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BL
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| Record Number
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851686
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| Main Entry
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Thioulouse, Jean, (Biologist)
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| Title & Author
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Multivariate analysis of ecological data with ade4 /\ Jean Thioulouse [and five others].
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| Publication Statement
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New York, NY :: Springer,, 2018.
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| Page. NO
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1 online resource (xi, 329 pages) :: illustrations
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| ISBN
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1493988506
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: 9781493988501
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1493988484
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9781493988488
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| Bibliographies/Indexes
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Includes bibliographical references and index.
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| Contents
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Intro; Foreword; Contents; 1 Introduction; 1.1 Intended Readership; 1.2 Evolutions of ade4; 1.2.1 The ade4 Add-On Package for R; 1.2.2 Previous Versions of ade4; 1.3 Using ade4; 1.3.1 Computer Hardware; 1.3.2 Installing R; 1.3.3 Installing ade4; 1.3.4 Dependencies; 1.3.5 Packages of the ade4 Family; 1.3.5.1 adegraphics; 1.3.5.2 ade4TkGUI; 1.3.5.3 adespatial; 1.3.5.4 adephylo; 1.3.6 Version of the Packages Used in This Book; 1.3.7 The adelist Forum; 1.3.8 Using the Help System; 1.4 Interactive Code Snippets; 1.5 Ecological Data Sets; 2 Useful R Functions and Data Structures; 2.1 Introduction.
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2.2 Basic Data Import and Export Functions2.2.1 read.table; 2.2.2 write.table; 2.2.3 Data; 2.3 Vectors; 2.4 Data Frames; 2.4.1 Dimensions; 2.4.2 Row and Column Names; 2.4.3 Accessing Data Frame Elements; 2.4.4 Row and Column Sums and Means; 2.4.5 Row and Column Selection; 2.4.6 Changing Values; 2.4.7 Missing Values in Data Frames; 2.4.8 Data Transformation; 2.4.9 Apply; 2.4.10 Summary; 2.4.11 Other Functions; 2.5 Factors; 2.5.1 Using Factors; 2.5.2 Generating Factors; 2.5.3 Re-ordering Levels; 3 The dudi Class; 3.1 Introduction; 3.2 Principles of Multivariate Analysis; 3.3 Structure.
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3.4 Functions3.5 Elements of dudi Objects; 3.5.1 pca1tab; 3.5.2 pca1cw and pca1lw; 3.5.3 pca1eig, pca1rank and pca1nf; 3.5.4 pca1c1, pca1l1, pca1co and pca1li; 3.5.5 pca1cent and pca1norm; 3.6 Using dudi Objects; 3.6.1 The print and summary Functions; 3.6.2 The scatter and biplot Functions; 3.6.3 The score Function; 3.6.4 The s.label and plot Functions; 3.6.5 The inertia Function; 3.6.6 Other Graphical Functions; 3.7 Exporting dudi Elements; 4 Multivariate Analysis Graphs; 4.1 Introduction; 4.2 Basics of adegraphics; 4.2.1 ADEg and ADEgS Objects; 4.2.2 Graphical Parameters.
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4.2.3 Main Functions and Methods4.2.4 (Big) Data Storage; 4.3 Simple Examples; 4.4 Spatial Representations; 4.5 Automatic Graph Collections; 4.5.1 Splitting Individuals with the facets Argument; 4.5.2 Multiple Variables; 4.5.3 Outputs of Multivariate Methods; 4.6 Step-by-Step Creation of an ADEgS; 4.6.1 Graphical Representations of One Axis; 4.6.2 Graphical Representations of Two Axes; 4.7 Conclusion; 5 Description of Environmental Variables Structures; 5.1 Introduction; 5.2 Standardised Principal Component Analysis (PCA); 5.3 Multiple Correspondence Analysis (MCA).
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5.4 Hill and Smith Analysis (HSA)5.5 Other Simple Methods; 6 Description of Species Structures; 6.1 Introduction; 6.2 Correspondence Analysis (CA); 6.3 Centred PCA (cPCA); 6.4 Standardised and Non-centred PCA; 6.5 Principal Coordinate Analysis (PCoA); 6.6 Other Simple Methods; 7 Taking into Account Groups of Sites; 7.1 Introduction; 7.2 An Environmental Situation; 7.3 Between-Class Analysis: Analysing Differences Between Groups; 7.3.1 Between-Site Analysis; 7.3.2 Between-Season Analysis; 7.4 Within-Class Analysis: Removing Differences Between Groups of Sites; 7.5 Discriminant Analysis.
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| Abstract
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This book introduces the ade4 package for R which provides multivariate methods for the analysis of ecological data. It is implemented around the mathematical concept of the duality diagram, and provides a unified framework for multivariate analysis. The authors offer a detailed presentation of the theoretical framework of the duality diagram and also of its application to real-world ecological problems. These two goals may seem contradictory, as they concern two separate groups of scientists, namely statisticians and ecologists. However, statistical ecology has become a scientific discipline of its own, and the good use of multivariate data analysis methods by ecologists implies a fair knowledge of the mathematical properties of these methods. The organization of the book is based on ecological questions, but these questions correspond to particular classes of data analysis methods. The first chapters present both usual and multiway data analysis methods. Further chapters are dedicated for example to the analysis of spatial data, of phylogenetic structures, and of biodiversity patterns. One chapter deals with multivariate data analysis graphs. In each chapter, the basic mathematical definitions of the methods and the outputs of the R functions available in ade4 are detailed in two different boxes. The text of the book itself can be read independently from these boxes. Thus the book offers the opportunity to find information about the ecological situation from which a question raises alongside the mathematical properties of methods that can be applied to answer this question, as well as the details of software outputs. Each example and all the graphs in this book come with executable R code.--
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| Subject
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Ecology-- Statistical methods.
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| Subject
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Multivariate analysis.
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Ecology-- Statistical methods.
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Multivariate analysis.
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NATURE-- Ecology.
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NATURE-- Ecosystems Habitats-- Wilderness.
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Probability statistics.
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| Subject
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SCIENCE-- Environmental Science.
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| Subject
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SCIENCE-- Life Sciences-- Ecology.
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| Dewey Classification
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577.015195
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| LC Classification
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QH541.15.S72
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| Added Entry
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Dray, Stéphane.
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Dufour, Anne-Béatrice.
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Jombart, Thibaut.
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Pavoine, Sanne.
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Siberchicot, Aurélie.
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