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: 0520294742

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.

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

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: 2014-04-14
Genre: Mathematics
ISBN: 1466561599

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.

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

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.

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

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

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

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

Psychological Science Under Scrutiny

Psychological Science Under Scrutiny
Author: Scott O. Lilienfeld
Publisher: John Wiley & Sons
Total Pages: 444
Release: 2017-01-03
Genre: Psychology
ISBN: 1118661044

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

R for Data Science

R for Data Science
Author: Hadley Wickham
Publisher: "O'Reilly Media, Inc."
Total Pages: 521
Release: 2016-12-12
Genre: Computers
ISBN: 1491910364

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

Engaging Researchers with Data Management: The Cookbook

Engaging Researchers with Data Management: The Cookbook
Author: Connie Clare
Publisher: Open Book Publishers
Total Pages: 111
Release: 2019-10-09
Genre: Computers
ISBN: 1783748001

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.

Reproducible Research with R and R Studio

Reproducible Research with R and R Studio
Author: Christopher Gandrud
Publisher: CRC Press
Total Pages: 316
Release: 2018-09-03
Genre: Business & Economics
ISBN: 1315360721

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.