Statistical Analysis Of Microbiome Data

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Statistical Analysis of Microbiome Data

Author : Somnath Datta
Publisher : Springer Nature
ISBN 13 : 3030733513
Total Pages : 349 pages
Book Rating : 4.0/5 (37 download)

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Book Synopsis Statistical Analysis of Microbiome Data by : Somnath Datta

Download or read book Statistical Analysis of Microbiome Data written by Somnath Datta and published by Springer Nature. This book was released on 2021-10-27 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microbiome research has focused on microorganisms that live within the human body and their effects on health. During the last few years, the quantification of microbiome composition in different environments has been facilitated by the advent of high throughput sequencing technologies. The statistical challenges include computational difficulties due to the high volume of data; normalization and quantification of metabolic abundances, relative taxa and bacterial genes; high-dimensionality; multivariate analysis; the inherently compositional nature of the data; and the proper utilization of complementary phylogenetic information. This has resulted in an explosion of statistical approaches aimed at tackling the unique opportunities and challenges presented by microbiome data. This book provides a comprehensive overview of the state of the art in statistical and informatics technologies for microbiome research. In addition to reviewing demonstrably successful cutting-edge methods, particular emphasis is placed on examples in R that rely on available statistical packages for microbiome data. With its wide-ranging approach, the book benefits not only trained statisticians in academia and industry involved in microbiome research, but also other scientists working in microbiomics and in related fields.

Statistical Analysis of Microbiome Data with R

Author : Yinglin Xia
Publisher : Springer
ISBN 13 : 9811315345
Total Pages : 505 pages
Book Rating : 4.8/5 (113 download)

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Book Synopsis Statistical Analysis of Microbiome Data with R by : Yinglin Xia

Download or read book Statistical Analysis of Microbiome Data with R written by Yinglin Xia and published by Springer. This book was released on 2018-10-06 with total page 505 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique book addresses the statistical modelling and analysis of microbiome data using cutting-edge R software. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of R for data analysis step by step. The data and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter, so that these new methods can be readily applied in their own research. The book also discusses recent developments in statistical modelling and data analysis in microbiome research, as well as the latest advances in next-generation sequencing and big data in methodological development and applications. This timely book will greatly benefit all readers involved in microbiome, ecology and microarray data analyses, as well as other fields of research.

Bioinformatic and Statistical Analysis of Microbiome Data

Author : Yinglin Xia
Publisher : Springer Nature
ISBN 13 : 3031213912
Total Pages : 717 pages
Book Rating : 4.0/5 (312 download)

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Book Synopsis Bioinformatic and Statistical Analysis of Microbiome Data by : Yinglin Xia

Download or read book Bioinformatic and Statistical Analysis of Microbiome Data written by Yinglin Xia and published by Springer Nature. This book was released on 2023-06-16 with total page 717 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique book addresses the bioinformatic and statistical modelling and also the analysis of microbiome data using cutting-edge QIIME 2 and R software. It covers core analysis topics in both bioinformatics and statistics, which provides a complete workflow for microbiome data analysis: from raw sequencing reads to community analysis and statistical hypothesis testing. It includes real-world data from the authors’ research and from the public domain, and discusses the implementation of QIIME 2 and R for data analysis step-by-step. The data as well as QIIME 2 and R computer programs are publicly available, allowing readers to replicate the model development and data analysis presented in each chapter so that these new methods can be readily applied in their own research. Bioinformatic and Statistical Analysis of Microbiome Data is an ideal book for advanced graduate students and researchers in the clinical, biomedical, agricultural, and environmental fields, as well as those studying bioinformatics, statistics, and big data analysis.

