitute function (base), Turning Code into Strings, Turning Code into Strings

using deparse with, Turning Code into Strings

using eval with, Turning Code into Strings

substr function (base), Extracting Substrings

substring function (base), Extracting Substrings, Cleaning Strings

subtracting dates, Arithmetic with Dates and Times

sum function (base), Mathematical Operations and Vectors

summary function (base), Examining Variables, Arithmetic with Dates and Times, Summary Statistics, A First Model: Linear Regressions

summary statistics, Arithmetic with Dates and Times, Exploring and Visualizing–Summary, Summary Statistics–Summary Statistics, Scatterplots–Line Plots, Line Plots–Line Plots, Histograms–Histograms, Bar Charts–Bar Charts

bar charts, Bar Charts–Bar Charts

histograms, Histograms–Histograms

line plots of, Line Plots–Line Plots

scatterplots of, Scatterplots–Line Plots

summary statistics, Summary Statistics–Summary Statistics

switch function (base), Multiple Selection, Turning Strings into Code

switch statements, Multiple Selection–Multiple Selection

system testing, Testing

T

t function (base), Array Arithmetic, Basic Data Frame Manipulation

tab-delimited files, CSV and Tab-Delimited Files–CSV and Tab-Delimited Files

table function (base), Converting Continuous Variables to Categorical, Summary Statistics

tapply function (base), Split-Apply-Combine, Split-Apply-Combine

wrapper functions to, Split-Apply-Combine

testing programs, Testing–testthat, Testing, Testing, Testing, RUnit–RUnit, RUnit, testthat

integration, Testing

system, Testing

test directory, RUnit

unit, Testing

with RUnit, RUnit–RUnit

with testthat, testthat

tests directory, RUnit

testthat, testthat

test_file function (testthat), testthat

text file formats, Reading Text Files–JSON and YAML Files, CSV and Tab-Delimited Files–CSV and Tab-Delimited Files, CSV and Tab-Delimited Files–CSV and Tab-Delimited Files, XML and HTML Files, XML and HTML Files, JSON and YAML Files–JSON and YAML Files, JSON and YAML Files–JSON and YAML Files

CSV, CSV and Tab-Delimited Files–CSV and Tab-Delimited Files

HTML, XML and HTML Files

JSON, JSON and YAML Files–JSON and YAML Files

reading, Reading Text Files–JSON and YAML Files

tab-delimited, CSV and Tab-Delimited Files–CSV and Tab-Delimited Files

XML, XML and HTML Files

YAML, JSON and YAML Files–JSON and YAML Files

time classes from add-on packages, Other Date Classes

time zones, Parsing Dates, Time Zones–Time Zones

time(s), Dates and Times–Summary, POSIX Dates and Times, The Date Class, Conversion to and from Strings, Parsing Dates, Formatting Dates, Time Zones–Time Zones, Arithmetic with Dates and Times, Lubridate–Lubridate

arithmetic with, Arithmetic with Dates and Times

Date class, The Date Class

formatting, Formatting Dates

lubridate package and, Lubridate–Lubridate

parsing, Parsing Dates

POSIX package, POSIX Dates and Times

strings, converting to/from, Conversion to and from Strings

time zones, Time Zones–Time Zones

Tinn-R, Other IDEs and Editors

tolower function (base), Changing Case

toString function (base), Constructing and Printing Strings

toupper function (base), Changing Case

trace method, Reference Classes

traceback function (base), Debugging

transposing data frames, Basic Data Frame Manipulation

transposing matrices, Array Arithmetic

TRUE, Logical Vectors

try function (base), Error Handling

try-error, Error Handling

tryapply function (plyr), Error Handling

tryCatch function (base), Error Handling

Twitter, Sites with an API

two-dimensional arrays, Other Common Classes

type argument, Histograms

U

unclass function, Examining Variables, POSIX Dates and Times, Arithmetic with Dates and Times

combining class and, Arithmetic with Dates and Times

unit testing, Testing

University of Auckland, What Is R?

