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.

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.

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.

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.

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 212 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

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

Download or read book Psychological Science Under Scrutiny written by Scott O. Lilienfeld and published by John Wiley & Sons. This book was released on 2017-01-03 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: Psychological Science Under Scrutiny explores a range of contemporary challenges to the assumptions and methodologies of psychology, in order to encourage debate and ground the discipline in solid science. Discusses the pointed challenges posed by critics to the field of psychological research, which have given pause to psychological researchers across a broad spectrum of sub-fields Argues that those conducting psychological research need to fundamentally change the way they think about data and results, in order to ensure that psychology has a firm basis in empirical science Places the recent challenges discussed into a broad historical and conceptual perspective, and considers their implications for the future of psychological methodology and research Challenges discussed include confirmation bias, the effects of grant pressure, false-positive findings, overestimating the efficacy of medications, and high correlations in functional brain imaging Chapters are authored by internationally recognized experts in their fields, and are written with a minimum of specialized terminology to ensure accessibility to students and lay readers

Download or read book Reproducibility written by Harald Atmanspacher and published by John Wiley & Sons. This book was released on 2016-07-05 with total page 612 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book R for Data Science written by Hadley Wickham and published by "O'Reilly Media, Inc.". This book was released on 2016-12-12 with total page 521 pages. Available in PDF, EPUB and Kindle. Book excerpt: Learn how to use R to turn raw data into insight, knowledge, and understanding. This book introduces you to R, RStudio, and the tidyverse, a collection of R packages designed to work together to make data science fast, fluent, and fun. Suitable for readers with no previous programming experience, R for Data Science is designed to get you doing data science as quickly as possible. Authors Hadley Wickham and Garrett Grolemund guide you through the steps of importing, wrangling, exploring, and modeling your data and communicating the results. You'll get a complete, big-picture understanding of the data science cycle, along with basic tools you need to manage the details. Each section of the book is paired with exercises to help you practice what you've learned along the way. You'll learn how to: Wrangle—transform your datasets into a form convenient for analysis Program—learn powerful R tools for solving data problems with greater clarity and ease Explore—examine your data, generate hypotheses, and quickly test them Model—provide a low-dimensional summary that captures true "signals" in your dataset Communicate—learn R Markdown for integrating prose, code, and results

Download or read book Engaging Researchers with Data Management The Cookbook written by Connie Clare and published by Open Book Publishers. This book was released on 2019-10-09 with total page 111 pages. Available in PDF, EPUB and Kindle. Book excerpt: Effective Research Data Management (RDM) is a key component of research integrity and reproducible research, and its importance is increasingly emphasised by funding bodies, governments, and research institutions around the world. However, many researchers are unfamiliar with RDM best practices, and research support staff are faced with the difficult task of delivering support to researchers across different disciplines and career stages. What strategies can institutions use to solve these problems? Engaging Researchers with Data Management is an invaluable collection of 24 case studies, drawn from institutions across the globe, that demonstrate clearly and practically how to engage the research community with RDM. These case studies together illustrate the variety of innovative strategies research institutions have developed to engage with their researchers about managing research data. Each study is presented concisely and clearly, highlighting the essential ingredients that led to its success and challenges encountered along the way. By interviewing key staff about their experiences and the organisational context, the authors of this book have created an essential resource for organisations looking to increase engagement with their research communities. This handbook is a collaboration by research institutions, for research institutions. It aims not only to inspire and engage, but also to help drive cultural change towards better data management. It has been written for anyone interested in RDM, or simply, good research practice.

Download or read book Statistics Done Wrong written by Alex Reinhart and published by No Starch Press. This book was released on 2015-03-01 with total page 177 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific progress depends on good research, and good research needs good statistics. But statistical analysis is tricky to get right, even for the best and brightest of us. You'd be surprised how many scientists are doing it wrong. Statistics Done Wrong is a pithy, essential guide to statistical blunders in modern science that will show you how to keep your research blunder-free. You'll examine embarrassing errors and omissions in recent research, learn about the misconceptions and scientific politics that allow these mistakes to happen, and begin your quest to reform the way you and your peers do statistics. You'll find advice on: –Asking the right question, designing the right experiment, choosing the right statistical analysis, and sticking to the plan –How to think about p values, significance, insignificance, confidence intervals, and regression –Choosing the right sample size and avoiding false positives –Reporting your analysis and publishing your data and source code –Procedures to follow, precautions to take, and analytical software that can help Scientists: Read this concise, powerful guide to help you produce statistically sound research. Statisticians: Give this book to everyone you know. The first step toward statistics done right is Statistics Done Wrong.

