Reproducibility

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Reproducibility and Replicability in Science

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309486165
Total Pages : 257 pages
Book Rating : 4.3/5 (94 download)

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Book Synopsis Reproducibility and Replicability in Science by : National Academies of Sciences, Engineering, and Medicine

Download or read book Reproducibility and Replicability in Science written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2019-10-20 with total page 257 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 Problem with Science

Author : R. Barker Bausell
Publisher : Oxford University Press
ISBN 13 : 0197536549
Total Pages : pages
Book Rating : 4.1/5 (975 download)

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Book Synopsis The Problem with Science by : R. Barker Bausell

Download or read book The Problem with Science written by R. Barker Bausell and published by Oxford University Press. This book was released on 2021-01-26 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Implementing Reproducible Research

Author : Victoria Stodden
Publisher : CRC Press
ISBN 13 : 1466561599
Total Pages : 450 pages
Book Rating : 4.4/5 (665 download)

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Book Synopsis Implementing Reproducible Research by : Victoria Stodden

Download or read book Implementing Reproducible Research written by Victoria Stodden and published by CRC Press. This book was released on 2014-04-14 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Author : Justin Kitzes
Publisher : Univ of California Press
ISBN 13 : 0520294750
Total Pages : 364 pages
Book Rating : 4.5/5 (22 download)

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Book Synopsis The Practice of Reproducible Research by : Justin Kitzes

Download or read book The Practice of Reproducible Research written by Justin Kitzes and published by Univ of California Press. This book was released on 2018 with total page 364 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Reproducible Research with R and RStudio

Author : Christopher Gandrud
Publisher : CRC Press
ISBN 13 : 0429627955
Total Pages : 211 pages
Book Rating : 4.4/5 (296 download)

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Book Synopsis Reproducible Research with R and RStudio by : Christopher Gandrud

Download or read book Reproducible Research with R and RStudio written by Christopher Gandrud and published by CRC Press. This book was released on 2020-02-21 with total page 211 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309664063
Total Pages : 143 pages
Book Rating : 4.3/5 (96 download)

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Book Synopsis Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting by : National Academies of Sciences, Engineering, and Medicine

Download or read book Enhancing Scientific Reproducibility in Biomedical Research Through Transparent Reporting written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2020-04-28 with total page 143 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sharing knowledge is what drives scientific progress - each new advance or innovation in biomedical research builds on previous observations. However, for experimental findings to be broadly accepted as credible by the scientific community, they must be verified by other researchers. An essential step is for researchers to report their findings in a manner that is understandable to others in the scientific community and provide sufficient information for others to validate the original results and build on them. In recent years, concern has been growing over a number of studies that have failed to replicate previous results and evidence from larger meta-analyses, which have pointed to the lack of reproducibility in biomedical research. On September 25 and 26, 2019, the National Academies of Science, Engineering, and Medicine hosted a public workshop in Washington, DC, to discuss the current state of transparency in the reporting of preclinical biomedical research and to explore opportunities for harmonizing reporting guidelines across journals and funding agencies. Convened jointly by the Forum on Drug Discovery, Development, and Translation; the Forum on Neuroscience and Nervous System Disorders; the National Cancer Policy Forum; and the Roundtable on Genomics and Precision Health, the workshop primarily focused on transparent reporting in preclinical research, but also considered lessons learned and best practices from clinical research reporting. This publication summarizes the presentation and discussion of the workshop.

