Advanced R: Data Programming and the Cloud

282 Pages·2016·11.614 MB·English

by  Matt Wiley, Joshua F. Wiley (auth.)

Advanced R
Data Programming and the Cloud
—
Matt Wiley
Joshua F. Wiley
Advanced R

Data Programming and the Cloud

Matt Wiley

Joshua F. Wiley
Advanced R: Data Programming and the Cloud
Matt Wiley Joshua F. Wiley
Elkhart Group Ltd. & Victoria College Elkhart Group Ltd. & Victoria College
Columbia City, Indiana Columbia City, Indiana
USA USA
ISBN-13 (pbk): 978-1-4842-2076-4 ISBN-13 (electronic): 978-1-4842-2077-1
DOI 10.1007/978-1-4842-2077-1
Library of Congress Control Number: 2016959581
Copyright © 2016 by Matt Wiley and Joshua F. Wiley
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To Family.
Contents at a Glance
About the Authors ..................................................................................................xiii
About the Technical Reviewer .................................................................................xv
Acknowledgments .................................................................................................xvii
Introduction ............................................................................................................xix
■ Chapter 1: Programming Basics ............................................................................1
■ Chapter 2: Programming Utilities ........................................................................17
■ Chapter 3: Programming Automation ..................................................................29
■ Chapter 4: Writing Functions ...............................................................................43
■ Chapter 5: Writing Classes and Methods.............................................................61
■ Chapter 6: Writing a Package ..............................................................................83
■ Chapter 7: Introduction to Data Management Using data.table ........................115
■ Chapter 8: Data Munging with data.table ..........................................................141
■ Chapter 9: Other Tools for Data Management ....................................................159
■ Chapter 10: Reading Big Data(bases) ................................................................181
■ Chapter 11: Getting a Cloud ...............................................................................199
■ Chapter 12: Cloud Ubuntu for Windows Users ...................................................211
■ Chapter 13: Every Cloud has a Shiny Lining ......................................................225
■ Chapter 14: Shiny Dashboard Sampler ..............................................................239
■ Chapter 15: Dynamic Reports and the Cloud .....................................................253
■ References .........................................................................................................271
Index .....................................................................................................................275
v
Contents
About the Authors ..................................................................................................xiii
About the Technical Reviewer .................................................................................xv
Acknowledgments .................................................................................................xvii
Introduction ............................................................................................................xix
■ Chapter 1: Programming Basics ............................................................................1
Advanced R Software Choices .........................................................................................1
Reproducing Results ........................................................................................................2
Types of Objects ...............................................................................................................2
Base Operators and Functions .........................................................................................5
Mathematical Operators and Functions .........................................................................11
References .....................................................................................................................15
■ Chapter 2: Programming Utilities ........................................................................17
Help and Documentation ................................................................................................17
System and Files ............................................................................................................18
Input ...............................................................................................................................23
Output .............................................................................................................................25
References .....................................................................................................................27
■ Chapter 3: Programming Automation ..................................................................29
Loops ..............................................................................................................................29
Flow Control ...................................................................................................................32
*apply Family of Functions .............................................................................................35
Final Thoughts ................................................................................................................42
vii
■ CONTENTS
■ Chapter 4: Writing Functions ...............................................................................43
Components of a Function .............................................................................................43
Scoping ..........................................................................................................................44
Functions for Functions ..................................................................................................47
Debugging ......................................................................................................................52
Summary ........................................................................................................................59
■ Chapter 5: Writing Classes and Methods.............................................................61
S3 System ......................................................................................................................61
S3 Classes ............................................................................................................................................61
S3 Methods ...........................................................................................................................................64
S4 System ......................................................................................................................71
S4 Classes ............................................................................................................................................72
S4 Class Inheritance .............................................................................................................................76
S4 Methods ...........................................................................................................................................77
Summary ........................................................................................................................80
■ Chapter 6: Writing a Package ..............................................................................83
Before You Get Started ...................................................................................................83
Version Control .....................................................................................................................................84
R Package Basics ...........................................................................................................89
Starting a Package by Using DevTools .................................................................................................90
Adding R Code ......................................................................................................................................92
Tests .....................................................................................................................................................93
Documentation Using roxygen2 .....................................................................................98
Functions ..............................................................................................................................................99
Data ....................................................................................................................................................102
Classes ...............................................................................................................................................103
Methods ..............................................................................................................................................104
Building, Installing, and Distributing an R Package ......................................................107
Summary ......................................................................................................................112
viii
■ CONTENTS
■ Chapter 7: Introduction to Data Management Using data.table ........................115
Introduction to data.table .............................................................................................115
