Reproducible research with R and RStudio:
"Preface This book has its genesis in my PhD research at the London School of Economics. I started the degree with questions about the 2008/09 financial crisis and planned to spend most of my time researching about capital adequacy requirements. But I quickly realized much of my time would actu...
Gespeichert in:
1. Verfasser: | |
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Format: | Buch |
Sprache: | English |
Veröffentlicht: |
Boca Raton, Fla. [u.a.]
CRC Press
2014
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Schriftenreihe: | The R series
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Schlagworte: | |
Online-Zugang: | Inhaltsverzeichnis Cover Inhaltsverzeichnis |
Zusammenfassung: | "Preface This book has its genesis in my PhD research at the London School of Economics. I started the degree with questions about the 2008/09 financial crisis and planned to spend most of my time researching about capital adequacy requirements. But I quickly realized much of my time would actually be spent learning the day-to-day tasks of data gathering, analysis, and results presentation. After plodding through for awhile, the breaking point came while reentering results into a regression table after I had tweaked one of my statistical models, yet again. Surely there was a better way to do research that would allow me to spend more time answering my research questions. Making research reproducible for others also means making it better organized and efficient for yourself. So, my search for a better way led me straight to the tools for reproducible computational research. The reproducible research community is very active, knowledgeable and helpful. Nonetheless, I often encountered holes in this collective knowledge, or at least had no resource to bring it all together as a whole. That is my intention for this book: to bring together the skills I have picked up for actually doing and presenting computational research. Hopefully, the book along with making reproducible research more common, will save researchers hours of Googling, so they can spend more time addressing their research questions. I would not have been able to write this book without many people's advice and support. Foremost is John Kimmel, acquisitions editor at Chapman & Hall. He approached me with in Spring 2012 with the general idea and opportunity for this book"-- |
Beschreibung: | Literaturverz. S. 271 - 277 |
Beschreibung: | XXV, 288 S. Ill., graph. Darst. |
ISBN: | 1466572841 9781466572843 |
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adam_text | Titel: Reproducible research with R and RStudio
Autor: Gandrud, Christopher
Jahr: 2014
Contents
Preface vii
Stylistic Conventions xv
Required R Packages xvii
Additional Resources xix
Chapter Examples................................................xix
Short Example Project............................................xix
List of Figures xxiii
List of Tables xxv
I Getting Started 1
1 Introducing Reproducible Research 3
1.1 What is Reproducible Research?................................3
1.2 Why Should Research Be Reproducible? ......................5
1.2.1 For science ................................................5
1.2.2 For you....................................................6
1.3 Who Should Read This Book? ..................................7
1.3.1 Academic researchers......................................8
1.3.2 Students....................................................8
1.3.3 Instructors ................................................8
1.3.4 Editors ....................................................9
1.3.5 Private sector researchers................................9
1.4 The Tools of Reproducible Research............................10
1.5 Why Use R, knitr, and RStudio for Reproducible Research? 11
1.5.1 Installing the main software..............................13
1.6 Book Overview....................................................14
1.6.1 How to read this book....................................15
1.6.2 Reproduce this book......................................16
1.6.3 Contents overview........................................16
ix
X
2 Getting Started with Reproducible Research 17
2.1 The Big Picture: A Workflow for Reproducible Research . . 17
2.1.1 Reproducible theory......................................18
2.2 Practical Tips for Reproducible Research ......................20
2.2.1 Document everything!....................................20
2.2.2 Everything is a (text) file................................22
2.2.3 All files should be human readable......................22
2.2.4 Explicitly tie your files together..........................24
2.2.5 Have a plan to organize, store, make your files avail-
able ........................................................25
3 Getting Started with R, RStudio, and knitr 27
3.1 Using R: the Basics ..............................................27
3.1.1 Objects....................................................28
3.1.2 Component selection......................................34
3.1.3 Subscripts..................................................36
