Data Integration Manipulation And Visualization Of Phylogenetic Trees

Author : Guangchuang Yu
Publisher : CRC Press
Page : 298 pages
File Size : 49,9 Mb
Release : 2022-08-26
Category : Medical
ISBN : 9781000613018

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Data Integration, Manipulation and Visualization of Phylogenetic Trees by Guangchuang Yu Pdf

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

Author : Emmanuel Paradis
Publisher : Springer Science & Business Media
Page : 221 pages
File Size : 50,8 Mb
Release : 2006-11-25
Category : Science
ISBN : 9780387351001

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Analysis of Phylogenetics and Evolution with R by Emmanuel Paradis Pdf

This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.

Author : Julia Silge,David Robinson
Publisher : "O'Reilly Media, Inc."
Page : 193 pages
File Size : 40,7 Mb
Release : 2017-06-12
Category : Computers
ISBN : 9781491981627

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Text Mining with R by Julia Silge,David Robinson Pdf

Chapter 7. Case Study : Comparing Twitter Archives; Getting the Data and Distribution of Tweets; Word Frequencies; Comparing Word Usage; Changes in Word Use; Favorites and Retweets; Summary; Chapter 8. Case Study : Mining NASA Metadata; How Data Is Organized at NASA; Wrangling and Tidying the Data; Some Initial Simple Exploration; Word Co-ocurrences and Correlations; Networks of Description and Title Words; Networks of Keywords; Calculating tf-idf for the Description Fields; What Is tf-idf for the Description Field Words?; Connecting Description Fields to Keywords; Topic Modeling.

Author : Florencio Pazos,Mónica Chagoyen
Publisher : Springer
Page : 111 pages
File Size : 53,9 Mb
Release : 2014-11-28
Category : Science
ISBN : 9783319127279

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Practical Protein Bioinformatics by Florencio Pazos,Mónica Chagoyen Pdf

This book describes more than 60 web-accessible computational tools for protein analysis and is totally practical, with detailed explanations on how to use these tools and interpret their results and minimal mentions to their theoretical basis (only when that is required for making a better use of them). It covers a wide range of tools for dealing with different aspects of proteins, from their sequences, to their three-dimensional structures, and the biological networks they are immersed in. The selection of tools is based on the experience of the authors that lead a protein bioinformatics facility in a large research centre, with the additional constraint that the tools should be accessible through standard web browsers without requiring the local installation of specific software, command-line tools, etc. The web tools covered include those aimed to retrieve protein information, look for similar proteins, generate pair-wise and multiple sequence alignments of protein sequences, work with protein domains and motifs, study the phylogeny of a family of proteins, retrieve, manipulate and visualize protein three-dimensional structures, predict protein structural features as well as whole three-dimensional structures, extract biological information from protein structures, summarize large protein sets, study protein interaction and metabolic networks, etc. The book is associated to a dynamic web site that will reflect changes in the web addresses of the tools, updates of these, etc. It also contains QR codes that can be scanned with any device to direct its browser to the tool web site. This monograph will be most valuable for researchers in experimental labs without specific knowledge on bioinformatics or computing.

Author : Nathan G. Swenson
Publisher : Springer Science & Business Media
Page : 217 pages
File Size : 55,8 Mb
Release : 2014-03-26
Category : Computers
ISBN : 9781461495420

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Functional and Phylogenetic Ecology in R by Nathan G. Swenson Pdf

Functional and Phylogenetic Ecology in R is designed to teach readers to use R for phylogenetic and functional trait analyses. Over the past decade, a dizzying array of tools and methods were generated to incorporate phylogenetic and functional information into traditional ecological analyses. Increasingly these tools are implemented in R, thus greatly expanding their impact. Researchers getting started in R can use this volume as a step-by-step entryway into phylogenetic and functional analyses for ecology in R. More advanced users will be able to use this volume as a quick reference to understand particular analyses. The volume begins with an introduction to the R environment and handling relevant data in R. Chapters then cover phylogenetic and functional metrics of biodiversity; null modeling and randomizations for phylogenetic and functional trait analyses; integrating phylogenetic and functional trait information; and interfacing the R environment with a popular C-based program. This book presents a unique approach through its focus on ecological analyses and not macroevolutionary analyses. The author provides his own code, so that the reader is guided through the computational steps to calculate the desired metrics. This guided approach simplifies the work of determining which package to use for any given analysis. Example datasets are shared to help readers practice, and readers can then quickly turn to their own datasets.