Download or read book Reproducible Research with R and R Studio written by Christopher Gandrud and published by CRC Press. This book was released on 2018-09-03 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Learning Statistics with R written by Daniel Navarro and published by Lulu.com. This book was released on 2013-01-13 with total page 617 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Learning Statistics with R" covers the contents of an introductory statistics class, as typically taught to undergraduate psychology students, focusing on the use of the R statistical software and adopting a light, conversational style throughout. The book discusses how to get started in R, and gives an introduction to data manipulation and writing scripts. From a statistical perspective, the book discusses descriptive statistics and graphing first, followed by chapters on probability theory, sampling and estimation, and null hypothesis testing. After introducing the theory, the book covers the analysis of contingency tables, t-tests, ANOVAs and regression. Bayesian statistics are covered at the end of the book. For more information (and the opportunity to check the book out before you buy!) visit http://ua.edu.au/ccs/teaching/lsr or http://learningstatisticswithr.com

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.

Download or read book Doing Developmental Research written by Tricia Striano and published by Guilford Publications. This book was released on 2016-02-19 with total page 192 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Subject Areas/Keywords: child development, children, developmental psychology, developmental research methods, developmental science, early childhood, infancy research, infants, parents, preschoolers, research laboratory, research studies DESCRIPTION Addressing practical issues rarely covered in methods texts, this userfriendly, jargonfree book helps students and beginning researchers plan infant and child development studies and get them done. The author provides stepbystep guidance for getting involved in a developmental laboratory and crafting effective research questions and proposals. Tips on recruiting study participants cover access issues--such as how to overcome language and cultural barriers--and include helpful sample scripts. The book offers time management strategies, pointers for organizing and communicating data, and a roadmap of the journal publication process, complete with an annotated sample article. Numerous concrete examples, checklists, worksheets, and exercises are featured. Reproducible forms can be downloaded and printed in a convenient 8 1/2" x 11" size"--

Download or read book R Markdown written by Yihui Xie and published by CRC Press. This book was released on 2018-07-27 with total page 307 pages. Available in PDF, EPUB and Kindle. Book excerpt: R Markdown: The Definitive Guide is the first official book authored by the core R Markdown developers that provides a comprehensive and accurate reference to the R Markdown ecosystem. With R Markdown, you can easily create reproducible data analysis reports, presentations, dashboards, interactive applications, books, dissertations, websites, and journal articles, while enjoying the simplicity of Markdown and the great power of R and other languages. In this book, you will learn Basics: Syntax of Markdown and R code chunks, how to generate figures and tables, and how to use other computing languages Built-in output formats of R Markdown: PDF/HTML/Word/RTF/Markdown documents and ioslides/Slidy/Beamer/PowerPoint presentations Extensions and applications: Dashboards, Tufte handouts, xaringan/reveal.js presentations, websites, books, journal articles, and interactive tutorials Advanced topics: Parameterized reports, HTML widgets, document templates, custom output formats, and Shiny documents. Yihui Xie is a software engineer at RStudio. He has authored and co-authored several R packages, including knitr, rmarkdown, bookdown, blogdown, shiny, xaringan, and animation. He has published three other books, Dynamic Documents with R and knitr, bookdown: Authoring Books and Technical Documents with R Markdown, and blogdown: Creating Websites with R Markdown. J.J. Allaire is the founder of RStudio and the creator of the RStudio IDE. He is an author of several packages in the R Markdown ecosystem including rmarkdown, flexdashboard, learnr, and radix. Garrett Grolemund is the co-author of R for Data Science and author of Hands-On Programming with R. He wrote the lubridate R package and works for RStudio as an advocate who trains engineers to do data science with R and the Tidyverse.

Download or read book Literate Programming written by Donald Ervin Knuth and published by Stanford Univ Center for the Study. This book was released on 1992-01 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Literate programming is a programming methodology that combines a programming language with a documentation language, making programs more easily maintained than programs written only in a high-level language. A literate programmer is an essayist who writes programs for humans to understand. When programs are written in the recommended style they can be transformed into documents by a document compiler and into efficient code by an algebraic compiler. This anthology of essays includes Knuth's early papers on related topics such as structured programming as well as the Computer Journal article that launched literate programming. Many examples are given, including excerpts from the programs for TeX and METAFONT. The final essay is an example of CWEB, a system for literate programming in C and related languages. Index included.