3.1.4 Functions and commands................................37
3.1.5 Arguments................................................38
3.1.0 The workspace history ................................39
3.1.7 Global R options..........................................41
3.1.8 Installing new packages and loading commands .... 42
3.2 Using RStudio ....................................................43
3.3 Using knitr-. the Basics ..........................................44
3.3.1 What knitr does..........................................45
3.3.2 File extensions............................................45
3.3.3 Code chunks..............................................47
3.3.4 Global chunk options......................................49
3.3.5 knitr package options....................................51
3.3.6 Hooks......................................................52
3.3.7 knitr RStudio..........................................52
3.3.8 knitr R..................................................55
4 Getting Started with File Management 59
4.1 File Paths c Naming Conventions..............................60
4.1.1 Root directories............................................60
4.1.2 Subdirectories parent directories......................60
4.1.3 Spaces in directory file names ........................61
4.1.4 Working directories........................................61
4.2 Organizing Your Research Project ..............................63
4.3 Setting Directories as RStudio Projects ........................64
4.4 R File Manipulation Commands ................................64
4.5 Unix-like Shell Commands for File Management ..............67
4.6 File Navigation in RStudio ......................................72
II Data Gathering and Storage 73
xi
5 Storing, Collaborating, Accessing Files, Versioning 75
5.1 Saving Data in Reproducible Formats..........................76
5.2 Storing Your Files in the Cloud: Dropbox......................77
5.2.1 Storage....................................................78
5.2.2 Accessing data............................................78
5.2.3 Collaboration..............................................80
5.2.4 Version control............................................80
5.3 Storing Your Files in the Cloud: GitHub ......................81
5.3.1 Setting up GitHub: basic ................................83
5.3.2 Version control with Git..................................84
5.3.3 Remote storage on GitHub..............................91
5.3.4 Accessing on GitHub......................................94
5.3.4.1 Collaboration with GitHub....................96
5.3.5 Summing up the GitHub workflow......................96
5.4 RStudio k, GitHub ..............................................97
5.4.1 Setting up Git/GitHub with Projects ..................98
5.4.2 Using Git in RStudio Projects ..........................99
6 Gathering Data with R 101
6.1 Organize Your Data Gathering: Makefiles......................101
6.1.1 R Make-like files..........................................102
6.1.2 GNU Make................................................103
6.1.2.1 Example makefile..............................104
6.1.2.2 Makefiles and RStudio Projects ..............108
6.1.2.3 Other information about makefiles............109
6.2 Importing Locally Stored Data Sets ............................109
6.3 Importing Data Sets from the Internet ........................110
6.3.1 Data from non-secure (http) URLs......................Ill
6.3.2 Data from secure (https) URLs........................Ill
6.3.3 Compressed data stored online..........................114
6.3.4 Data APIs feeds........................................115
6.4 Advanced Automatic Data Gathering: Web Scraping..........117
7 Preparing Data for Analysis 121
7.1 Cleaning Data for Merging ......................................121
7.1.1 Get a handle on your data................................121
7.1.2 Reshaping data............................................123
7.1.3 Renaming variables........................................126
7.1.4 Ordering data..............................................126
7.1.5 Subsetting data............................................127
7.1.6 Recoding string/numeric variables......................129
7.1.7 Creating new variables from old ........................131
7.1.8 Changing variable types..................................134
7.2 Merging Data Sets................................................135
7.2.1 Binding....................................................135
xii
7.2.2 The merge command......................................135
7.2.3 Duplicate values..........................................138
7.2.4 Duplicate columns........................................139
III Analysis and Results 143
8 Statistical Modelling and knitr 145
8.1 Incorporating Analyses into the Markup ......................140
8.1.1 Full code chunks..........................................140
8.1.2 Showing code results inline............................148
8.1.2.1 LaTeX ..........................................M8
8.1.2.2 Markdown......................................150
