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Reproducibility and Replicability in Science

Reproducibility and Replicability in Science
Author: National Academies of Sciences, Engineering, and Medicine
Publisher: National Academies Press
Total Pages: 257
Release: 2019-10-20
Genre: Science
ISBN: 0309486165

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One of the pathways by which the scientific community confirms the validity of a new scientific discovery is by repeating the research that produced it. When a scientific effort fails to independently confirm the computations or results of a previous study, some fear that it may be a symptom of a lack of rigor in science, while others argue that such an observed inconsistency can be an important precursor to new discovery. Concerns about reproducibility and replicability have been expressed in both scientific and popular media. As these concerns came to light, Congress requested that the National Academies of Sciences, Engineering, and Medicine conduct a study to assess the extent of issues related to reproducibility and replicability and to offer recommendations for improving rigor and transparency in scientific research. Reproducibility and Replicability in Science defines reproducibility and replicability and examines the factors that may lead to non-reproducibility and non-replicability in research. Unlike the typical expectation of reproducibility between two computations, expectations about replicability are more nuanced, and in some cases a lack of replicability can aid the process of scientific discovery. This report provides recommendations to researchers, academic institutions, journals, and funders on steps they can take to improve reproducibility and replicability in science.


The Practice of Reproducible Research

The Practice of Reproducible Research
Author: Justin Kitzes
Publisher: Univ of California Press
Total Pages: 364
Release: 2018
Genre: Computers
ISBN: 0520294750

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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.


Implementing Reproducible Research

Implementing Reproducible Research
Author: Victoria Stodden
Publisher: CRC Press
Total Pages: 450
Release: 2018-12-14
Genre: Mathematics
ISBN: 131536039X

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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 Problem with Science

The Problem with Science
Author: R. Barker Bausell
Publisher: Oxford University Press
Total Pages:
Release: 2021-01-26
Genre: Psychology
ISBN: 0197536549

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Recent events have vividly underscored the societal importance of science, yet the majority of the public are unaware that a large proportion of published scientific results are simply wrong. The Problem with Science is an exploration of the manifestations and causes of this scientific crisis, accompanied by a description of the very promising corrective initiatives largely developed over the past decade to stem the spate of irreproducible results that have come to characterize many of our sciences. More importantly, Dr. R. Barker Bausell has designed it to provide guidance to practicing and aspiring scientists regarding how (a) to change the way in which science has come to be both conducted and reported in order to avoid producing false positive, irreproducible results in their own work and (b) to change those institutional practices (primarily but not exclusively involving the traditional journal publishing process and the academic reward system) that have unwittingly contributed to the present crisis. There is a need for change in the scientific culture itself. A culture which prioritizes conducting research correctly in order to get things right rather than simply getting it published.


Reproducible Research with R and RStudio

Reproducible Research with R and RStudio
Author: Christopher Gandrud
Publisher: CRC Press
Total Pages: 211
Release: 2020-02-21
Genre: Business & Economics
ISBN: 0429627955

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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


Transparent and Reproducible Social Science Research

Transparent and Reproducible Social Science Research
Author: Garret Christensen
Publisher: University of California Press
Total Pages: 266
Release: 2019-07-23
Genre: Social Science
ISBN: 0520296958

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Recently, social science has had numerous episodes of influential research that was found invalid when placed under rigorous scrutiny. The growing sense that many published results are potentially erroneous has made those conducting social science research more determined to ensure the underlying research is sound. Transparent and Reproducible Social Science Research is the first book to summarize and synthesize new approaches to combat false positives and non-reproducible findings in social science research, document the underlying problems in research practices, and teach a new generation of students and scholars how to overcome them. Understanding that social science research has real consequences for individuals when used by professionals in public policy, health, law enforcement, and other fields, the book crystallizes new insights, practices, and methods that help ensure greater research transparency, openness, and reproducibility. Readers are guided through well-known problems and are encouraged to work through new solutions and practices to improve the openness of their research. Created with both experienced and novice researchers in mind, Transparent and Reproducible Social Science Research serves as an indispensable resource for the production of high quality social science research.


Development Research in Practice

Development Research in Practice
Author: Kristoffer Bjärkefur
Publisher: World Bank Publications
Total Pages: 388
Release: 2021-07-16
Genre: Business & Economics
ISBN: 1464816956