Unix grep tool, Cleaning Strings

unlist function (base), Converting Between Vectors and Lists

untrace method, Reference Classes

updating packages, Maintaining Packages

UseMethod function, S3 Classes

user workspace, Environments

(see also global environment)

UTC, Parsing Dates (see coordinated universal time)

V

vapply function (base), Looping Over Lists

variables, How to Get Help in R, Assigning Variables–Assigning Variables, Assigning Variables, Inspecting Variables and Your Workspace–The Workspace, Classes, Classes, Classes, Different Types of Numbers, Checking and Changing Classes–Checking and Changing Classes, Examining Variables–Examining Variables, The Workspace–The Workspace, The Workspace, Atomic and Recursive Variables, Atomic and Recursive Variables, NULL, Environments–Environments, Environments, Variable Scope–Variable Scope, Converting Continuous Variables to Categorical, Magic, Properties of Variables, Properties of Variables, Properties of Variables, Properties of Variables

assigning, Assigning Variables–Assigning Variables

atomic, Atomic and Recursive Variables, Properties of Variables

classes of, Classes

classes, checking/changing, Checking and Changing Classes–Checking and Changing Classes

continuous vs. categorical, Converting Continuous Variables to Categorical

creating, How to Get Help in R

empty, NULL

environments and, Environments–Environments

examining, Examining Variables–Examining Variables

functions and, Properties of Variables

internal storage type, Classes

language types, Magic

local, Assigning Variables

number types, Different Types of Numbers

recursive, Atomic and Recursive Variables, Properties of Variables

removing, The Workspace

scope, Variable Scope–Variable Scope

storage mode, Classes

storing, Environments

values returned by modes, Properties of Variables

in workspace, The Workspace–The Workspace

VCF files, Reading Other File Types

vector function (base), Vectors

vector inputs, Looping Over Lists

Vectorize function (base), Instant Vectorization

vectorized arguments, Looping Over Lists

vectorized flow control, Vectorized if

vectorized operation, for Loops

vectorizing, Mathematical Operations and Vectors, Mathematical Operations and Vectors, Logical Vectors

logical operators, Logical Vectors

over arguments, Mathematical Operations and Vectors

vectors, Your First Program, Mathematical Operations and Vectors–Mathematical Operations and Vectors, Mathematical Operations and Vectors, Logical Vectors–Logical Vectors, Classes, Other Common Classes, Vectors–Vector Recycling and Repetition, Vectors, Sequences, Lengths, Lengths, Lengths, Names, Names, Indexing Vectors–Indexing Vectors, Indexing Vectors, Vector Recycling and Repetition, Vector Recycling and Repetition, Vector Recycling and Repetition, Combining Matrices, Converting Between Vectors and Lists, Creating and Calling Functions, Properties of Variables

accessing parts of, Indexing Vectors

adding, Mathematical Operations and Vectors, Vector Recycling and Repetition

atomic types and, Properties of Variables

character, Lengths

classes of, Other Common Classes

converting matrices to, Combining Matrices

creating, Vectors, Names

elements, naming, Names

elements, recycling, Vector Recycling and Repetition

elements, repetition of, Vector Recycling and Repetition

indexing, Indexing Vectors–Indexing Vectors

lengths, Lengths

lists, converting to/from, Converting Between Vectors and Lists

logical, Logical Vectors–Logical Vectors

scaling, Creating and Calling Functions

sequences, Sequences

shorten, Lengths

View function (utils), Examining Variables

vignette function (utils), How to Get Help in R

vignettes, How to Get Help in R

vignettes directory, The Package Directory Structure

Vim-R, Other IDEs and Editors

W

warn option, RUnit

warnings, Messages, Warnings, and Errors–Messages, Warnings, and Errors

warnings function (base), Messages, Warnings, and Errors

web data, Web Data–Scraping Web Pages, Sites with an API, Scraping Web Pages–Scraping Web Pages

APIs, sites with, Sites with an API

scraping pages, Scraping Web Pages–Scraping Web Pages

which function (base), Indexing Vectors

while loops, while Loops

with function (base), Adding and Replacing Columns

within function (base), Adding and Replacing Columns

workspace, The Workspace–The Workspace

write.csv function (utils), CSV and Tab-Delimited Files

write.table function (utils), CSV and Tab-Delimited Files

writeLines function (base), Unstructured Text Files

X

XEmacs, Emacs + ESS

xlsReadWrite package, Reading Excel Files

xlsx package, Reading Excel Files

XML files, XML and HTML Files, XML and HTML Files, JSON and YAML Files

importing, XML and HTML Files

problems with, JSON and YAML Files

xmlParse function (XML), XML and HTML Files, XML and HTML Files

internal nodes and, XML and HTML Files

XPath, XML and HTML Files

xyplot function (lattice), Take 2: lattice Graphics

Y

YAML files, JSON and YAML Files–JSON and YAML Files, JSON and YAML Files

importing, JSON and YAML Files

ymd function (lubridate), Lubridate