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E-grāmata: Statistical Methods for Field and Laboratory Studies in Behavioral Ecology

(Cornell University), (Bayer Healthcare, Whippany, New Jersey, USA)
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Statistical Methods for Field and Laboratory Studies in Behavioral Ecology focuses on how statistical methods may be used to make sense of behavioral ecology and other data. It presents fundamental concepts in statistical inference and intermediate topics such as multiple least squares regression and ANOVA. The objective is to teach students to recognize situations where various statistical methods should be used, understand the strengths and limitations of the methods, and to show how they are implemented in R code. Examples are based on research described in the literature of behavioral ecology, with data sets and analysis code provided.



Features:











This intermediate to advanced statistical methods text was written with the behavioral ecologist in mind





Computer programs are provided, written in the R language.





Datasets are also provided, mostly based, at least to some degree, on real studies.





Methods and ideas discussed include multiple regression and ANOVA, logistic and Poisson regression, machine learning and model identification, time-to-event modeling, time series and stochastic modeling, game-theoretic modeling, multivariate methods, study design/sample size, and what to do when things go wrong.

It is assumed that the reader has already had exposure to statistics through a first introductory course at least, and also has sufficient knowledge of R. However, some introductory material is included to aid the less initiated reader.

Scott Pardo, Ph.D., is an accredited professional statistician (PStat®) by the American Statistical Association. Michael Pardo is a Ph.D. is a candidate in behavioral ecology at Cornell University, specializing in animal communication and social behavior.
Preface xi
Acknowledgments xiii
About the Authors xv
1 Statistical Foundations
1(16)
Some Probability Concepts
2(4)
Some Statistical Concepts
6(9)
Key Points for
Chapter 1
15(2)
2 Binary Results: Single Samples and 2 × 2 Tables
17(8)
General Ideas
17(2)
Single Proportion
17(1)
2 × 2 Tables
18(1)
Examples with R Code
19(2)
Single Proportion
19(1)
2 × 2 Tables
20(1)
Theoretical Aspects
21(3)
Single Proportion
21(2)
2 × 2 Tables
23(1)
Key Points for
Chapter 2
24(1)
3 Continuous Variables
25(16)
General Ideas
25(1)
Examples with R Code
26(7)
Theoretical Aspects
33(6)
Key Points for
Chapter 3
39(2)
4 The Linear Model: Continuous Variables
41(20)
General Ideas
41(1)
Examples with R Code
42(10)
Theoretical Aspects
52(6)
Key Points for
Chapter 4
58(3)
5 The Linear Model: Discrete Regressor Variables
61(20)
General Ideas
61(1)
Examples with R Code
62(14)
More Than One Treatment: Multiple Factors
67(3)
Blocking Factors
70(3)
ANOVA and Permutation Tests
73(2)
Nested Factors
75(1)
Analysis of Covariance: Models with Both Discrete and Continuous Regressors
76(2)
Theoretical Aspects
78(1)
Multiple Groupings: One-Way ANOVA
78(2)
Key Points for
Chapter 5
80(1)
6 The Linear Model: Random Effects and Mixed Models
81(12)
General Ideas
81(1)
Simple Case: One Fixed and One Random Effect
82(1)
Examples with R Code
82(3)
More Complex Case: Multiple Fixed and Random Effects
85(5)
Theoretical Aspects
90(1)
Key Points for
Chapter 6
91(2)
7 Polytomous Discrete Variables: R x C Contingency Tables
93(12)
General Ideas
93(5)
Independence of Two Discrete Variables
93(1)
Examples with R Code
93(5)
A Goodness-of-Fit Test
98(4)
A Special Goodness-of-Fit Test: Test for Random Allocation
100(2)
Theoretical Aspects
102(1)
Key Points for
Chapter 7
103(2)
8 The Generalized Linear Model: Logistic and Poisson Regression
105(24)
General Ideas
105(2)
