The practice of reproducible research: case studies and lessons from the data-intensive sciences
"The Practice of Reproducible Research presents concrete examples of how researchers in the data-intensive sciences are working to improve the reproducibility of their research projects. Each of the thirty-one case studies in this volume describes the workflow that an author used to complete a...
Gespeichert in:
| Weitere Verfasser: | , , |
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| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Oakland, California
University of California Press
[2018]
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis Inhaltsverzeichnis |
| Zusammenfassung: | "The Practice of Reproducible Research presents concrete examples of how researchers in the data-intensive sciences are working to improve the reproducibility of their research projects. Each of the thirty-one case studies in this volume describes the workflow that an author used to complete a real-world research project, highlighting how particular tools, ideas, and practices have been combined to support reproducibility. Authors emphasize the very practical how, rather than the why or what, of conducting reproducible research. Part 1 contains an accessible introduction to reproducible research, a basic reproducible research project template, and a synthesis of lessons learned from across the thirty-one case studies. Parts 2 and 3 focus on the case studies. The Practice of Reproducible Research is an invaluable resource for students and researchers who wish to better understand the practice of data-intensive sciences and learn how to make their own research more reproducible."...Provided by publisher |
| Beschreibung: | Includes bibliographical references and index |
| Beschreibung: | xxv, 337 Seiten Diagramme |
| ISBN: | 9780520294745 9780520294752 |
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| adam_text |
THE PRACTICE OF REPRODUCIBLE RESEARCH
/
: 2018
TABLE OF CONTENTS / INHALTSVERZEICHNIS
PRACTICING REPRODUCIBILITY
HIGH-LEVEL CASE STUDIES
LOW-LEVEL CASE STUDIES
DIESES SCHRIFTSTUECK WURDE MASCHINELL ERZEUGT.
Contents
Contributors xi
Preface: Nullius in Verba xvii
Philip B. Stark
Introduction xxi
Justin Kitzes
PART I: PRACTICING REPRODUCIBILITY 1
Assessing Reproducibility 3
Ariel Rohem, Ben Marwick, and Valentina Staneva
The Basic Reproducible Workflow Template 19
Justin Kitzes
Case Studies in Reproducible Research 31
Daniel Turek and Fatma Deniz
Lessons Learned 41
Kathryn Huff
Building toward a Future Where Reproducible,
Open Science Is the Norm 61
Karthik Ram and Ben Marwick
Glossary
Ariel Rokem and Fernando Chirigati
71
PART II: HIGH-LEVEL CASE STUDIES 93
Case Study 1: Processing of Airborne Laser Altimetry
Data Using Cloud-Based Python and Relational
Database Tools 95
Anthony Arendt, Christian Kienholz, Christopher Larsen,
Justin Rich, and Evan Burgess
Case Study 2: The Trade-Off between Reproducibility
and Privacy in the Use of Social Media Data to Study
Political Behavior 103
Pablo Barberd
Case Study 3: A Reproducible R Notebook Using Docker 109
Carl Boettiger
Case Study 4: Estimating the Effect of Soldier Deaths
on the Military Labor Supply 119
Garret Christensen
Case Study 5: Turning Simulations of Quantum Many-
Body Systems into a Provenance-Rich Publication 125
Jan Gukelberger and Matthias Troyer
Case Study 6: Validating Statistical Methods to Detect
Data Fabrication 131
Chris Hartgerink
Case Study 7: Feature Extraction and Data Wrangling
for Predictive Models of the Brain in Python 139
Chris Holdgraf
Case Study 8: Using Observational Data and Numerical
Modeling to Make Scientific Discoveries in Climate Science 149
David Holland and Denise Holland
Case Study 9: Analyzing Bat Distributions in a Human-
Dominated Landscape with Autonomous Acoustic Detectors
and Machine Learning Models IS5
Justin Kitzes
Case Study 10: An Analysis of Household Location Choice
in Major US Metropolitan Areas Using R 161
Andy Krause and Hossein Estiri
Case Study 11: Analyzing Cosponsorship Data to Detect
Networking Patterns in Peruvian Legislators 169
José Manuel Magallanes