Author : Javier Luraschi,Kevin Kuo,Edgar Ruiz
Publisher : "O'Reilly Media, Inc."
Page : 296 pages
File Size : 55,9 Mb
Release : 2019-10-07
Category : Computers
ISBN : 9781492046325

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Mastering Spark with R by Javier Luraschi,Kevin Kuo,Edgar Ruiz Pdf

If you’re like most R users, you have deep knowledge and love for statistics. But as your organization continues to collect huge amounts of data, adding tools such as Apache Spark makes a lot of sense. With this practical book, data scientists and professionals working with large-scale data applications will learn how to use Spark from R to tackle big data and big compute problems. Authors Javier Luraschi, Kevin Kuo, and Edgar Ruiz show you how to use R with Spark to solve different data analysis problems. This book covers relevant data science topics, cluster computing, and issues that should interest even the most advanced users. Analyze, explore, transform, and visualize data in Apache Spark with R Create statistical models to extract information and predict outcomes; automate the process in production-ready workflows Perform analysis and modeling across many machines using distributed computing techniques Use large-scale data from multiple sources and different formats with ease from within Spark Learn about alternative modeling frameworks for graph processing, geospatial analysis, and genomics at scale Dive into advanced topics including custom transformations, real-time data processing, and creating custom Spark extensions

Author : SUSAN. HUBER HOLMES (WOLFGANG.),Wolfgang Huber
Publisher : Cambridge University Press
Page : 407 pages
File Size : 55,9 Mb
Release : 2018
Category : Electronic
ISBN : 9781108427029

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Modern Statistics for Modern Biology by SUSAN. HUBER HOLMES (WOLFGANG.),Wolfgang Huber Pdf

Author : Ben Fry
Publisher : "O'Reilly Media, Inc."
Page : 384 pages
File Size : 49,8 Mb
Release : 2008
Category : Computers
ISBN : 9780596519308

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Visualizing Data by Ben Fry Pdf

Provides information on the methods of visualizing data on the Web, along with example projects and code.

Author : Carson Sievert
Publisher : CRC Press
Page : 278 pages
File Size : 48,9 Mb
Release : 2020-01-30
Category : Business & Economics
ISBN : 9780429824203

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Interactive Web-Based Data Visualization with R, plotly, and shiny by Carson Sievert Pdf

The richly illustrated Interactive Web-Based Data Visualization with R, plotly, and shiny focuses on the process of programming interactive web graphics for multidimensional data analysis. It is written for the data analyst who wants to leverage the capabilities of interactive web graphics without having to learn web programming. Through many R code examples, you will learn how to tap the extensive functionality of these tools to enhance the presentation and exploration of data. By mastering these concepts and tools, you will impress your colleagues with your ability to quickly generate more informative, engaging, and reproducible interactive graphics using free and open source software that you can share over email, export to pdf, and more. Key Features: Convert static ggplot2 graphics to an interactive web-based form Link, animate, and arrange multiple plots in standalone HTML from R Embed, modify, and respond to plotly graphics in a shiny app Learn best practices for visualizing continuous, discrete, and multivariate data Learn numerous ways to visualize geo-spatial data This book makes heavy use of plotly for graphical rendering, but you will also learn about other R packages that support different phases of a data science workflow, such as tidyr, dplyr, and tidyverse. Along the way, you will gain insight into best practices for visualization of high-dimensional data, statistical graphics, and graphical perception. The printed book is complemented by an interactive website where readers can view movies demonstrating the examples and interact with graphics.

Author : Wolfgang Aigner,Silvia Miksch,Heidrun Schumann,Christian Tominski
Publisher : Springer Nature
Page : 453 pages
File Size : 55,5 Mb
Release : 2023-12-21
Category : Computers
ISBN : 9781447175278

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Visualization of Time-Oriented Data by Wolfgang Aigner,Silvia Miksch,Heidrun Schumann,Christian Tominski Pdf

This is an open access book. Time is an exceptional dimension with high relevance in medicine, engineering, business, science, biography, history, planning, or project management. Understanding time-oriented data via visual representations enables us to learn from the past in order to predict, plan, and build the future. This second edition builds upon the great success of the first edition. It maintains a brief introduction to visualization and a review of historical time-oriented visual representations. At its core, the book develops a systematic view of the visualization of time-oriented data. Separate chapters discuss interaction techniques and computational methods for supporting the visual data analysis. Many examples and figures illustrate the introduced concepts and techniques. So, what is new for the second edition? First of all, the second edition is now published as an open-access book so that anyone interested in the visualization of time and time-oriented data can read it. Second, the entire content has been revised and expanded to represent state-of-the-art knowledge. The chapter on interaction support now includes advanced methods for interacting with visual representations of time-oriented data. The second edition also covers the topics of data quality as well as segmentation and labeling. The comprehensive survey of classic and contemporary visualization techniques now provides more than 150 self-contained descriptions accompanied by illustrations and corresponding references. A completely new chapter describes how the structured survey can be used for the guided selection of suitable visualization techniques. For the second edition, our TimeViz Browser, the digital pendant to the survey of visualization techniques, received a major upgrade. It includes the same set of techniques as the book, but comes with additional filter and search facilities allowing scientists and practitioners to find exactly the solutions they are interested in.