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Development Research in Practice leads the reader through a complete empirical research project, providing links to continuously updated resources on the DIME Wiki as well as illustrative examples from the Demand for Safe Spaces study. The handbook is intended to train users of development data how to handle data effectively, efficiently, and ethically. “In the DIME Analytics Data Handbook, the DIME team has produced an extraordinary public good: a detailed, comprehensive, yet easy-to-read manual for how to manage a data-oriented research project from beginning to end. It offers everything from big-picture guidance on the determinants of high-quality empirical research, to specific practical guidance on how to implement specific workflows—and includes computer code! I think it will prove durably useful to a broad range of researchers in international development and beyond, and I learned new practices that I plan on adopting in my own research group.†? —Marshall Burke, Associate Professor, Department of Earth System Science, and Deputy Director, Center on Food Security and the Environment, Stanford University “Data are the essential ingredient in any research or evaluation project, yet there has been too little attention to standardized practices to ensure high-quality data collection, handling, documentation, and exchange. Development Research in Practice: The DIME Analytics Data Handbook seeks to fill that gap with practical guidance and tools, grounded in ethics and efficiency, for data management at every stage in a research project. This excellent resource sets a new standard for the field and is an essential reference for all empirical researchers.†? —Ruth E. Levine, PhD, CEO, IDinsight “Development Research in Practice: The DIME Analytics Data Handbook is an important resource and a must-read for all development economists, empirical social scientists, and public policy analysts. Based on decades of pioneering work at the World Bank on data collection, measurement, and analysis, the handbook provides valuable tools to allow research teams to more efficiently and transparently manage their work flows—yielding more credible analytical conclusions as a result.†? —Edward Miguel, Oxfam Professor in Environmental and Resource Economics and Faculty Director of the Center for Effective Global Action, University of California, Berkeley “The DIME Analytics Data Handbook is a must-read for any data-driven researcher looking to create credible research outcomes and policy advice. By meticulously describing detailed steps, from project planning via ethical and responsible code and data practices to the publication of research papers and associated replication packages, the DIME handbook makes the complexities of transparent and credible research easier.†? —Lars Vilhuber, Data Editor, American Economic Association, and Executive Director, Labor Dynamics Institute, Cornell University


Big Data Meets Survey Science

Big Data Meets Survey Science
Author: Craig A. Hill
Publisher: John Wiley & Sons
Total Pages: 784
Release: 2020-09-29
Genre: Social Science
ISBN: 1118976320

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Offers a clear view of the utility and place for survey data within the broader Big Data ecosystem This book presents a collection of snapshots from two sides of the Big Data perspective. It assembles an array of tangible tools, methods, and approaches that illustrate how Big Data sources and methods are being used in the survey and social sciences to improve official statistics and estimates for human populations. It also provides examples of how survey data are being used to evaluate and improve the quality of insights derived from Big Data. Big Data Meets Survey Science: A Collection of Innovative Methods shows how survey data and Big Data are used together for the benefit of one or more sources of data, with numerous chapters providing consistent illustrations and examples of survey data enriching the evaluation of Big Data sources. Examples of how machine learning, data mining, and other data science techniques are inserted into virtually every stage of the survey lifecycle are presented. Topics covered include: Total Error Frameworks for Found Data; Performance and Sensitivities of Home Detection on Mobile Phone Data; Assessing Community Wellbeing Using Google Street View and Satellite Imagery; Using Surveys to Build and Assess RBS Religious Flag; and more. Presents groundbreaking survey methods being utilized today in the field of Big Data Explores how machine learning methods can be applied to the design, collection, and analysis of social science data Filled with examples and illustrations that show how survey data benefits Big Data evaluation Covers methods and applications used in combining Big Data with survey statistics Examines regulations as well as ethical and privacy issues Big Data Meets Survey Science: A Collection of Innovative Methods is an excellent book for both the survey and social science communities as they learn to capitalize on this new revolution. It will also appeal to the broader data and computer science communities looking for new areas of application for emerging methods and data sources.


Statistical Challenges in Assessing and Fostering the Reproducibility of Scientific Results

Statistical Challenges in Assessing and Fostering the Reproducibility of Scientific Results
Author: National Academies of Sciences, Engineering, and Medicine
Publisher: National Academies Press
Total Pages: 133
Release: 2016-03-29
Genre: Mathematics
ISBN: 0309392020

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Questions about the reproducibility of scientific research have been raised in numerous settings and have gained visibility through several high-profile journal and popular press articles. Quantitative issues contributing to reproducibility challenges have been considered (including improper data measurement and analysis, inadequate statistical expertise, and incomplete data, among others), but there is no clear consensus on how best to approach or to minimize these problems. A lack of reproducibility of scientific results has created some distrust in scientific findings among the general public, scientists, funding agencies, and industries. While studies fail for a variety of reasons, many factors contribute to the lack of perfect reproducibility, including insufficient training in experimental design, misaligned incentives for publication and the implications for university tenure, intentional manipulation, poor data management and analysis, and inadequate instances of statistical inference. The workshop summarized in this report was designed not to address the social and experimental challenges but instead to focus on the latter issues of improper data management and analysis, inadequate statistical expertise, incomplete data, and difficulties applying sound statistic inference to the available data. Many efforts have emerged over recent years to draw attention to and improve reproducibility of scientific work. This report uniquely focuses on the statistical perspective of three issues: the extent of reproducibility, the causes of reproducibility failures, and the potential remedies for these failures.


Reproducible Research in Pattern Recognition

Reproducible Research in Pattern Recognition
Author: Bertrand Kerautret
Publisher: Springer
Total Pages: 184
Release: 2017-04-04
Genre: Computers
ISBN: 3319564145

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This book constitutes the thoroughly refereed post-proceedings of the First International Workshop on Reproducible Research in Pattern Recognition, RRPR 2016, held in Cancún, Mexico, in December 2016. The 12 revised full papers, among them 2 invited talks, presented were carefully reviewed and selected from 16 submissions. They focus on pattern recognition algorithms; reproducible research frameworks; reproducible research results, previous works on reproducible research.