8.1.3 Dynamically including non-R code in code chunks . . 150
8.2 Dynamically Including Modular Analysis Files ................152
8.2.1 Source from a local file....................................152
8.2.2 Source from a non-secure URL (http)..................153
8.2.3 Source from a secure URL (https)......................151
8.3 Reproducibly Random: set.seed ..............................155
8.4 Computationally Intensive Analyses............................157
9 Showing Results with Tables 159
9.1 Basic knitr Syntax for Tables....................................160
9.2 Table Basics ......................................................160
9.2.1 Tables in LaTeX..........................................161
9.2.2 Tables in Markdown/HTML ............................165
9.3 Creating Tables from R Objects ................................169
9.3.1 xtable apsrtable basics with supported class objects 169
9.3.1.1 apsrtable for LaTeX............................172
9.3.2 xtable with non-supported class objects ................175
9.3.3 Creating variable description documents with xtable . 177
10 Showing Results with Figures 181
10.1 Including Non-knitted Graphics ................................181
10.1.1 Including graphics in LaTeX ............................182
10.1.2 Including graphics in Markdown/HTML................184
10.2 Basic knitr Figure Options ......................................185
10.2.1 Chunk options............................................185
10.2.2 Global options............................................187
10.3 Knitting R s Default Graphics ..................................187
10.4 Including ggplotë Graphics ......................................192
10.4.1 Showing regression results with caterpillar plots .... 195
10.5 JavaScript Graphs with yoogleVis ..............................198
IV Presentation Documents 203
xiii
11 Presenting with LaTeX 205
11.1 The Basics ........................................................205
11.1.1 Getting started with LaTeX editors ....................205
11.1.2 Basic LaTeX command syntax..........................206
11.1.3 The LaTeX preamble body............................207
11.1.4 Headings ..................................................210
11.1.5 Paragraphs spacing....................................210
11.1.6 Horizontal lines............................................211
11.1.7 Text formatting............................................211
11.1.8 Math ......................................................212
11.1.9 Lists........................................................213
11.1.10 Footnotes..................................................214
11.1.11 Cross-references............................................214
11.2 Bibliographies with BibTeX ....................................215
11.2.1 The .bib file................................................215
11.2.2 Including citations in LaTeX documents................216
11.2.3 Generating a BibTeX file of R package citations . . . 217
11.3 Presentations with LaTeX Beamer..............................220
11.3.1 Beamer basics ............................................220
11.3.2 knitr with LaTeX slideshows............................223
12 Large LaTeX Documents: Theses, Books, Batch Reports 225
12.1 Planning Large Documents......................................225
12.2 Large Documents with Traditional LaTeX ....................226
12.2.1 Inputting/including children ............................227
12.2.2 Other common features of large documents............228
12.3 knitr and Large Documents......................................229
12.3.1 The parent document....................................229
12.3.2 Knitting child documents................................230
12.4 Child Documents in a Different Markup Language............231
12.5 Creating Batch Reports..........................................232
13 Presenting on the Web with Markdown 239
13.1 The Basics ........................................................239
13.1.1 Getting started with Markdown editors................240
13.1.2 Preamble and document structure......................240
13.1.3 Headers....................................................243
13.1.4 Horizontal lines............................................243
13.1.5 Paragraphs and new lines................................243
13.1.6 Italics and bold............................................244
13.1.7 Links ......................................................244
13.1.8 Special characters and font customization..............244
13.1.9 Lists........................................................244
13.1.10Escape characters ........................................245
13.1.11 Math with MathJax......................................245
xiv
13.2 Markdown witli Pandoc and Custom CSS......................246
13.2.1 Pandoc....................................................246
13.2.2 CSS style files and Markdown............................250
13.2.3 knitr s pandoc command ................................251
13.3 Slideshows with Markdown, knitr, and HTML ................254