Author : Sharon Machlis
Publisher : CRC Press
Page : 379 pages
File Size : 49,9 Mb
Release : 2018-12-21
Category : Mathematics
ISBN : 9780429681752

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Practical R for Mass Communication and Journalism by Sharon Machlis Pdf

Do you want to use R to tell stories? This book was written for you—whether you already know some R or have never coded before. Most R texts focus only on programming or statistical theory. Practical R for Mass Communication and Journalism gives you ideas, tools, and techniques for incorporating data and visualizations into your narratives. You’ll see step by step how to: Analyze airport flight delays, restaurant inspections, and election results Map bank locations, median incomes, and new voting districts Compare campaign contributions to final election results Extract data from PDFs Whip messy data into shape for analysis Scrape data from a website Create graphics ranging from simple, static charts to interactive visualizations for the Web If you work or plan to work in a newsroom, government office, non-profit policy organization, or PR office, Practical R for Mass Communication and Journalism will help you use R in your world. This book has a companion website with code, links to additional resources, and searchable tables by function and task. Sharon Machlis is the author of Computerworld’s Beginner’s Guide to R, host of InfoWorld’s Do More With R video screencast series, admin for the R for Journalists Google Group, and is well known among Twitter users who follow the #rstats hashtag. She is Director of Editorial Data and Analytics at IDG Communications (parent company of Computerworld, InfoWorld, PC World and Macworld, among others) and a frequent speaker at data journalism and R conferences.

Author : Michael J. Crawley
Publisher : John Wiley & Sons
Page : 953 pages
File Size : 47,7 Mb
Release : 2007-06-13
Category : Mathematics
ISBN : 0470515066

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The R Book by Michael J. Crawley Pdf

The high-level language of R is recognized as one of the mostpowerful and flexible statistical software environments, and israpidly becoming the standard setting for quantitative analysis,statistics and graphics. R provides free access to unrivalledcoverage and cutting-edge applications, enabling the user to applynumerous statistical methods ranging from simple regression to timeseries or multivariate analysis. Building on the success of the author’s bestsellingStatistics: An Introduction using R, The R Book ispacked with worked examples, providing an all inclusive guide to R,ideal for novice and more accomplished users alike. The bookassumes no background in statistics or computing and introduces theadvantages of the R environment, detailing its applications in awide range of disciplines. Provides the first comprehensive reference manual for the Rlanguage, including practical guidance and full coverage of thegraphics facilities. Introduces all the statistical models covered by R, beginningwith simple classical tests such as chi-square and t-test. Proceeds to examine more advance methods, from regression andanalysis of variance, through to generalized linear models,generalized mixed models, time series, spatial statistics,multivariate statistics and much more. The R Book is aimed at undergraduates, postgraduates andprofessionals in science, engineering and medicine. It is alsoideal for students and professionals in statistics, economics,geography and the social sciences.

Author : Ward Wheeler
Publisher : Unknown
Page : 380 pages
File Size : 47,5 Mb
Release : 2006
Category : Nature
ISBN : UVA:X030204917

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Dynamic Homology and Phylogenetic Systematics by Ward Wheeler Pdf

Author : Paola Zuccolotto,Marica Manisera
Publisher : CRC Press
Page : 245 pages
File Size : 41,6 Mb
Release : 2020-01-03
Category : Business & Economics
ISBN : 9780429894268

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Basketball Data Science by Paola Zuccolotto,Marica Manisera Pdf

Using data from one season of NBA games, Basketball Data Science: With Applications in R is the perfect book for anyone interested in learning and applying data analytics in basketball. Whether assessing the spatial performance of an NBA player's shots or doing an analysis of the impact of high pressure game situations on the probability of scoring, this book discusses a variety of case studies and hands-on examples using a custom R package. The codes are supplied so readers can reproduce the analyses themselves or create their own. Assuming a basic statistical knowledge, Basketball Data Science with R is suitable for students, technicians, coaches, data analysts and applied researchers. Features: One of the first books to provide statistical and data mining methods for the growing field of analytics in basketball Presents tools for modelling graphs and figures to visualize the data Includes real world case studies and examples, such as estimations of scoring probability using the Golden State Warriors as a test case Provides the source code and data so readers can do their own analyses on NBA teams and players

Author : Greg Wilson
Publisher : CRC Press
Page : 250 pages
File Size : 45,8 Mb
Release : 2019-10-08
Category : Computers
ISBN : 9781000728156

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Teaching Tech Together by Greg Wilson Pdf

Hundreds of grassroots groups have sprung up around the world to teach programming, web design, robotics, and other skills outside traditional classrooms. These groups exist so that people don't have to learn these things on their own, but ironically, their founders and instructors are often teaching themselves how to teach. There's a better way. This book presents evidence-based practices that will help you create and deliver lessons that work and build a teaching community around them. Topics include the differences between different kinds of learners, diagnosing and correcting misunderstandings, teaching as a performance art, what motivates and demotivates adult learners, how to be a good ally, fostering a healthy community, getting the word out, and building alliances with like-minded groups. The book includes over a hundred exercises that can be done individually or in groups, over 350 references, and a glossary to help you navigate educational jargon.