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El. knyga: Eco-Stats: Data Analysis in Ecology: From t-tests to Multivariate Abundances

  • Formatas: EPUB+DRM
  • Serija: Methods in Statistical Ecology
  • Išleidimo metai: 10-Aug-2022
  • Leidėjas: Springer Nature Switzerland AG
  • Kalba: eng
  • ISBN-13: 9783030884437
  • Formatas: EPUB+DRM
  • Serija: Methods in Statistical Ecology
  • Išleidimo metai: 10-Aug-2022
  • Leidėjas: Springer Nature Switzerland AG
  • Kalba: eng
  • ISBN-13: 9783030884437

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This book introduces ecologists to the wonderful world of modern tools for data analysis, especially multivariate analysis.

Assuming only a vague recollection of an introductory statistics course, the book begins by reviewing some core principles in statistics, and relates common methods to the linear model, a general framework for modeling data where the response is continuous.  This is then extended to discrete data using generalized linear models, to designs with multiple sampling levels via mixed models, and to situations where there are multiple response variables via model-based approaches to multivariate analysis.  Along the way there is an introduction to: important principles in model selection; adaptations of the model to handle non-linearity and cyclical variables; dependence due to structured correlation in time, space or phylogeny; and design-based techniques for inference that can relax some of the modelling assumptions.  Examples span a variety of applications including environmental monitoring, species distribution modeling, global-scale surveys of plant traits, and small field experiments on biological controls.  Maths Boxes throughout the book explain some of the core ideas mathematically for readers who want to delve deeper, and R code is used throughout.  Accompanying code and data can be found in the ecostats R package on CRAN.