Microbiome Analysis

Author : Robert G. Beiko
Publisher :
ISBN 13 : 9781493987283
Total Pages : 324 pages
Book Rating : 4.9/5 (872 download)

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Book Synopsis Microbiome Analysis by : Robert G. Beiko

Download or read book Microbiome Analysis written by Robert G. Beiko and published by . This book was released on 2018 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Handbook of Statistical Genomics

Author : David J. Balding
Publisher : John Wiley & Sons
ISBN 13 : 1119429250
Total Pages : 1828 pages
Book Rating : 4.1/5 (194 download)

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Book Synopsis Handbook of Statistical Genomics by : David J. Balding

Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.

Statistical Data Analysis of Microbiomes and Metabolomics

Author : Yinglin Xia
Publisher : American Chemical Society
ISBN 13 : 0841299161
Total Pages : 229 pages
Book Rating : 4.8/5 (412 download)

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Book Synopsis Statistical Data Analysis of Microbiomes and Metabolomics by : Yinglin Xia

Download or read book Statistical Data Analysis of Microbiomes and Metabolomics written by Yinglin Xia and published by American Chemical Society. This book was released on 2022-02-03 with total page 229 pages. Available in PDF, EPUB and Kindle. Book excerpt: Compared with other research fields, both microbiome and metabolomics data are complicated and have some unique characteristics, respectively. Thus, choosing an appropriate statistical test or method is a very important step in the analysis of microbiome and metabolomics data. However, this is still a difficult task for those biomedical researchers without a statistical background and for those biostatisticians who do not have research experiences in these fields. Graduate students studying microbiome and metabolomics; statisticians, working on microbiome and metabolomics projects, either for their own research, or for their collaborative research for experimental design, grant application, and data analysis; and researchers who investigate biomedical and biochemical projects with the microbiome, metabolome, and multi-omics data analysis will benefit from reading this work.

Applied Microbiome Statistics

Author : Yinglin Xia
Publisher : CRC Press
ISBN 13 : 1040045669
Total Pages : 457 pages
Book Rating : 4.0/5 (4 download)

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Book Synopsis Applied Microbiome Statistics by : Yinglin Xia

Download or read book Applied Microbiome Statistics written by Yinglin Xia and published by CRC Press. This book was released on 2024-07-22 with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique book officially defines microbiome statistics as a specific new field of statistics and addresses the statistical analysis of correlation, association, interaction, and composition in microbiome research. It also defines the study of the microbiome as a hypothesis-driven experimental science and describes two microbiome research themes and six unique characteristics of microbiome data, as well as investigating challenges for statistical analysis of microbiome data using the standard statistical methods. This book is useful for researchers of biostatistics, ecology, and data analysts. Presents a thorough overview of statistical methods in microbiome statistics of parametric and nonparametric correlation, association, interaction, and composition adopted from classical statistics and ecology and specifically designed for microbiome research. Performs step-by-step statistical analysis of correlation, association, interaction, and composition in microbiome data. Discusses the issues of statistical analysis of microbiome data: high dimensionality, compositionality, sparsity, overdispersion, zero-inflation, and heterogeneity. Investigates statistical methods on multiple comparisons and multiple hypothesis testing and applications to microbiome data. Introduces a series of exploratory tools to visualize composition and correlation of microbial taxa by barplot, heatmap, and correlation plot. Employs the Kruskal–Wallis rank-sum test to perform model selection for further multi-omics data integration. Offers R code and the datasets from the authors’ real microbiome research and publicly available data for the analysis used. Remarks on the advantages and disadvantages of each of the methods used.

Metagenomics for Microbiology

Author : Jacques Izard
Publisher : Academic Press
ISBN 13 : 0124105084
Total Pages : 188 pages
Book Rating : 4.1/5 (241 download)

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Book Synopsis Metagenomics for Microbiology by : Jacques Izard

Download or read book Metagenomics for Microbiology written by Jacques Izard and published by Academic Press. This book was released on 2014-11-07 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications. With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future. Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.

Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry

Author : Susmita Datta
Publisher : Springer
ISBN 13 : 3319458094
Total Pages : 295 pages
Book Rating : 4.3/5 (194 download)

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Book Synopsis Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry by : Susmita Datta

Download or read book Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry written by Susmita Datta and published by Springer. This book was released on 2016-12-15 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of computational and statistical design and analysis of mass spectrometry-based proteomics, metabolomics, and lipidomics data. This contributed volume provides an introduction to the special aspects of statistical design and analysis with mass spectrometry data for the new omic sciences. The text discusses common aspects of design and analysis between and across all (or most) forms of mass spectrometry, while also providing special examples of application with the most common forms of mass spectrometry. Also covered are applications of computational mass spectrometry not only in clinical study but also in the interpretation of omics data in plant biology studies. Omics research fields are expected to revolutionize biomolecular research by the ability to simultaneously profile many compounds within either patient blood, urine, tissue, or other biological samples. Mass spectrometry is one of the key analytical techniques used in these new omic sciences. Liquid chromatography mass spectrometry, time-of-flight data, and Fourier transform mass spectrometry are but a selection of the measurement platforms available to the modern analyst. Thus in practical proteomics or metabolomics, researchers will not only be confronted with new high dimensional data types—as opposed to the familiar data structures in more classical genomics—but also with great variation between distinct types of mass spectral measurements derived from different platforms, which may complicate analyses, comparison, and interpretation of results.

The Human Microbiome, Diet, and Health

Author : Food Forum
Publisher : National Academies Press
ISBN 13 : 030926586X
Total Pages : 197 pages
Book Rating : 4.3/5 (92 download)

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Book Synopsis The Human Microbiome, Diet, and Health by : Food Forum

Download or read book The Human Microbiome, Diet, and Health written by Food Forum and published by National Academies Press. This book was released on 2013-02-27 with total page 197 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Food Forum convened a public workshop on February 22-23, 2012, to explore current and emerging knowledge of the human microbiome, its role in human health, its interaction with the diet, and the translation of new research findings into tools and products that improve the nutritional quality of the food supply. The Human Microbiome, Diet, and Health: Workshop Summary summarizes the presentations and discussions that took place during the workshop. Over the two day workshop, several themes covered included: The microbiome is integral to human physiology, health, and disease. The microbiome is arguably the most intimate connection that humans have with their external environment, mostly through diet. Given the emerging nature of research on the microbiome, some important methodology issues might still have to be resolved with respect to undersampling and a lack of causal and mechanistic studies. Dietary interventions intended to have an impact on host biology via their impact on the microbiome are being developed, and the market for these products is seeing tremendous success. However, the current regulatory framework poses challenges to industry interest and investment.

Introduction to Statistics in Human Performance

Author : Dale P. Mood
Publisher : Taylor & Francis
ISBN 13 : 1351818821
Total Pages : 406 pages
Book Rating : 4.3/5 (518 download)

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Book Synopsis Introduction to Statistics in Human Performance by : Dale P. Mood

Download or read book Introduction to Statistics in Human Performance written by Dale P. Mood and published by Taylor & Francis. This book was released on 2017-06-30 with total page 406 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Our goal is to give readers the knowledge and skill to use statistics effectively in their professional lives and feel comfortable doing so."--From the Preface This new textbook, by two renowned authors with many years of teaching experience, provides: A sound overview of statistical procedures and introduction to the basics of statistical analyses An informal perspective that enables students to read, interpret, and use statistics directly related to their chosen careers in the kinesiology field (e.g., exercise physiology, physical therapy, medicine, personal training, nurse practitioner, physician’s assistant, and more) Relevant examples, review questions, practice problems, and SPSS activities, which help to make the material understandable and interesting A student website with videos, interactive concept reviews, image bank, and PowerPoint slides offers students the tools they need to understand the statistical concepts and learn at their own pace

Evolutionary Genomics

Author : Maria Anisimova
Publisher :
ISBN 13 : 9781617795824
Total Pages : pages
Book Rating : 4.7/5 (958 download)

