Chapters in this book

1. Frontmatter i
2. Contents v
3. List of Contributors xi
4. Preface: Nullius in Verba xvii
5. Introduction xxi
6. PART I: PRACTICING REPRODUCIBILITY
7. Assessing Reproducibility 1
8. The Basic Reproducible Workflow Template 19
9. Case Studies in Reproducible Research 31
10. Lessons Learned 41
11. Building toward a Future Where Reproducible, Open Science Is the Norm 61
12. Glossary 71
13. PART II: HIGH-LEVEL CASE STUDIES
14. Case Study 1: Processing of Airborne Laser Altimetry Data Using Cloud-Based Python and Relational Database Tools 95
15. Case Study 2: The Trade-Off between Reproducibility and Privacy in the Use of Social Media Data to Study Political Behavior 103
16. Case Study 3: A Reproducible R Notebook Using Docker 109
17. Case Study 4: Estimating the Effect of Soldier Deaths on the Military Labor Supply 119
18. Case Study 5: Turning Simulations of Quantum Many- Body Systems into a Provenance-Rich Publication 125
19. Case Study 6: Validating Statistical Methods to Detect Data Fabrication 131
20. Case Study 7: Feature Extraction and Data Wrangling for Predictive Models of the Brain in Python 139
21. Case Study 8: Using Observational Data and Numerical Modeling to Make Scientific Discoveries in Climate Science 149
22. Case Study 9: Analyzing Bat Distributions in a Human- Dominated Landscape with Autonomous Acoustic Detectors and Machine Learning Models 155
23. Case Study 10: An Analysis of Household Location Choice in Major US Metropolitan Areas Using R 161
24. Case Study 11: Analyzing Cosponsorship Data to Detect Networking Patterns in Peruvian Legislators 169
25. Case Study 12: Using R and Related Tools for Reproducible Research in Archaeology 181
26. Case Study 13: Achieving Full Replication of Our Own Published CFD Results, with Four Different Codes 191
27. Case Study 14: Reproducible Applied Statistics: Is Tagging of Therapist-Patient Interactions Reliable? 201
28. Case Study 15: A Dissection of Computational Methods Used in a Biogeographic Study 215
29. Case Study 16: A Statistical Analysis of Salt and Mortality at the Level of Nations 221
30. Case Study 17: Reproducible Workflows for Understanding Large-Scale Ecological Effects of Climate Change 227
31. Case Study 18: Reproducibility in Human Neuroimaging Research: A Practical Example from the Analysis of Diffusion MRI 233
32. Case Study 19: Reproducible Computational Science on High-Performance Computers: A View from Neutron Transport 241
33. Case Study 20: Detection and Classification of Cervical Cells 247
34. Case Study 21: Enabling Astronomy Image Processing with Cloud Computing Using Apache Spark 253
35. PART III: LOW-LEVEL CASE STUDIES
36. Case Study 22: Software for Analyzing Supernova Light Curve Data for Cosmology 265
37. Case Study 23: pyMooney: Generating a Database of Two-Tone Mooney Images 271
38. Case Study 24: Problem-Specific Analysis of Molecular Dynamics Trajectories for Biomolecules 277
39. Case Study 25: Developing an Open, Modular Simulation Framework for Nuclear Fuel Cycle Analysis 285
40. Case Study 26: Producing a Journal Article on Probabilistic Tsunami Hazard Assessment 291
41. Case Study 27: A Reproducible Neuroimaging Workflow Using the Automated Build Tool “Make” 297
42. Case Study 28: Generation of Uniform Data Products for AmeriFlux and FLUXNET 305
43. Case Study 29: Developing a Reproducible Workflow for Large-Scale Phenotyping 311
44. Case Study 30: Developing and Testing Stochastic Filtering Methods for Tracking Objects in Videos 317
45. Case Study 31: Developing, Testing, and Deploying Efficient MCMC Algorithms for Hierarchical Models Using R 323
46. Index 329