Table of Contents

• Front Matter
• Table of Contents
• Preface (Stark)
• Introduction (Kitzes)

Part I: Practicing Reproducibility

• Assessing Reproducibility (Rokem, Marwick, Staneva)
• The Basic Reproducible Workflow Template (Kitzes)
• Case Studies in Reproducible Research (Turek, Deniz)
• Lessons Learned (Huff)
• Building Towards a Future Where Reproducible, Open Science is the Norm (Ram, Marwick)
• Glossary (Rokem, Chirigati)

Part II: High-level Case Studies

• Processing of Airborne Laser Altimetry Data Using Cloud-based Python and Relational Database Tools (Arendt)
• The Trade-Off Between Reproducibility and Privacy in the Use of Social Media Data to Study Political Behavior (Barberá)
• A Reproducible R Notebook Using Docker (Boettiger)
• Estimating the Effect of Soldier Deaths on the Military Labor Supply (Christensen)
• Developing and Analyzing Exact-Diagonalization Simulations for Quantum Many-Body Systems and Creating a Provenance-Rich Publication from the Results (Gukelberger)
• Validating Statistical Methods to Detect Data Fabrication (Hartgerink)
• Feature Extraction and Data Wrangling for Predictive Models of the Brain in Python (Holdgraf)
• Using Observational Data and Numerical Modeling to Make Scientific Discoveries in Climate Science (Holland, Holland)
• Analyzing Bat Distributions in a Human-Dominated Landscape with Autonomous Acoustic Detectors and Machine Learning Models (Kitzes)
• An Analysis of Household Location Choice in Major U.S. Metropolitan Areas Using R (Krause)
• Analyzing Cosponsorship Data to Detect Networking Patterns in Peruvian Legislators (Magallanes)
• Using R and Related Tools for Reproducible Research in Archaeology (Marwick)
• Achieving Full Replication of our Own Published CFD Results, with Four Different Codes (Mesnard, Barba)
• Reproducible Applied Statistics: Is Tagging of Therapist-Patient Interactions Reliable? (Millman, Ottoboni, Stark, Stark)
• A Dissection of Computational Methods Used in a Biogeographic Study (Mislan)
• A Statistical Analysis of Salt and Mortality at the Level of Nations (Ottoboni)
• Reproducible Workflows For Understanding Large Scale Ecological Effects Of Climate Change (Ram)
• Reproducibility in Human Neuroimaging Research: A Practical Example from the Analysis of Diffusion MRI (Rokem)
• Reproducible Computational Science on High Performance Computers: A View from Neutron Transport (Slaybaugh)
• Detection and Classification of Cervical Cells (Ushizima)
• Enabling Astronomy Image Processing With Cloud Computing Using Apache Spark (Zhang)

Part III: Low-level Case Studies

• Software for Analyzing Supernova Light Curve Data for Cosmology (Barbary)
• pyMooney: Generating a Database of Two-Tone, Mooney Images (Deniz)
• Problem-Specific Analysis of Molecular Dynamics Trajectories for Biomolecules (Hinsen)
• Developing an Open, Modular Simulation Framework for Nuclear Fuel Cycle Analysis (Huff)
• Producing a Journal Article on Probabilistic Tsunami Hazard Assessment (LeVeque)
• A Reproducible Neuroimaging Workflow using the Automated Build Tool "make" (Madhyastha, Koh, Askren)
• Generation of Uniform Data Products for AmeriFlux and FLUXNET (Pastorello)
• Developing a Reproducible Workflow for Large-scale Phenotyping (Poldrack)
• Developing and Testing Stochastic Filtering Methods for Tracking Objects in Videos (Staneva)
• Developing, Testing, and Deploying Efficient MCMC Algorithms for Hierarchical Models Using R (Turek)

Appendix

• Maintaining a Reproducible Database on Political Parties, Elections, and Governments (Krause)
• Developing R Code for the Processing and Analysis of Optic Flow Data (Seisler)
• All or Nothing! Public Goods Provision under Partial versus Full Decentralization in Indonesia (Singhania)