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Book Synopsis Evolutionary Genomics by : Maria Anisimova

Download or read book Evolutionary Genomics written by Maria Anisimova and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Compositional Data Analysis

Author : Vera Pawlowsky-Glahn
Publisher : John Wiley & Sons
ISBN 13 : 0470711353
Total Pages : 401 pages
Book Rating : 4.4/5 (77 download)

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Book Synopsis Compositional Data Analysis by : Vera Pawlowsky-Glahn

Download or read book Compositional Data Analysis written by Vera Pawlowsky-Glahn and published by John Wiley & Sons. This book was released on 2011-09-19 with total page 401 pages. Available in PDF, EPUB and Kindle. Book excerpt: It is difficult to imagine that the statistical analysis of compositional data has been a major issue of concern for more than 100 years. It is even more difficult to realize that so many statisticians and users of statistics are unaware of the particular problems affecting compositional data, as well as their solutions. The issue of ``spurious correlation'', as the situation was phrased by Karl Pearson back in 1897, affects all data that measures parts of some whole, such as percentages, proportions, ppm and ppb. Such measurements are present in all fields of science, ranging from geology, biology, environmental sciences, forensic sciences, medicine and hydrology. This book presents the history and development of compositional data analysis along with Aitchison's log-ratio approach. Compositional Data Analysis describes the state of the art both in theoretical fields as well as applications in the different fields of science. Key Features: Reflects the state-of-the-art in compositional data analysis. Gives an overview of the historical development of compositional data analysis, as well as basic concepts and procedures. Looks at advances in algebra and calculus on the simplex. Presents applications in different fields of science, including, genomics, ecology, biology, geochemistry, planetology, chemistry and economics. Explores connections to correspondence analysis and the Dirichlet distribution. Presents a summary of three available software packages for compositional data analysis. Supported by an accompanying website featuring R code. Applied scientists working on compositional data analysis in any field of science, both in academia and professionals will benefit from this book, along with graduate students in any field of science working with compositional data.

Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases

Author : Jun Sun
Publisher : Springer
ISBN 13 : 149397534X
Total Pages : 381 pages
Book Rating : 4.4/5 (939 download)

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Book Synopsis Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases by : Jun Sun

Download or read book Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases written by Jun Sun and published by Springer. This book was released on 2018-01-26 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: Only recently have we begun to appreciate the role of microbiome in health and disease. Environmental factors and change of life style including diet significantly shape human microbiome that in turn appears to modify gut barrier function affecting nutrient & electrolyte absorption and inflammation. Approaches that can reverse the gut dysbiosis represent as reasonable and novel strategies for restoring the balance between host and microbes. In the book, we offer summary and discussion on the advances in understanding of pathophysiological mechanisms of microbial host interactions in human diseases. We will not only discuss intestinal bacterial community, but also viruses, fungi and oral microbiome. Microbiome studies will facilitate diagnosis, functional studies, drug development and personalized medicine. Thus, this book will further highlight the microbiome in the context of health and disease, focusing on mechanistic concepts that underlie the complex relationships between host and microbes.

Encyclopedia of Metagenomics

Author : Karen E. Nelson
Publisher : Springer
ISBN 13 : 9781461446743
Total Pages : 1528 pages
Book Rating : 4.4/5 (467 download)

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Book Synopsis Encyclopedia of Metagenomics by : Karen E. Nelson