Case Study 12: Using R and Related Tools
for Reproducible Research in Archaeology 181
Ben Marwick
Case Study 13: Achieving Full Replication of Our Own
Published CFD Results, with Four Different Codes 191
Olivier Mesnard and Lorena A. Barba
Case Study 14: Reproducible Applied Statistics:
Is Tagging of Therapist-Patient Interactions Reliable? 201
K. Jarrod Millman, Kellie Otto boni, Naomi A. P. Stark,
and Philip B. Stark
Case Study 15: A Dissection of Computational Methods
Used in a Biogeographic Study 215
K. A. S. Mislan
Case Study 16: A Statistical Analysis of Salt and Mortality
at the Level of Nations 221
Kellie Ottoboni
Case Study 17: Reproducible Workflows for Understanding
Large-Scale Ecological Effects of Climate Change 227
Karthik Ram
Case Study 18: Reproducibility in Human Neuroimaging
Research: A Practical Example from the Analysis of
Diffusion MRI 233
Ariel Rokem
Case Study 19: Reproducible Computational Science
on High-Performance Computers: A View from Neutron
Transport 241
Rachel Slaybaugh
Case Study 20: Detection and Classification of Cervical Cells 247
Daniela Ushizima
Case Study 21: Enabling Astronomy Image Processing
with Cloud Computing Using Apache Spark 253
Zhao Zhang
PART III: LOW-LEVEL CASE STUDIES 263
Case Study 22: Software for Analyzing Supernova Light
Curve Data for Cosmology 265
Kyle Barbary
Case Study 23: pyMooney: Generating a Database
of Two-Tone Mooney Images 271
Fatma Deniz
Case Study 24: Problem-Specific Analysis of Molecular
Dynamics Trajectories for Biomolecules 277
Konrad Hinsen
Case Study 25: Developing an Open, Modular Simulation
Framework for Nuclear Fuel Cycle Analysis 285
Kathryn Huff
Case Study 26: Producing a Journal Article on Probabilistic
Tsunami Hazard Assessment 291
Randall J. LeVeque
Case Study 27: A Reproducible Neuroimaging Workflow
Using the Automated Build Tool “Make” 297
Tara Madhyastha, Natalie Koh, and Mary K. Askren
Case Study 28: Generation of Uniform Data Products
for AmeriFlux and FLUXNET 305
Gilberto Pastorello
Case Study 29: Developing a Reproducible Workflow
for Large-Scale Phenotyping 311
Russell Poldrack
Case Study 30: Developing and Testing Stochastic
Filtering Methods for Tracking Objects in Videos 317
Valentina Staneva
Case Study 31: Developing, Testing, and Deploying
Efficient MCMC Algorithms for Hierarchical Models Using R 323
Daniel Turek
Index 329 |
| any_adam_object | 1 |
| author2 | Kitzes, Justin 1982- Turek, Daniel 1980- Deniz, Fatma |
| author2_role | edt edt edt |
| author2_variant | j k jk d t dt f d fd |
| author_GND | (DE-588)1166366278 (DE-588)1166366359 |
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| building | Verbundindex |
| bvnumber | BV044932082 |
| callnumber-first | Q - Science |
| callnumber-label | Q180 |
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| callnumber-search | Q180.55.S7 |
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| dewey-full | 507.2/1 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 507 - Education, research, related topics |
| dewey-raw | 507.2/1 |
| dewey-search | 507.2/1 |
| dewey-sort | 3507.2 11 |
| dewey-tens | 500 - Natural sciences and mathematics |
| discipline | Allgemeine Naturwissenschaft Allgemeines Physik Biologie Soziologie Mathematik Geographie |
| format | Book |
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| language | English |
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| spelling | The practice of reproducible research case studies and lessons from the data-intensive sciences edited by Justin Kitzes, Daniel Turek, and Fatma Deniz Oakland, California University of California Press [2018] © 2018 xxv, 337 Seiten Diagramme txt rdacontent n rdamedia nc rdacarrier Includes bibliographical references and index "The Practice of Reproducible Research presents concrete examples of how researchers in the data-intensive sciences are working to improve the reproducibility of their research projects. Each of the thirty-one case studies in this volume describes the workflow that an author used to complete a real-world research project, highlighting how particular tools, ideas, and practices have been combined to support reproducibility. Authors emphasize the very practical how, rather than the why or what, of conducting reproducible research. Part 1 contains an accessible introduction to reproducible research, a basic reproducible research project template, and a synthesis of lessons learned from across the thirty-one case studies. Parts 2 and 3 focus on the case studies. The Practice of Reproducible Research is an invaluable resource for students and researchers who wish to better understand the practice of data-intensive sciences and learn how to make their own research more reproducible."