The Practice Of Reproducible Research
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The Practice Of Reproducible Research
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Author : Justin Kitzes
language : en
Publisher: Univ of California Press
Release Date : 2018
The Practice Of Reproducible Research written by Justin Kitzes and has been published by Univ of California Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018 with Computers categories.
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
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Author : Victoria Stodden
language : en
Publisher: CRC Press
Release Date : 2018-12-14
Implementing Reproducible Research written by Victoria Stodden and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-12-14 with Mathematics categories.
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.
Reproducible Research With R And Rstudio
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Author : Christopher Gandrud
language : en
Publisher: CRC Press
Release Date : 2020-02-21
Reproducible Research With R And Rstudio written by Christopher Gandrud and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-02-21 with Business & Economics categories.
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
Stochastic Modeling In Hydrogeology
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Author : J. Jaime Gómez-Hernández
language : en
Publisher: Frontiers Media SA
Release Date : 2021-07-14
Stochastic Modeling In Hydrogeology written by J. Jaime Gómez-Hernández and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-07-14 with Science categories.
Dr. Andres Alcolea is employed by Geo-Energie Suisse AG and is the funder and CEO of HydroGeoModels. All other Topic Editors declare no competing interests with regards to the Research Topic subject
Bioinformatics Data Skills
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Author : Vince Buffalo
language : en
Publisher: "O'Reilly Media, Inc."
Release Date : 2015-07
Bioinformatics Data Skills written by Vince Buffalo and has been published by "O'Reilly Media, Inc." this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-07 with Computers categories.
Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, youâ??ll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand lifeâ??s complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, youâ??re ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM Manage your bioinformatics project with the Git version control system Tackle tedious data processing tasks with with Bash scripts and Makefiles
Ontology Epistemology And Teleology For Modeling And Simulation
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Author : Andreas Tolk
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-08-10
Ontology Epistemology And Teleology For Modeling And Simulation written by Andreas Tolk and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-08-10 with Technology & Engineering categories.
In this book, internationally recognized experts in philosophy of science, computer science, and modeling and simulation are contributing to the discussion on how ontology, epistemology, and teleology will contribute to enable the next generation of intelligent modeling and simulation applications. It is well understood that a simulation can provide the technical means to display the behavior of a system over time, including following observed trends to predict future possible states, but how reliable and trustworthy are such predictions? The questions about what we can know (ontology), how we gain new knowledge (epistemology), and what we do with this knowledge (teleology) are therefore illuminated from these very different perspectives, as each experts uses a different facet to look at these challenges. The result of bringing these perspectives into one book is a challenging compendium that gives room for a spectrum of challenges: from general philosophy questions, such as can we use modeling and simulation and other computational means at all to discover new knowledge, down to computational methods to improve semantic interoperability between systems or methods addressing how to apply the recent insights of service oriented approaches to support distributed artificial intelligence. As such, this book has been compiled as an entry point to new domains for students, scholars, and practitioners and to raise the curiosity in them to learn more to fully address the topics of ontology, epistemology, and teleology from philosophical, computational, and conceptual viewpoints.
Opening Science
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Author : Sönke Bartling
language : en
Publisher: Springer
Release Date : 2013-12-16
Opening Science written by Sönke Bartling and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-12-16 with Science categories.
Modern information and communication technologies, together with a cultural upheaval within the research community, have profoundly changed research in nearly every aspect. Ranging from sharing and discussing ideas in social networks for scientists to new collaborative environments and novel publication formats, knowledge creation and dissemination as we know it is experiencing a vigorous shift towards increased transparency, collaboration and accessibility. Many assume that research workflows will change more in the next 20 years than they have in the last 200. This book provides researchers, decision makers, and other scientific stakeholders with a snapshot of the basics, the tools, and the underlying visions that drive the current scientific (r)evolution, often called ‘Open Science.’
Computational Frameworks
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Author : Mamadou Kaba Traore
language : en
Publisher: Elsevier
Release Date : 2017-07-07
Computational Frameworks written by Mamadou Kaba Traore and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-07-07 with Computers categories.
Computational Frameworks: Systems, Models and Applications provides an overview of advanced perspectives that bridges the gap between frontline research and practical efforts. It is unique in showing the interdisciplinary nature of this area and the way in which it interacts with emerging technologies and techniques. As computational systems are a dominating part of daily lives and a required support for most of the engineering sciences, this book explores their usage (e.g. big data, high performance clusters, databases and information systems, integrated and embedded hardware/software components, smart devices, mobile and pervasive networks, cyber physical systems, etc.). - Provides a unique presentation on the views of frontline researchers on computational systems theory and applications in one holistic scope - Cover both computational science and engineering - Bridges the gap between frontline research and practical efforts
Beginner S Guide To R Programming
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Author : Agasti Khatri
language : en
Publisher: Educohack Press
Release Date : 2025-02-20
Beginner S Guide To R Programming written by Agasti Khatri and has been published by Educohack Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-02-20 with Computers categories.
Discover the world of data analysis with "Beginner's Guide to R Programming." This comprehensive resource is crafted to help individuals learn the R programming language and explore its diverse applications. Whether you're a complete beginner or an experienced analyst, our book offers a structured learning path that starts with the basics and progresses to advanced topics like statistical analysis, data visualization, and machine learning. Each chapter includes practical examples, exercises, and real-world case studies, encouraging hands-on experimentation with R code. You'll delve into data types, functions, data manipulation, statistical analysis, data visualization, and more, building a solid foundation in R programming and data analysis. Complex concepts are explained in clear, easy-to-understand language, with visual aids, code snippets, and step-by-step tutorials to help you grasp key ideas effectively. The book emphasizes practical applications of R in real-world scenarios, showcasing how you can use R to solve problems, analyze data, make informed decisions, and communicate insights. With access to supplementary resources, including downloadable datasets, code samples, and additional exercises, you'll further enhance your learning experience and practice your skills.
Scientific Research And Methodology
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Author : Peter K. Dunn
language : en
Publisher: CRC Press
Release Date : 2025-08-19
Scientific Research And Methodology written by Peter K. Dunn and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-08-19 with Mathematics categories.
This textbook is designed for teaching quantitative research in the scientific, health and engineering disciplines at first-year undergraduate level, with an emphasis on statistics. It covers the research process, including asking research questions, research design, data collection, summarising data, analysis and communication. Many real journal articles are used throughout the text as examples that demonstrate the use of the techniques. Students are introduced to statistics as a method for answering questions. Descriptive research questions lead to analysis of single proportions and means. Repeated-measures research questions are answered using paired quantitative data. Relational research questions compare proportions, odds and means in different groups. Correlational research questions are studied using correlation and regression techniques. Statistical topics include numerical summary methods (such as means, odds ratios and identification of outliers), graphing (such as histograms, case-profile plots and scatterplots), confidence intervals and hypothesis testing. Emphasis is placed on understanding and concepts; while calculations are shown in simple situations, they are deferred to software when the computations become tedious and disruptive to understanding. Almost every dataset used is a real dataset, and is available online or in an associated R package SRMData. Software output is often used when calculations become onerous. The output is sufficiently generic that the book can be used in conjunction with any statistical software.