Implementing Reproducible Research

In computational science, reproducibility requires that researchers make code and data available to others so that the data can be analyzed in a similar manner as in the original publication. Code must be available to be distributed, data must be accessible in a readable format, and a platform must be available for widely distributing the data and code. In addition, both data and code need to be licensed permissively enough so that others can reproduce the work without a substantial legal burden. Implementing Reproducible Research covers many of the elements necessary for conducting and distributing reproducible research. It explains how to accurately reproduce a scientific result. Divided into three parts, the book discusses the tools, practices, and dissemination platforms for ensuring reproducibility in computational science. It describes: Computational tools, such as Sweave, knitr, VisTrails, Sumatra, CDE, and the Declaratron system Open source practices, good programming practices, trends in open science, and the role of cloud computing in reproducible research Software and methodological platforms, including open source software packages, RunMyCode platform, and open access journals Each part presents contributions from leaders who have developed software and other products that have advanced the field. Supplementary material is available at www.ImplementingRR.org.

In computational science, reproducibility requires that researchers make code and data available to others so that the data can be analyzed in a similar manner as in the original publication. Code must be available to be distributed, data must be accessible in a readable format, and a platform must be available for widely distributing the data and code. In addition, both data and code need to be licensed permissively enough so that others can reproduce the work without a substantial legal burden. Implementing Reproducible Research covers many of the elements necessary for conducting and distributing reproducible research. It explains how to accurately reproduce a scientific result. Divided into three parts, the book discusses the tools, practices, and dissemination platforms for ensuring reproducibility in computational science. It describes: Computational tools, such as Sweave, knitr, VisTrails, Sumatra, CDE, and the Declaratron system Open source practices, good programming practices, trends in open science, and the role of cloud computing in reproducible research Software and methodological platforms, including open source software packages, RunMyCode platform, and open access journals Each part presents contributions from leaders who have developed software and other products that have advanced the field. Supplementary material is available at www.ImplementingRR.org.

In computational science, reproducibility requires that researchers make code and data available to others so that the data can be analyzed in a similar manner as in the original publication. Code must be available to be distributed, data must be accessible in a readable format, and a platform must be available for widely distributing the data and code. In addition, both data and code need to be licensed permissively enough so that others can reproduce the work without a substantial legal burden. Implementing Reproducible Research covers many of the elements necessary for conducting and distributing reproducible research. It explains how to accurately reproduce a scientific result. Divided into three parts, the book discusses the tools, practices, and dissemination platforms for ensuring reproducibility in computational science. It describes: Computational tools, such as Sweave, knitr, VisTrails, Sumatra, CDE, and the Declaratron system Open source practices, good programming practices, trends in open science, and the role of cloud computing in reproducible research Software and methodological platforms, including open source software packages, RunMyCode platform, and open access journals Each part presents contributions from leaders who have developed software and other products that have advanced the field. Supplementary material is available at www.ImplementingRR.org.

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.

2017 PROSE Award Honorable Mention The PROSE Awards draw attention to pioneering works of research and for contributions to the conception, production, and design of landmark works in their fields. Featuring peer-reviewed contributions from noted experts in their fields of research, Reproducibility: Principles, Problems, Practices, and Prospects presents state-of-the-art approaches to reproducibility, the gold standard of sound science, from multi- and interdisciplinary perspectives. Including comprehensive coverage for implementing and reflecting the norm of reproducibility in various pertinent fields of research, the book focuses on how the reproducibility of results is applied, how it may be limited, and how such limitations can be understood or even controlled in the natural sciences, computational sciences, life sciences, social sciences, and studies of science and technology. The book presents many chapters devoted to a variety of methods and techniques, as well as their epistemic and ontological underpinnings, which have been developed to safeguard reproducible research and curtail deficits and failures. The book also investigates the political, historical, and social practices that underlie reproducible research in contemporary science studies, including the difficulties of good scientific practice and the ethos of reproducibility in modern innovation societies. Reproducibility: Principles, Problems, Practices, and Prospects is a guide for researchers who are interested in the general and overarching questions behind the concept of reproducibility; for active scientists who are confronted with practical reproducibility problems in their everyday work; and for economic stakeholders and political decision makers who need to better understand the challenges of reproducibility. In addition, the book is a useful in-depth primer for undergraduate and graduate-level courses in scientific methodology and basic issues in the philosophy and sociology of science from a modern perspective. “A comprehensive, insightful treatment of the reproducibility challenges facing science today and of ways in which the scientific community can address them.” Kathleen Hall Jamieson, Elizabeth Ware Packard Professor of Communication, University of Pennsylvania “How can we make sure that reproducible research remains a key imperative of scientific communication under increasing commercialization, media attention, and publication pressure? This handbook offers the first interdisciplinary and fundamental treatment of this important question.”Torsten Hothorn, Professor of Biostatistics, University of Zurich Harald Atmanspacher, PhD, is Associate Fellow and staff member at Collegium Helveticum, ETH and University Zurich and is also President of the Society for Mind-Matter Research. He has pioneered advances in complex dynamical systems research and in a number of topics concerned with the relation between the mental and physical. Sabine Maasen, PhD, is Professor for Sociology of Science and Director of the Munich Center for Technology in Society (TU Munich) and Associate Fellow at Collegium Helveticum (ETH and University Zurich). Her research focuses on the interface of science, technology, and society, notably with respect to neuroscience and its applications.

