The practice of reproducible research : case studies and lessons from the data-intensive sciences / Justin Kitzes.

Format:

Book

Contributor:

Kitzes, Justin, editor.

Language:

English

Subjects (All):

Electronic data processing.

Research--Statistical methods.

Research.

R (Computer program language).

Reproducible research.

Physical Description:

1 online resource (365 pages)

Place of Publication:

Berkeley, CA : University of California Press, [2017]

Language Note:

In English.

Summary:

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.

Contents:

Frontmatter

Contents

List of Contributors

Preface: Nullius in Verba / Stark, Philip B.

Introduction / Kitzes, Justin

PART I: PRACTICING REPRODUCIBILITY

Assessing Reproducibility / Rokem, Ariel / Marwick, Ben / Staneva, Valentina

The Basic Reproducible Workflow Template / Kitzes, Justin

Case Studies in Reproducible Research / Turek, Daniel / Deniz, Fatma

Lessons Learned / Huff, Kathryn

Building toward a Future Where Reproducible, Open Science Is the Norm / Ram, Karthik / Marwick, Ben

Glossary / Rokem, Ariel / Chirigati, Fernando

PART II: HIGH-LEVEL CASE STUDIES

Case Study 1: Processing of Airborne Laser Altimetry Data Using Cloud-Based Python and Relational Database Tools / Arendt, Anthony / Kienholz, Christian / Larsen, Christopher / Rich, Justin / Burgess, Evan

Case Study 2: The Trade-Off between Reproducibility and Privacy in the Use of Social Media Data to Study Political Behavior / Barberá, Pablo

Case Study 3: A Reproducible R Notebook Using Docker / Boettiger, Carl

Case Study 4: Estimating the Effect of Soldier Deaths on the Military Labor Supply / Christensen, Garret

Case Study 5: Turning Simulations of Quantum Many- Body Systems into a Provenance-Rich Publication / Gukelberger, Jan / Troyer, Matthias

Case Study 6: Validating Statistical Methods to Detect Data Fabrication / Hartgerink, Chris

Case Study 7: Feature Extraction and Data Wrangling for Predictive Models of the Brain in Python / Holdgraf, Chris

Case Study 8: Using Observational Data and Numerical Modeling to Make Scientific Discoveries in Climate Science / Holland, David / Holland, Denise

Case Study 9: Analyzing Bat Distributions in a Human- Dominated Landscape with Autonomous Acoustic Detectors and Machine Learning Models / Kitzes, Justin

Case Study 10: An Analysis of Household Location Choice in Major US Metropolitan Areas Using R / Krause, Andy / Estiri, Hossein

Case Study 11: Analyzing Cosponsorship Data to Detect Networking Patterns in Peruvian Legislators / Magallanes, José Manuel

Case Study 12: Using R and Related Tools for Reproducible Research in Archaeology / Marwick, Ben

Case Study 13: Achieving Full Replication of Our Own Published CFD Results, with Four Different Codes / Mesnard, Olivier / Barba, Lorena A.

Case Study 14: Reproducible Applied Statistics: Is Tagging of Therapist-Patient Interactions Reliable? / Millman, K. Jarrod / Ottoboni, Kellie / Stark, Naomi A. P. / Stark, Philip B.

Case Study 15: A Dissection of Computational Methods Used in a Biogeographic Study / Mislan, K. A. S.

Case Study 16: A Statistical Analysis of Salt and Mortality at the Level of Nations / Ottoboni, Kellie

Case Study 17: Reproducible Workflows for Understanding Large-Scale Ecological Effects of Climate Change / Ram, Karthik

Case Study 18: Reproducibility in Human Neuroimaging Research: A Practical Example from the Analysis of Diffusion MRI / Rokem, Ariel

Case Study 19: Reproducible Computational Science on High-Performance Computers: A View from Neutron Transport / Slaybaugh, Rachel

Case Study 20: Detection and Classification of Cervical Cells / Ushizima, Daniela

Case Study 21: Enabling Astronomy Image Processing with Cloud Computing Using Apache Spark / Zhang, Zhao

PART III: LOW-LEVEL CASE STUDIES

Case Study 22: Software for Analyzing Supernova Light Curve Data for Cosmology / Barbary, Kyle

Case Study 23: pyMooney: Generating a Database of Two-Tone Mooney Images / Deniz, Fatma

Case Study 24: Problem-Specific Analysis of Molecular Dynamics Trajectories for Biomolecules / Hinsen, Konrad

Case Study 25: Developing an Open, Modular Simulation Framework for Nuclear Fuel Cycle Analysis / Huff, Kathryn

Case Study 26: Producing a Journal Article on Probabilistic Tsunami Hazard Assessment / LeVeque, Randall J.

Case Study 27: A Reproducible Neuroimaging Workflow Using the Automated Build Tool "Make" / Madhyastha, Tara / Koh, Natalie / Askren, Mary K.

Case Study 28: Generation of Uniform Data Products for AmeriFlux and FLUXNET / Pastorello, Gilberto

Case Study 29: Developing a Reproducible Workflow for Large-Scale Phenotyping / Poldrack, Russell

Case Study 30: Developing and Testing Stochastic Filtering Methods for Tracking Objects in Videos / Staneva, Valentina

Case Study 31: Developing, Testing, and Deploying Efficient MCMC Algorithms for Hierarchical Models Using R / Turek, Daniel

Index

Notes:

Includes index.

Description based on online resource; title from PDF title page (publisher's Web site, viewed 20. Sep 2019)

ISBN:

9780520967779

0520967771

OCLC:

1004199317