Presented to you through Paradigm Publishing Services
University of California Press
Book
Licensed
Unlicensed
Requires Authentication
The Practice of Reproducible Research
Case Studies and Lessons from the Data-Intensive Sciences
-
Edited by:
Language:
English
Published/Copyright:
2018
About this book
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. In each of the thirty-one case studies in this volume, the author or team describes the workflow that they used to complete a real-world research project. Authors highlight how they utilized particular tools, ideas, and practices to support reproducibility, emphasizing the very practical how, rather than the why or what, of conducting reproducible research.
Part 1 provides 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 themselves. 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.
Part 1 provides 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 themselves. 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.
Author / Editor information
Contributor: Justin Kitzes
Justin Kitzes is Assistant Professor of Biology at the University of Pittsburgh.
Daniel Turek is Assistant Professor of Statistics at Williams College.
Fatma Deniz is Postdoctoral Scholar at the Helen Wills Neuroscience Institute and the International Computer Science Institute, and Data Science Fellow at the University of California, Berkeley.
Daniel Turek is Assistant Professor of Statistics at Williams College.
Fatma Deniz is Postdoctoral Scholar at the Helen Wills Neuroscience Institute and the International Computer Science Institute, and Data Science Fellow at the University of California, Berkeley.
Topics
-
Download PDFPublicly Available
Frontmatter
i -
Download PDFPublicly Available
Contents
v -
Download PDFPublicly Available
List of Contributors
xi -
Download PDFPublicly Available
Preface: Nullius in Verba
xvii -
Download PDFPublicly Available
Introduction
xxi - PART I: PRACTICING REPRODUCIBILITY
-
Download PDFRequires Authentication UnlicensedLicensed
Assessing Reproducibility
1 -
Download PDFRequires Authentication UnlicensedLicensed
The Basic Reproducible Workflow Template
19 -
Download PDFRequires Authentication UnlicensedLicensed
Case Studies in Reproducible Research
31 -
Download PDFRequires Authentication UnlicensedLicensed
Lessons Learned
41 -
Download PDFRequires Authentication UnlicensedLicensed
Building toward a Future Where Reproducible, Open Science Is the Norm
61 -
Download PDFRequires Authentication UnlicensedLicensed
Glossary
71 - PART II: HIGH-LEVEL CASE STUDIES
-
Download PDFRequires Authentication UnlicensedLicensed
Case Study 1: Processing of Airborne Laser Altimetry Data Using Cloud-Based Python and Relational Database Tools
95 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 2: The Trade-Off between Reproducibility and Privacy in the Use of Social Media Data to Study Political Behavior
103 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 3: A Reproducible R Notebook Using Docker
109 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 4: Estimating the Effect of Soldier Deaths on the Military Labor Supply
119 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 5: Turning Simulations of Quantum Many- Body Systems into a Provenance-Rich Publication
125 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 6: Validating Statistical Methods to Detect Data Fabrication
131 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 7: Feature Extraction and Data Wrangling for Predictive Models of the Brain in Python
139 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 8: Using Observational Data and Numerical Modeling to Make Scientific Discoveries in Climate Science
149 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 9: Analyzing Bat Distributions in a Human- Dominated Landscape with Autonomous Acoustic Detectors and Machine Learning Models
155 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 10: An Analysis of Household Location Choice in Major US Metropolitan Areas Using R
161 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 11: Analyzing Cosponsorship Data to Detect Networking Patterns in Peruvian Legislators
169 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 12: Using R and Related Tools for Reproducible Research in Archaeology
181 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 13: Achieving Full Replication of Our Own Published CFD Results, with Four Different Codes
191 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 14: Reproducible Applied Statistics: Is Tagging of Therapist-Patient Interactions Reliable?
201 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 15: A Dissection of Computational Methods Used in a Biogeographic Study
215 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 16: A Statistical Analysis of Salt and Mortality at the Level of Nations
221 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 17: Reproducible Workflows for Understanding Large-Scale Ecological Effects of Climate Change
227 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 18: Reproducibility in Human Neuroimaging Research: A Practical Example from the Analysis of Diffusion MRI
233 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 19: Reproducible Computational Science on High-Performance Computers: A View from Neutron Transport
241 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 20: Detection and Classification of Cervical Cells
247 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 21: Enabling Astronomy Image Processing with Cloud Computing Using Apache Spark
253 - PART III: LOW-LEVEL CASE STUDIES
-
Download PDFRequires Authentication UnlicensedLicensed
Case Study 22: Software for Analyzing Supernova Light Curve Data for Cosmology
265 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 23: pyMooney: Generating a Database of Two-Tone Mooney Images
271 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 24: Problem-Specific Analysis of Molecular Dynamics Trajectories for Biomolecules
277 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 25: Developing an Open, Modular Simulation Framework for Nuclear Fuel Cycle Analysis
285 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 26: Producing a Journal Article on Probabilistic Tsunami Hazard Assessment
291 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 27: A Reproducible Neuroimaging Workflow Using the Automated Build Tool “Make”
297 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 28: Generation of Uniform Data Products for AmeriFlux and FLUXNET
305 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 29: Developing a Reproducible Workflow for Large-Scale Phenotyping
311 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 30: Developing and Testing Stochastic Filtering Methods for Tracking Objects in Videos
317 -
Download PDFRequires Authentication UnlicensedLicensed
Case Study 31: Developing, Testing, and Deploying Efficient MCMC Algorithms for Hierarchical Models Using R
323 -
Download PDFRequires Authentication UnlicensedLicensed
Index
329
Publishing information
Pages and Images/Illustrations in book
eBook published on:
April 15, 2019
eBook ISBN:
9780520967779
Pages and Images/Illustrations in book
Main content:
368
eBook ISBN:
9780520967779
Keywords for this book
research skills; researchers; data; scientific data; research projects; case studies; workflow; real world; academic research; academic study; practical; research project; social media; research ethics; politics; political behavior; statistical methods; statistics; statistical analysis; ecology; climate change; anthology; reproducible research; science