...Provided by publisher Reproducible research Electronic data processing Research Statistical methods Statistics Data processing Empirische Forschung (DE-588)4300400-3 gnd rswk-swf Datenanalyse (DE-588)4123037-1 gnd rswk-swf Reproduzierbarkeit (DE-588)4586094-4 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content (DE-588)4522595-3 Fallstudiensammlung gnd-content Empirische Forschung (DE-588)4300400-3 s Datenanalyse (DE-588)4123037-1 s Reproduzierbarkeit (DE-588)4586094-4 s DE-604 Kitzes, Justin 1982- (DE-588)1166366278 edt Turek, Daniel 1980- (DE-588)1166366359 edt Deniz, Fatma edt Erscheint auch als Online-Ausgabe Practice of reproducible research Oakland, California : University of California Press, [2018] 9780520967779 LoC Fremddatenuebernahme application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030325121&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis Digitalisierung UB Augsburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030325121&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | The practice of reproducible research case studies and lessons from the data-intensive sciences Reproducible research Electronic data processing Research Statistical methods Statistics Data processing Empirische Forschung (DE-588)4300400-3 gnd Datenanalyse (DE-588)4123037-1 gnd Reproduzierbarkeit (DE-588)4586094-4 gnd |
| subject_GND | (DE-588)4300400-3 (DE-588)4123037-1 (DE-588)4586094-4 (DE-588)4143413-4 (DE-588)4522595-3 |
| title | The practice of reproducible research case studies and lessons from the data-intensive sciences |
| title_auth | The practice of reproducible research case studies and lessons from the data-intensive sciences |
| title_exact_search | The practice of reproducible research case studies and lessons from the data-intensive sciences |
| title_full | The practice of reproducible research case studies and lessons from the data-intensive sciences edited by Justin Kitzes, Daniel Turek, and Fatma Deniz |
| title_fullStr | The practice of reproducible research case studies and lessons from the data-intensive sciences edited by Justin Kitzes, Daniel Turek, and Fatma Deniz |
| title_full_unstemmed | The practice of reproducible research case studies and lessons from the data-intensive sciences edited by Justin Kitzes, Daniel Turek, and Fatma Deniz |
| title_short | The practice of reproducible research |
| title_sort | the practice of reproducible research case studies and lessons from the data intensive sciences |
| title_sub | case studies and lessons from the data-intensive sciences |
| topic | Reproducible research Electronic data processing Research Statistical methods Statistics Data processing Empirische Forschung (DE-588)4300400-3 gnd Datenanalyse (DE-588)4123037-1 gnd Reproduzierbarkeit (DE-588)4586094-4 gnd |
| topic_facet | Reproducible research Electronic data processing Research Statistical methods Statistics Data processing Empirische Forschung Datenanalyse Reproduzierbarkeit Aufsatzsammlung Fallstudiensammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030325121&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030325121&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT kitzesjustin thepracticeofreproducibleresearchcasestudiesandlessonsfromthedataintensivesciences AT turekdaniel thepracticeofreproducibleresearchcasestudiesandlessonsfromthedataintensivesciences AT denizfatma thepracticeofreproducibleresearchcasestudiesandlessonsfromthedataintensivesciences |
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Inhaltsverzeichnis