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Data Integration, Manipulation and Visualization of Phylogenetic Trees

Author : Guangchuang Yu
Publisher :
ISBN 13 : 9781032245546
Total Pages : 0 pages
Book Rating : 4.2/5 (455 download)

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Book Synopsis Data Integration, Manipulation and Visualization of Phylogenetic Trees by : Guangchuang Yu

Download or read book Data Integration, Manipulation and Visualization of Phylogenetic Trees written by Guangchuang Yu and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Data Integration, Manipulation and Visualization of Phylogenetic Trees introduces and demonstrates data integration, manipulation and visualization of phylogenetic trees using a suite of R packages, tidytree, treeio, ggtree and ggtreeExtra. Using the most comprehensive packages for phylogenetic data integration and visualization, contains numerous examples that can be used for teaching and learning. Ideal for undergraduate readers and researchers with a working knowledge of R and ggplot2. Key Features: Manipulating phylogenetic tree with associated data using tidy verbs Integrating phylogenetic data from diverse sources Visualizing phylogenetic data using grammar of graphics

R Markdown

Author : Yihui Xie
Publisher : CRC Press
ISBN 13 : 0429782969
Total Pages : 307 pages
Book Rating : 4.4/5 (297 download)

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Book Synopsis R Markdown by : Yihui Xie

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.

bookdown

Author : Yihui Xie
Publisher : CRC Press
ISBN 13 : 1351792601
Total Pages : 140 pages
Book Rating : 4.3/5 (517 download)

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Book Synopsis bookdown by : Yihui Xie

Download or read book bookdown written by Yihui Xie and published by CRC Press. This book was released on 2016-12-12 with total page 140 pages. Available in PDF, EPUB and Kindle. Book excerpt: bookdown: Authoring Books and Technical Documents with R Markdown presents a much easier way to write books and technical publications than traditional tools such as LaTeX and Word. The bookdown package inherits the simplicity of syntax and flexibility for data analysis from R Markdown, and extends R Markdown for technical writing, so that you can make better use of document elements such as figures, tables, equations, theorems, citations, and references. Similar to LaTeX, you can number and cross-reference these elements with bookdown. Your document can even include live examples so readers can interact with them while reading the book. The book can be rendered to multiple output formats, including LaTeX/PDF, HTML, EPUB, and Word, thus making it easy to put your documents online. The style and theme of these output formats can be customized. We used books and R primarily for examples in this book, but bookdown is not only for books or R. Most features introduced in this book also apply to other types of publications: journal papers, reports, dissertations, course handouts, study notes, and even novels. You do not have to use R, either. Other choices of computing languages include Python, C, C++, SQL, Bash, Stan, JavaScript, and so on, although R is best supported. You can also leave out computing, for example, to write a fiction. This book itself is an example of publishing with bookdown and R Markdown, and its source is fully available on GitHub.

EnvStats

Author : Steven P. Millard
Publisher : Springer Science & Business Media
ISBN 13 : 1461484561
Total Pages : 305 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis EnvStats by : Steven P. Millard

Download or read book EnvStats written by Steven P. Millard and published by Springer Science & Business Media. This book was released on 2013-10-16 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes EnvStats, a new comprehensive R package for environmental statistics and the successor to the S-PLUS module EnvironmentalStats for S-PLUS (first released in 1997). EnvStats and R provide an open-source set of powerful functions for performing graphical and statistical analyses of environmental data, bringing major environmental statistical methods found in the literature and regulatory guidance documents into one statistical package, along with an extensive hypertext help system that explains what these methods do, how to use these methods, and where to find them in the environmental statistics literature. EnvStats also includes numerous built-in data sets from regulatory guidance documents and the environmental statistics literature. This book shows how to use EnvStats and R to easily: * graphically display environmental data * plot probability distributions * estimate distribution parameters and construct confidence intervals on the original scale for commonly used distributions such as the lognormal and gamma, as well as do this nonparametrically * estimate and construct confidence intervals for distribution percentiles or do this nonparametrically (e.g., to compare to an environmental protection standard) * perform and plot the results of goodness-of-fit tests * compute optimal Box-Cox data transformations * compute prediction limits and simultaneous prediction limits (e.g., to assess compliance at multiple sites for multiple constituents) * perform nonparametric estimation and test for seasonal trend (even in the presence of correlated observations) * perform power and sample size computations and create companion plots for sampling designs based on confidence intervals, hypothesis tests, prediction intervals, and tolerance intervals * deal with non-detect (censored) data * perform Monte Carlo simulation and probabilistic risk assessment * reproduce specific examples in EPA guidance documents EnvStats combined with other R packages (e.g., for spatial analysis) provides the environmental scientist, statistician, researcher, and technician with tools to “get the job done!”