13.3.1 Slideshows with Markdown, knitr, and RStudio s R Pre-
sentations ..................................................254
13.3.2 Slideshows with Markdown, knitr, and slidify .... 256
13.4 Publishing Markdown Documents ..............................262
13.4.1 Stand alone HTML files..................................262
13.4.2 Hosting webpages with Dropbox........................263
13.4.3 GitHub Pages..............................................263
14 Conclusion 265
14.1 Citing Reproducible Research ..................................265
14.2 Licensing Your Reproducible Research..........................267
14.3 Sharing Your Code in Packages ................................267
14.4 Project Development: Public or Private? ......................268
14.5 Is it Possible to Completely Future Proof Your Research? . . 269
Bibliography 271
Index 279
|
any_adam_object | 1 |
author | Gandrud, Christopher |
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ctrlnum | (OCoLC)881874121 (DE-599)GBV750605561 |
discipline | Informatik |
format | Book |
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id | DE-604.BV041413299 |
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language | English |
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record_format | marc |
series2 | The R series |
spelling | Gandrud, Christopher Verfasser (DE-588)1044135131 aut Reproducible research with R and RStudio Christopher Gandrud Boca Raton, Fla. [u.a.] CRC Press 2014 XXV, 288 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier The R series Literaturverz. S. 271 - 277 "Preface This book has its genesis in my PhD research at the London School of Economics. I started the degree with questions about the 2008/09 financial crisis and planned to spend most of my time researching about capital adequacy requirements. But I quickly realized much of my time would actually be spent learning the day-to-day tasks of data gathering, analysis, and results presentation. After plodding through for awhile, the breaking point came while reentering results into a regression table after I had tweaked one of my statistical models, yet again. Surely there was a better way to do research that would allow me to spend more time answering my research questions. Making research reproducible for others also means making it better organized and efficient for yourself. So, my search for a better way led me straight to the tools for reproducible computational research. The reproducible research community is very active, knowledgeable and helpful. Nonetheless, I often encountered holes in this collective knowledge, or at least had no resource to bring it all together as a whole. That is my intention for this book: to bring together the skills I have picked up for actually doing and presenting computational research. Hopefully, the book along with making reproducible research more common, will save researchers hours of Googling, so they can spend more time addressing their research questions. I would not have been able to write this book without many people's advice and support. Foremost is John Kimmel, acquisitions editor at Chapman & Hall. He approached me with in Spring 2012 with the general idea and opportunity for this book"-- Empirische Forschung (DE-588)4300400-3 gnd rswk-swf Quantitative Methode (DE-588)4232139-6 gnd rswk-swf R Programm (DE-588)4705956-4 gnd rswk-swf Empirische Forschung (DE-588)4300400-3 s Quantitative Methode (DE-588)4232139-6 s R Programm (DE-588)4705956-4 s DE-604 DE-601 pdf/application http://www.gbv.de/dms/ilmenau/toc/750605561.PDF Inhaltsverzeichnis http://images.tandf.co.uk/common/jackets/websmall/978146657/9781466572843.jpg Cover HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026860551&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
spellingShingle | Gandrud, Christopher Reproducible research with R and RStudio Empirische Forschung (DE-588)4300400-3 gnd Quantitative Methode (DE-588)4232139-6 gnd R Programm (DE-588)4705956-4 gnd |
subject_GND | (DE-588)4300400-3 (DE-588)4232139-6 (DE-588)4705956-4 |
title | Reproducible research with R and RStudio |
title_auth | Reproducible research with R and RStudio |
title_exact_search | Reproducible research with R and RStudio |
title_full | Reproducible research with R and RStudio Christopher Gandrud |
title_fullStr | Reproducible research with R and RStudio Christopher Gandrud |
title_full_unstemmed | Reproducible research with R and RStudio Christopher Gandrud |
title_short | Reproducible research with R and RStudio |
title_sort | reproducible research with r and rstudio |
topic | Empirische Forschung (DE-588)4300400-3 gnd Quantitative Methode (DE-588)4232139-6 gnd R Programm (DE-588)4705956-4 gnd |
topic_facet | Empirische Forschung Quantitative Methode R Programm |
url | http://www.gbv.de/dms/ilmenau/toc/750605561.PDF http://images.tandf.co.uk/common/jackets/websmall/978146657/9781466572843.jpg http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026860551&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
work_keys_str_mv | AT gandrudchristopher reproducibleresearchwithrandrstudio |