SUMMARY.md

Summary

• Front Matter
• Table of Contents
• Preface
• Introduction

Part I: Practicing Reproducibility

• Assessing Reproducibility
• The Basic Reproducible Workflow Template
• Case Studies in Reproducible Research
• Lessons Learned
• Building Towards a Future Where Reproducible, Open Science is the Norm
• Glossary

Part II: High-level Case Studies

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

Part III: Low-level Case Studies

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

Appendix

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