Explanatory Model Analysis

Author : Przemyslaw Biecek
Publisher : CRC Press
ISBN 13 : 0429651376
Total Pages : 312 pages
Book Rating : 4.4/5 (296 download)

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Book Synopsis Explanatory Model Analysis by : Przemyslaw Biecek

Download or read book Explanatory Model Analysis written by Przemyslaw Biecek and published by CRC Press. This book was released on 2021-02-15 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: Explanatory Model Analysis Explore, Explain and Examine Predictive Models is a set of methods and tools designed to build better predictive models and to monitor their behaviour in a changing environment. Today, the true bottleneck in predictive modelling is neither the lack of data, nor the lack of computational power, nor inadequate algorithms, nor the lack of flexible models. It is the lack of tools for model exploration (extraction of relationships learned by the model), model explanation (understanding the key factors influencing model decisions) and model examination (identification of model weaknesses and evaluation of model's performance). This book presents a collection of model agnostic methods that may be used for any black-box model together with real-world applications to classification and regression problems.

Data Depth

Author : Regina Y. Liu
Publisher : American Mathematical Soc.
ISBN 13 : 0821835963
Total Pages : 264 pages
Book Rating : 4.8/5 (218 download)

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Book Synopsis Data Depth by : Regina Y. Liu

Download or read book Data Depth written by Regina Y. Liu and published by American Mathematical Soc.. This book was released on 2006 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book is a collection of some of the research presented at the workshop of the same name held in May 2003 at Rutgers University. The workshop brought together researchers from two different communities: statisticians and specialists in computational geometry. The main idea unifying these two research areas turned out to be the notion of data depth, which is an important notion both in statistics and in the study of efficiency of algorithms used in computational geometry. Many of the articles in the book lay down the foundations for further collaboration and interdisciplinary research. Information for our distributors: Co-published with the Center for Discrete Mathematics and Theoretical Computer Science beginning with Volume 8. Volumes 1-7 were co-published with the Association for Computer Machinery (ACM).

Pedigree Analysis in R

Author : Magnus Dehli Vigeland
Publisher : Elsevier
ISBN 13 : 0128244305
Total Pages : 184 pages
Book Rating : 4.1/5 (282 download)

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Book Synopsis Pedigree Analysis in R by : Magnus Dehli Vigeland

Download or read book Pedigree Analysis in R written by Magnus Dehli Vigeland and published by Elsevier. This book was released on 2021-04-27 with total page 184 pages. Available in PDF, EPUB and Kindle. Book excerpt: Pedigree Analysis in R gives an introduction to the theory of relatedness and covers a range of applications in forensic and medical genetics. The book's material was developed through teaching courses on genetic relatedness, pedigree analysis and R, and offers insights from a decade of research activities in forensic and medical genetics. The R code in the book uses the ped suite, a unified collection of packages for pedigree analysis, developed by the author. All code examples are given in full, allowing accurate reproduction of figures and results. At the end of each chapter, a selection of exercises encourages the reader to explore further and perform their own analyses. Introduction to the theory of genetic relatedness, richly illustrated with classic and novel examples In-depth case studies including kinship testing, pedigree reconstruction, linkage analysis and clinical segregation analysis Easy-to-follow R code with explanations Based on the ped suite packages for pedigree analysis in R Suitable for R users at all levels, including complete beginners Exercises after each chapter

Proteomics Data Analysis

Author : Daniela Cecconi
Publisher :
ISBN 13 : 9781071616413
Total Pages : 326 pages
Book Rating : 4.6/5 (164 download)

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Book Synopsis Proteomics Data Analysis by : Daniela Cecconi

Download or read book Proteomics Data Analysis written by Daniela Cecconi and published by . This book was released on 2021 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough book collects methods and strategies to analyze proteomics data. It is intended to describe how data obtained by gel-based or gel-free proteomics approaches can be inspected, organized, and interpreted to extrapolate biological information. Organized into four sections, the volume explores strategies to analyze proteomics data obtained by gel-based approaches, different data analysis approaches for gel-free proteomics experiments, bioinformatic tools for the interpretation of proteomics data to obtain biological significant information, as well as methods to integrate proteomics data with other omics datasets including genomics, transcriptomics, metabolomics, and other types of data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that will ensure high quality results in the lab. Authoritative and practical, Proteomics Data Analysis serves as an ideal guide to introduce researchers, both experienced and novice, to new tools and approaches for data analysis to encourage the further study of proteomics.