Selecting and Subsetting Data .....................................................................................120
Using the First Formal ........................................................................................................................120
Using the Second Formal ...................................................................................................................122
Using the Second and Third Formals ..................................................................................................123
Variable Renaming and Ordering..................................................................................125
Computing on Data and Creating Variables ..................................................................127
Merging and Reshaping Data .......................................................................................130
Merging Data ......................................................................................................................................130
Reshaping Data ..................................................................................................................................136
Summary ......................................................................................................................140
■ Chapter 8: Data Munging with data.table ..........................................................141
Data Munging / Cleaning ..............................................................................................142
Recoding Data ....................................................................................................................................143
Recoding Numeric Values ...................................................................................................................148
Creating New Variables ................................................................................................150
Fuzzy Matching ............................................................................................................152
Summary ......................................................................................................................157
■ Chapter 9: Other Tools for Data Management ....................................................159
Sorting ..........................................................................................................................160
Selecting and Subsetting .............................................................................................162
Variable Renaming and Ordering..................................................................................168
Computing on Data and Creating Variables ..................................................................170
Merging and Reshaping Data .......................................................................................173
Summary ......................................................................................................................178
ix
■ CONTENTS
■ Chapter 10: Reading Big Data(bases) ................................................................181
SQLite ...........................................................................................................................182
Installing SQLite on Windows .............................................................................................................182
SQLite and R .......................................................................................................................................183
PostgreSQL ...................................................................................................................186
Installing PostgreSQL on Windows .....................................................................................................186
PostgreSQL and R ...............................................................................................................................187
MongoDB ......................................................................................................................190
Installing MongoDB on Windows ........................................................................................................190
MongoDB and R ..................................................................................................................................192
Summary ......................................................................................................................196
■ Chapter 11: Getting a Cloud ...............................................................................199
Disclaimers ..................................................................................................................199
Starting Amazon Web Services ....................................................................................200
Accessing Your Instance’s Command Line ...................................................................205
Uploading Files to Your Instance ..................................................................................207
Final Thoughts ..............................................................................................................209
■ Chapter 12: Cloud Ubuntu for Windows Users ...................................................211
Common Commands ....................................................................................................211
Superuser and Security ................................................................................................213
Installing and Using R ...................................................................................................215
Installing and Using RStudio Server .............................................................................218
Installing Microsoft R ...................................................................................................222
Installing Java ..............................................................................................................224
Installing Shiny on Your Cloud ......................................................................................224
Final Thoughts ..............................................................................................................224
x
■ CONTENTS
■ Chapter 13: Every Cloud has a Shiny Lining ......................................................225
The Basics of Shiny ......................................................................................................225
Shiny in Motion ............................................................................................................232
Uploading a User File into Shiny ..................................................................................234
Hosting Shiny in the Cloud ..........................................................................................236
Final Thoughts ..............................................................................................................238
■ Chapter 14: Shiny Dashboard Sampler ..............................................................239
A Dashboard’s Bones ...................................................................................................239
Dashboard Header ..............................................................................................................................241
Dashboard Sidebar .............................................................................................................................241
Dashboard Body .................................................................................................................................243
Dashboard in the Cloud ................................................................................................245
Complete Sampler Code ...............................................................................................247
References ...................................................................................................................251
■ Chapter 15: Dynamic Reports and the Cloud .....................................................253
Needed Software ..........................................................................................................253
Local Machine ....................................................................................................................................253
Cloud Instance ....................................................................................................................................254
Dynamic Documents ....................................................................................................254
Dynamic Documents and Shiny ...................................................................................258
server.R ...............................................................................................................................................258
ui.R .....................................................................................................................................................261
report.Rmd ..........................................................................................................................................263
Uploading to the Cloud .................................................................................................269
Summary ......................................................................................................................269
■ References .........................................................................................................271
Index .....................................................................................................................275
xi