  • For biologists with relatively little prior knowledge of statistics - introducing a modern, advanced approach to data analysis in an intuitive and accessible way
  • Introduces modern methods of multivariate analysis to ecology - as direct extensions of univariate techniques
Introduces a range of advanced statistics topics relevant to the modern ecologist - including mixed models, model selection, design-based inference, spatial statistics, latent variable models.
Part I Regression Analysis for a Single Response Variable
1 "Stats 101" Revision
3(40)
1.1 Regression, Predictors, and Responses
4(1)
1.2 Study Design Is Critical
4(7)
1.3 When Do You Use a Given Method?
11(6)
1.4 Statistical Inference
17(5)
1.5 Mind Your Ps and Qs--Assumptions
22(13)
1.6 Transformations
35(8)
2 An Important Equivalence Result
43(20)
2.1 The Two-Sample r-Test
43(4)
2.2 Simple Linear Regression
47(10)
2.3 Equivalence of r-Test and Linear Regression
57(6)
3 Regression with Multiple Predictor Variables
63(18)
3.1 Multiple Regression
63(10)
3.2 ANOVA
73(8)
4 Linear Models--Anything Goes
81(26)
4.1 Paired and Blocked Designs
81(5)
4.2 Analysis of Covariance
86(4)
4.3 Factorial Experiments
90(9)
4.4 Interactions in Regression
99(3)
4.5 Robustness of Linear Models--What Could Go Wrong?
102(5)
5 Model Selection
107(26)
5.1 Understanding Model Selection
108(6)
5.2 Validation
114(3)
5.3 tf-fold Cross-Validation
117(2)
5.4 Information Criteria
119(2)
5.5 Ways to Do Subset Selection
121(3)
5.6 Penalised Estimation
124(2)
5.7 Variable Importance
126(5)
5.8 Summary
131(2)
6 Mixed Effects Models
133(18)
6.1 Fitting Models with Random Effects
135(1)
6.2 Linear Mixed Effects Model
136(3)
6.3 Likelihood Functions
139(3)
6.4 Inference from Mixed Effects Models
142(3)
6.5 What If I Want More Accurate Inferences?
145(1)
6.6 Design Considerations
146(2)
6.7 Situations Where Random Effects Are and Aren't Used
148(3)
7 Correlated Samples in Time, Space, Phylogeny
151(30)
7.1 Longitudinal Analysis of Repeated Measures Data
155(8)
7.2 Spatially Structured Data
163(7)
7.3 Phylogenetically Structured Data
170(7)
7.4 Confounding--Where Is the Fixed Effect You Love?
177(2)
7.5 Further Reading
179(2)
8 Wiggly Models
181(24)
8.1 Spline Smoothers
182(7)
8.2 Smoothers with Interactions
189(3)
8.3 A Smoother as a Diagnostic Tool in Residual Plots
192(1)
8.4 Cyclical Variables
193(12)
9 Design-Based Inference
205(26)
9.1 Permutation Tests
206(5)
9.2 Bootstrapping
211(3)
9.3 Do I Use the Bootstrap or a Permutation Test?
214(1)
9.4 Mind Your Ps and Qs!
215(2)
9.5 Resampling Residuals
217(4)
9.6 Limitations of Resampling: Still Mind Your Ps and Qs!
221(2)
9.7 Design-Based Inference for Dependent Data
223(8)
10 Analysing Discrete Data
231(36)
10.1 GLMs: Relaxing Linear Modelling Assumptions
236(4)
10.2 Fitting a GLM
240(4)
10.3 Checking GLM Assumptions
244(7)
10.4 Inference from Generalised Linear Models
251(8)
10.5 Don't Standardise Counts, Use Offsets!
259(2)
10.6 Extensions
261(6)
Part II Regression Analysis for Multiple Response Variables
11 Multivariate Analysis
267(28)
11.1 Do You Really Need to Go Multivariate? Really?
268(2)
11.2 MANOVA and Multivariate Linear Models
270(9)
11.3 Hierarchical Generalised Linear Models
279(14)
11.4 Other Approaches to Multivariate Analysis
293(2)
12 Visualising Many Responses
295(22)
12.1 One at a Time: Visualising Marginal Response
296(1)
12.2 Ordination for Multivariate Normal Data
297(11)
12.3 Generalised Latent Variable Models
308(4)
12.4 Multi-Dimensional Scaling and Algorithms Using Pairwise Dissimilarities
312(2)
12.5 Make Sure You Plot the Raw Data!
314(3)
13 Allometric Line Fitting
317(14)
13.1 Why Not Just Use a Linear Model?
319(1)
13.2 The (Standardised) Major Axis
320(7)
13.3 Controversies in the Allometry Literature
327(4)
Part III Regression Analysis for Multivariate Abundances
14 Multivariate Abundances and Environmental Association
331(26)
14.1 Generalised Estimating Equations
334(2)
14.2 Design-Based Inference Using GEEs
336(8)
14.3 Compositional Change and Diversity Partitioning
344(5)
14.4 In Which Taxa Is There an Effect?
349(2)
14.5 Random Factors
351(1)
14.6 Modelling Frameworks for Multivariate Abundances
351(6)
15 Predicting Multivariate Abundances
357(12)
15.1 Special Considerations for Multivariate Abundances
358(2)
15.2 Borrowing Strength Across Taxa
360(5)
15.3 Non-Linearity of Environmental Response and Interactions
365(1)
15.4 Relative Importance of Predictors
366(3)
16 Explaining Variation in Responses Across Taxa
369(18)
16.1 Classifying Species by Environmental Response
369(9)
16.2 Fourth Corner Models
378(9)
17 Studying Co-occurrence Patterns
387(18)
17.1 Copula Frameworks for Modelling Co-occurrence
389(3)
17.2 Inferring Co-occurrence Using Latent Variables
392(2)
17.3 Co-occurrence Induced by Environmental Variables
394(4)
17.4 Co-occurrence Induced by Mediator Taxa
398(2)
17.5 The Graphical LASSO for Multivariate Abundances
400(3)
17.6 Other Models for Co-occurrence
403(2)
18 Closing Advice
405(10)
18.1 A Framework for Data Analysis--Mind Your Ps and Qs
405(5)
18.2 Beyond the Methods Discussed in This Book
410(5)
References 415(14)
Index 429
David Warton is professor and leads the Eco-Stats group based in the School of Mathematics and Statistics and is affiliated with the Evolution & Ecology Research Centre at the University of New South Wales (Australia). He is an ecological statistician who advances methodology for data analysis in ecology and is one of quantitative ecologys great explainers. He has an unerring knack for identifying core concepts and packaging them in comprehensible ways.