Development Research in Practice

Author : Kristoffer Bjärkefur
Publisher : World Bank Publications
ISBN 13 : 1464816956
Total Pages : 388 pages
Book Rating : 4.4/5 (648 download)

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Book Synopsis Development Research in Practice by : Kristoffer Bjärkefur

Download or read book Development Research in Practice written by Kristoffer Bjärkefur and published by World Bank Publications. This book was released on 2021-07-16 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Transparent and Reproducible Social Science Research

Author : Garret Christensen
Publisher : University of California Press
ISBN 13 : 0520296931
Total Pages : 266 pages
Book Rating : 4.5/5 (22 download)

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Book Synopsis Transparent and Reproducible Social Science Research by : Garret Christensen

Download or read book Transparent and Reproducible Social Science Research written by Garret Christensen and published by University of California Press. This book was released on 2019-07-23 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Home Cage-based Phenotyping in Rodents: Innovation, Standardization, Reproducibility and Translational Improvement

Author : Stefano Gaburro
Publisher : Frontiers Media SA
ISBN 13 : 2889765989
Total Pages : 328 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis Home Cage-based Phenotyping in Rodents: Innovation, Standardization, Reproducibility and Translational Improvement by : Stefano Gaburro

Download or read book Home Cage-based Phenotyping in Rodents: Innovation, Standardization, Reproducibility and Translational Improvement written by Stefano Gaburro and published by Frontiers Media SA. This book was released on 2022-07-25 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Statistical Challenges in Assessing and Fostering the Reproducibility of Scientific Results

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309392020
Total Pages : 133 pages
Book Rating : 4.3/5 (93 download)

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Book Synopsis Statistical Challenges in Assessing and Fostering the Reproducibility of Scientific Results by : National Academies of Sciences, Engineering, and Medicine

Download or read book Statistical Challenges in Assessing and Fostering the Reproducibility of Scientific Results written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2016-03-29 with total page 133 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Research in the Biomedical Sciences

Author : Michael Williams
Publisher : Academic Press
ISBN 13 : 9780128047255
Total Pages : 0 pages
Book Rating : 4.0/5 (472 download)

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Book Synopsis Research in the Biomedical Sciences by : Michael Williams

Download or read book Research in the Biomedical Sciences written by Michael Williams and published by Academic Press. This book was released on 2017-10-10 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Research in the Biomedical Sciences: Transparent and Reproducible documents the widespread concerns related to reproducibility in biomedical research and provides a best practices guide to effective and transparent hypothesis generation, experimental design, reagent standardization (including validation and authentication), statistical analysis, and data reporting. The book addresses issues in the perceived value of the existing peer review process and calls for the need for improved transparency in data reporting. It reflects new guidelines for publication that include manuscript checklists, replication/reproducibility initiatives, and the potential consequences for the biomedical research community and societal health and well-being if training, mentoring, and funding of new generations of researchers and incentives for publications are not improved. This book offers real world examples, insights, and solutions to provide a thought-provoking and timely resource for all those learning about, or engaged in, performing and supervising research across the biomedical sciences.

Reproducible Research in Pattern Recognition

Author : Bertrand Kerautret
Publisher : Springer
ISBN 13 : 3319564145
Total Pages : 179 pages
Book Rating : 4.3/5 (195 download)

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Book Synopsis Reproducible Research in Pattern Recognition by : Bertrand Kerautret

Download or read book Reproducible Research in Pattern Recognition written by Bertrand Kerautret and published by Springer. This book was released on 2017-04-04 with total page 179 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Reproducible Finance with R

Author : Jonathan K. Regenstein, Jr.
Publisher : CRC Press
ISBN 13 : 1351052608
Total Pages : 248 pages
Book Rating : 4.3/5 (51 download)

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Book Synopsis Reproducible Finance with R by : Jonathan K. Regenstein, Jr.

Download or read book Reproducible Finance with R written by Jonathan K. Regenstein, Jr. and published by CRC Press. This book was released on 2018-09-24 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: Reproducible Finance with R: Code Flows and Shiny Apps for Portfolio Analysis is a unique introduction to data science for investment management that explores the three major R/finance coding paradigms, emphasizes data visualization, and explains how to build a cohesive suite of functioning Shiny applications. The full source code, asset price data and live Shiny applications are available at reproduciblefinance.com. The ideal reader works in finance or wants to work in finance and has a desire to learn R code and Shiny through simple, yet practical real-world examples. The book begins with the first step in data science: importing and wrangling data, which in the investment context means importing asset prices, converting to returns, and constructing a portfolio. The next section covers risk and tackles descriptive statistics such as standard deviation, skewness, kurtosis, and their rolling histories. The third section focuses on portfolio theory, analyzing the Sharpe Ratio, CAPM, and Fama French models. The book concludes with applications for finding individual asset contribution to risk and for running Monte Carlo simulations. For each of these tasks, the three major coding paradigms are explored and the work is wrapped into interactive Shiny dashboards.