All the Tools for Gathering and Analyzing Data and Presenting Results Reproducible Research with R and RStudio, Second Edition brings together the skills and tools needed for doing and presenting computational research. Using straightforward examples, the book takes you through an entire reproducible research workflow. This practical workflow enables you to gather and analyze data as well as dynamically present results in print and on the web. New to the Second Edition The rmarkdown package that allows you to create reproducible research documents in PDF, HTML, and Microsoft Word formats using the simple and intuitive Markdown syntax Improvements to RStudio’s interface and capabilities, such as its new tools for handling R Markdown documents Expanded knitr R code chunk capabilities The kable function in the knitr package and the texreg package for dynamically creating tables to present your data and statistical results An improved discussion of file organization, enabling you to take full advantage of relative file paths so that your documents are more easily reproducible across computers and systems The dplyr, magrittr, and tidyr packages for fast data manipulation Numerous modifications to R syntax in user-created packages Changes to GitHub’s and Dropbox’s interfaces Create Dynamic and Highly Reproducible Research This updated book provides all the tools to combine your research with the presentation of your findings. It saves you time searching for information so that you can spend more time actually addressing your research questions. Supplementary files used for the examples and a reproducible research project are available on the author’s website.

Science is allegedly in the midst of a reproducibility crisis, but questions of reproducibility and related principles date back nearly 80 years. Numerous controversies have arisen, especially since 2010, in a wide array of disciplines that stem from the failure to reproduce studies or their findings:biology, biomedical and preclinical research, business and organizational studies, computational sciences, drug discovery, economics, education, epidemiology and statistics, genetics, immunology, policy research, political science, psychology, and sociology. This monograph defines terms and constructs related to reproducible research, weighs key considerations and challenges in reproducing or replicating studies, and discusses transparency in publications that can support reproducible research goals. It attempts to clarify reproducible research, with its attendant (and confusing or even conflicting) lexicon and aims to provide useful background, definitions, and practical guidance for all readers. Among its conclusions: First, researchers must become better educated about these issues, particularly the differences between the concepts and terms. The main benefit is being able to communicate clearly within their own fields and, more importantly, across multiple disciplines. In addition, scientists need to embrace these concepts as part of their responsibilities as good stewards of research funding and as providers of credible information for policy decision making across many areas of public concern. Finally, although focusing on transparency and documentation is essential, ultimately the goal is achieving the most rigorous, high-quality science possible given limitations on time, funding, or other resources. “The authors have written a nuanced and thoughtful primer on scientific reproducibility. By highlighting the social, political, and technical importance of reproducibility, together with a precise description of the related concepts of reproducibility, replicability, and repeatability, this primer provides a significant resource that all practicing researchers should read.” Daniel Reed, Vice President for Research and Economic Development, University of Iowa and former Corporate Vice President, Microsoft “This is a well-written, clearly articulated, and timely primer on the developing and evolving rich terminology of reproducible research. The primer, put together by authors with deep experience and expertise in the topic area, focuses primarily on human-centric research in biomedicine, medicine, and the social sciences as well as reproducibility issues in analytics and computational science. The growing focus on reproducibility will open new vistas in research methodologies, meta analysis, comparative studies of research results, and reuse and adaptation of results from prior research. This primer provides an excellent overview of the subject area, and I would recommend it to anyone interested in coming up to speed on current issues in reproducible research.” Chaitan Baru, Distinguished Scientist and Associate Director for Data Initiatives, San Diego Supercomputing Center; current appointment as Senior Advisor for Data Science, Computer and Information Science and Engineering Directorate, National Science Foundation “Pellizzari et al. have taken on the Herculean task of collecting, synthesizing, and relating the various interpretations of reproducibility used in the research community today, and turned the result into an accessible must-read guide. This important work provides a Rosetta Stone for various stakeholders to discuss and implement solutions that make real progress toward a research enterprise that routinely produces reproducible findings.” Victoria Stodden, Associate Professor at the School of Information Sciences, University of Illinois at Urbana Champaign and co-editor of the books Implementing Reproducible Research and Privacy, Big Data, and the Public Good: Frameworks for Engagement

Praise for previous editions: "Gandrud has written a great outline of how a fully reproducible research project should look from start to finish, with brief explanations of each tool that he uses along the way... Advanced undergraduate students in mathematics, statistics, and similar fields as well as students just beginning their graduate studies would benefit the most from reading this book. Many more experienced R users or second-year graduate students might find themselves thinking, ‘I wish I’d read this book at the start of my studies, when I was first learning R!’...This book could be used as the main text for a class on reproducible research ..." (The American Statistician) Reproducible Research with R and R Studio, Third Edition brings together the skills and tools needed for doing and presenting computational research. Using straightforward examples, the book takes you through an entire reproducible research workflow. This practical workflow enables you to gather and analyze data as well as dynamically present results in print and on the web. Supplementary materials and example are available on the author’s website. New to the Third Edition Updated package recommendations, examples, URLs, and removed technologies no longer in regular use. More advanced R Markdown (and less LaTeX) in discussions of markup languages and examples. Stronger focus on reproducible working directory tools. Updated discussion of cloud storage services and persistent reproducible material citation. Added discussion of Jupyter notebooks and reproducible practices in industry. Examples of data manipulation with Tidyverse tibbles (in addition to standard data frames) and pivot_longer() and pivot_wider() functions for pivoting data. Features Incorporates the most important advances that have been developed since the editions were published Describes a complete reproducible research workflow, from data gathering to the presentation of results Shows how to automatically generate tables and figures using R Includes instructions on formatting a presentation document via markup languages Discusses cloud storage and versioning services, particularly Github Explains how to use Unix-like shell programs for working with large research projects