Download or read book Encyclopedia of Metagenomics written by Karen E. Nelson and published by Springer. This book was released on 2015-02-18 with total page 1528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metagenomics has taken off as one of the major cutting-edge fields of research. The field has broad implications for human health and disease, animal production, and environmental health. Metagenomics has opened up a wealth of data, tools, technologies and applications that allow us to access the majority of organisms that we still cannot access in pure culture (an estimated 99% of microbial life). Numerous research groups are developing tools, approaches and applications to deal with this new field, as larger data sets from environments including the human body, the oceans and soils are being generated. See for example the human microbiome initiative (HMP; http://nihroadmap.nih.gov/hmp/) which has become a world-wide effort, and the Global Ocean Sampling (GOS) surveys; http://www.jcvi.org/cms/research/projects/gos/overview/). The number of publications as measured through PubMed that are focused on metagenomics continues to increase. The field of metagenomics continues to evolve with large common datasets available to the scientific community. A concerted effort is needed to collate all this information in a centralized place. By having all the information in an Encyclopedia form, we have an opportunity to gather seminal contributions from the leaders in the field, and at the same time provide this information to a significant number of junior and senior scientists. It is anticipated that the Encyclopedia will also be used by many other groups including, clinicians, undergraduate and graduate level students, as well as ethical and legal groups associated with or interested in the issues surrounding metagenome science.

Microbiomes of the Built Environment

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309449839
Total Pages : 318 pages
Book Rating : 4.3/5 (94 download)

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Book Synopsis Microbiomes of the Built Environment by : National Academies of Sciences, Engineering, and Medicine

Download or read book Microbiomes of the Built Environment written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2017-10-06 with total page 318 pages. Available in PDF, EPUB and Kindle. Book excerpt: People's desire to understand the environments in which they live is a natural one. People spend most of their time in spaces and structures designed, built, and managed by humans, and it is estimated that people in developed countries now spend 90 percent of their lives indoors. As people move from homes to workplaces, traveling in cars and on transit systems, microorganisms are continually with and around them. The human-associated microbes that are shed, along with the human behaviors that affect their transport and removal, make significant contributions to the diversity of the indoor microbiome. The characteristics of "healthy" indoor environments cannot yet be defined, nor do microbial, clinical, and building researchers yet understand how to modify features of indoor environmentsâ€"such as building ventilation systems and the chemistry of building materialsâ€"in ways that would have predictable impacts on microbial communities to promote health and prevent disease. The factors that affect the environments within buildings, the ways in which building characteristics influence the composition and function of indoor microbial communities, and the ways in which these microbial communities relate to human health and well-being are extraordinarily complex and can be explored only as a dynamic, interconnected ecosystem by engaging the fields of microbial biology and ecology, chemistry, building science, and human physiology. This report reviews what is known about the intersection of these disciplines, and how new tools may facilitate advances in understanding the ecosystem of built environments, indoor microbiomes, and effects on human health and well-being. It offers a research agenda to generate the information needed so that stakeholders with an interest in understanding the impacts of built environments will be able to make more informed decisions.

Compositional Data Analysis in Practice

Author : Michael Greenacre
Publisher : CRC Press
ISBN 13 : 042984901X
Total Pages : 120 pages
Book Rating : 4.4/5 (298 download)

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Book Synopsis Compositional Data Analysis in Practice by : Michael Greenacre

Download or read book Compositional Data Analysis in Practice written by Michael Greenacre and published by CRC Press. This book was released on 2018-07-17 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: Compositional Data Analysis in Practice is a user-oriented practical guide to the analysis of data with the property of a constant sum, for example percentages adding up to 100%. Compositional data can give misleading results if regular statistical methods are applied, and are best analysed by first transforming them to logarithms of ratios. This book explains how this transformation affects the analysis, results and interpretation of this very special type of data. All aspects of compositional data analysis are considered: visualization, modelling, dimension-reduction, clustering and variable selection, with many examples in the fields of food science, archaeology, sociology and biochemistry, and a final chapter containing a complete case study using fatty acid compositions in ecology. The applicability of these methods extends to other fields such as linguistics, geochemistry, marketing, economics and finance. R Software The R package easyCODA, which accompanies this book, can be downloaded from R-Forge as follows: install.packages("easyCODA", repos="") and will be available on CRAN soon. Notice that the R packages ca and vegan also have to be installed (from CRAN in the usual way).