Binary Logistic Regression
105(2)
Examples with R Code
107(17)
The Logit Transformation
107(6)
Poisson Regression
113(3)
Overdispersion
116(4)
Zero-Inflated Data and Poisson Regression
120(4)
Theoretical Aspects
124(4)
Logistic Regression
124(2)
Poisson Regression
126(1)
Overdispersed Poisson
126(1)
Zero-Inflated Poisson
127(1)
Key Points for
Chapter 8
128(1)
9 Multivariate Analyses: Dimension Reduction, Clustering, and Discrimination
129(22)
General Ideas
129(1)
Dimension Reduction: Principal Components
130(2)
Clustering
131(1)
Discrimination
131(1)
MANOVA
132(1)
Examples with R Code
132(12)
Dimension Reduction: Principal Components
132(3)
Clustering
135(7)
Discrimination
142(1)
MANOVA
143(1)
Theoretical Aspects
144(5)
Principal Components
145(1)
Discrimination
145(3)
MANOVA
148(1)
Key Points for
Chapter 9
149(2)
10 Bayesian and Frequentist Philosophies
151(18)
General Ideas
151(6)
Bayes' Theorem: Not Controversial
151(2)
Conjugacy
153(1)
Beta, Binomial
153(1)
Poisson, Gamma
154(1)
Normal, Normal
155(1)
Monte Carlo Markov Chain (MCMC) Method
156(1)
Examples with R Code
157(5)
Exponential, Gamma
157(1)
Bayesian Regression Analysis
158(1)
Markov Chain Monte Carlo
159(3)
Theoretical Aspects
162(5)
Bayesian Regression Analysis
162(3)
A Slightly More Complicated Model
165(2)
An Afterword about Bayesian Methods
167(1)
Key Points for
Chapter 10
168(1)
11 Decision and Game Theory
169(20)
General Ideas
169(1)
Examples with R Code
170(15)
Discrete Choices, Discrete States
170(3)
Discrete Choices, Continuous States: Reward and Cost as a Function of Choice
173(3)
Discrete Choices, Continuous States: An Inverted Problem
176(5)
Game Theory: Types of Games and Evolutionarily Stable Strategies
181(4)
Theoretical Aspects
185(2)
Verifying Models: Frequentist and Bayesian Approaches
185(2)
Key Points for
Chapter 11
187(2)
12 Modern Prediction Methods and Machine Learning Models
189(22)
General Ideas
189(1)
Do Machines Learn?
189(1)
Examples with R Code
190(13)
Stepwise Regression
192(5)
Artificial Neural Networks
197(3)
Classification and Regression Trees (CART)
200(3)
Bayesian Model Averaging
203(4)
Theoretical Aspects
207(2)
Key Points for
Chapter 12
209(2)
13 Time-to-Event
211(18)
General Ideas
211(1)
Examples with R Code
212(3)
Comparison of Survival Curves
212(3)
Theoretical Aspects
215(9)
Obtaining an Empirical Survival Model
222(1)
Censored Time-to-Failure
223(1)
Comparison of Survival Distributions
224(3)
Mantel--Cox LogRank and Peto and Peto Procedures
224(1)
Cox Proportional Hazard Model
225(2)
Key Points for
Chapter 13
227(2)
14 Time Series Analysis and Stochastic Processes
229(24)
General Ideas
229(1)
Time Series
229(9)
Identifying Time Series Model Types and Orders
231(2)
The Box--Jenkins Approach
233(5)
Nonstationarity and Differencing
238(1)
Examples with R Code: Time Series
238(10)
Time Series
238(3)
Markov Chains
241(2)
Extensions of Markov Chains
243(1)
Examples with R Code: Markov Chains
244(4)
Theoretical Aspects
248(2)
Time Series
248(1)
Markov Chains
249(1)
Key Points for
Chapter 14
250(3)
15 Study Design and Sample Size Considerations
253(12)
Degrees of Freedom: The Accounting of Experimental Design
253(1)
Latin Squares and Partial Latin Squares: Useful Design Tools
254(4)
Power for ANOVA
255(3)
Sample Size and Confidence Intervals
258(1)
Confidence Intervals for Proportions
259(1)
Pseudo-Replicates
260(2)
Too Many p-Values: False Discovery Rate
262(2)
Key Points for
Chapter 15
264(1)
16 When Things Go Wrong
265(8)
Inadequate Measurement System
265(1)
Incorrect Assignment of Individuals to Groups
265(1)
An Undiscovered Covariate
266(1)
Unintended Order Effects
266(1)
Missing Data
267(2)
Imputation
269(2)
Summary
271(1)
Key Points for
Chapter 16
271(2)
Appendix A Matrices and Vectors 273(14)
Appendix B Solving Your Problem 287(2)
References 289(4)
Index 293
Scott Pardo, Michael Pardo