The Practice of Reproducible Research

Author : Justin Kitzes
Publisher : Univ of California Press
ISBN 13 : 0520294742
Total Pages : 364 pages
Book Rating : 4.5/5 (22 download)

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Book Synopsis The Practice of Reproducible Research by : Justin Kitzes

Statistics Applied to Clinical Trials

Author : Ton J. Cleophas
Publisher : Springer Science & Business Media
ISBN 13 : 1402095236
Total Pages : 550 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Statistics Applied to Clinical Trials by : Ton J. Cleophas

Download or read book Statistics Applied to Clinical Trials written by Ton J. Cleophas and published by Springer Science & Business Media. This book was released on 2008-12-16 with total page 550 pages. Available in PDF, EPUB and Kindle. Book excerpt: In clinical medicine appropriate statistics has become indispensable to evaluate treatment effects. Randomized controlled trials are currently the only trials that truly provide evidence-based medicine. Evidence based medicine has become crucial to optimal treatment of patients. We can define randomized controlled trials by using Christopher J. Bulpitt’s definition “a carefully and ethically designed experiment which includes the provision of adequate and appropriate controls by a process of randomization, so that precisely framed questions can be answered”. The answers given by randomized controlled trials constitute at present the way how patients should be clinically managed. In the setup of such randomized trial one of the most important issues is the statistical basis. The randomized trial will never work when the statistical grounds and analyses have not been clearly defined beforehand. All endpoints should be clearly defined in order to perform appropriate power calculations. Based on these power calculations the exact number of available patients can be calculated in order to have a sufficient quantity of individuals to have the predefined questions answered. Therefore, every clinical physician should be capable to understand the statistical basis of well performed clinical trials. It is therefore a great pleasure that Drs. T. J. Cleophas, A. H. Zwinderman, and T. F. Cleophas have published a book on statistical analysis of clinical trials. The book entitled “Statistics Applied to Clinical Trials” is clearly written and makes complex issues in statistical analysis transparant.

Big Data Meets Survey Science

Author : Craig A. Hill
Publisher : John Wiley & Sons
ISBN 13 : 1118976320
Total Pages : 784 pages
Book Rating : 4.1/5 (189 download)

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Book Synopsis Big Data Meets Survey Science by : Craig A. Hill

Download or read book Big Data Meets Survey Science written by Craig A. Hill and published by John Wiley & Sons. This book was released on 2020-09-29 with total page 784 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Methods to Foster Transparency and Reproducibility of Federal Statistics

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309486327
Total Pages : 125 pages
Book Rating : 4.3/5 (94 download)

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Book Synopsis Methods to Foster Transparency and Reproducibility of Federal Statistics by : National Academies of Sciences, Engineering, and Medicine

Download or read book Methods to Foster Transparency and Reproducibility of Federal Statistics written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2019-03-01 with total page 125 pages. Available in PDF, EPUB and Kindle. Book excerpt: In 2014 the National Science Foundation (NSF) provided support to the National Academies of Sciences, Engineering, and Medicine for a series of Forums on Open Science in response to a government-wide directive to support increased public access to the results of research funded by the federal government. However, the breadth of the work resulting from the series precluded a focus on any specific topic or discussion about how to improve public access. Thus, the main goal of the Workshop on Transparency and Reproducibility in Federal Statistics was to develop some understanding of what principles and practices are, or would be, supportive of making federal statistics more understandable and reviewable, both by agency staff and the public. This publication summarizes the presentations and discussions from the workshop.