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Table Of Contents

Working with Spatial Data
1.1 Introduction
1.2 Analysis of Spatial Data
1.2.1 Types of Spatial Data
1.2.2 Components of Spatial Data
1.2.3 Topics Covered in the Text
1.3 Data Sets Analyzed in This Book
1.3.1 Data Set 1: Yellow-Billed Cuckoo Habitat
1.3.2 Data Set 2: Environmental Characteristics of Oak Woodlands
1.3.3 Data Set 3: Uruguayan Rice Farmers
1.3.4 Data Set 4: Factors Underlying Yield in Two Fields
1.3.5 Comparing the Data Sets
1.4 Further Reading
R Programming Environment
2.1 Introduction
2.1.1 Introduction to R
2.1.2 Setting Up Yourself to Use This Book
2.2 R Basics
2.3 Programming Concepts
2.3.1 Looping and Branching
2.3.2 Functional Programming
2.4 Handling Data in R
2.4.1 Data Structures in R
2.4.2 Basic Data Input and Output
2.4.3 Spatial Data Structures
2.5 Writing Functions in R
2.6 Graphics in R
2.6.1 Traditional Graphics in R: Attribute Data
2.6.2 Traditional Graphics in R: Spatial Data
2.6.3 Trellis Graphics in R: Attribute Data
2.6.4 Trellis Graphics in R: Spatial Data
2.6.5 Using Color in R
2.7 Other Software Packages
2.8 Further Reading
Exercises
Statistical Properties of Spatially Autocorrelated Data
3.1 Introduction
3.2 Components of a Spatial Random Process
3.2.1 Spatial Trends in Data
3.2.2 Stationarity
3.3 Monte Carlo Simulation
3.4 Review of Hypothesis and Significance Testing
3.5 Modeling Spatial Autocorrelation
3.5.1 Monte Carlo Simulation of Time Series
3.5.2 Modeling Spatial Contiguity
3.5.3 Modeling Spatial Association in R
3.6 Application to Field Data
3.7 Further Reading
Measures of Spatial Autocorrelation
4.1 Introduction
4.2 Preliminary Considerations
4.2.1 Measurement Scale
4.2.1.1 Nominal Scale Data
4.2.1.2 Ordinal Scale Data
4.2.1.3 Interval Scale Data
4.2.1.4 Ratio Scale Data
4.2.2 Resampling and Randomization Assumptions
4.2.2.1 Resampling Assumption
4.2.2.2 Randomization Assumption
4.2.3 Testing the Null Hypothesis
4.3 Join-Count Statistics
4.4 Moran’s I and Geary’s c
4.5 Measures of Autocorrelation Structure
4.5.1 Moran Correlogram
4.5.2 Moran Scatterplot
4.5.3 Local Measures of Autocorrelation
4.5.4 Geographically Weighted Regression
4.6 Measuring Autocorrelation of Spatially Continuous Data
4.6.1 Variogram
4.6.2 Covariogram and Correlogram
4.7 Further Reading
Sampling and Data Collection
5.1 Introduction
5.2 Preliminary Considerations
5.2.1 Artificial Population
5.2.2 Accuracy, Bias, Precision, and Variance
5.2.3 Comparison Procedures
5.3 Developing the Sampling Patterns
5.3.1 Random Sampling
5.3.2 Geographically Stratified Sampling
5.3.3 Sampling on a Regular Grid
5.3.4 Stratification Based on a Covariate
5.3.5 Cluster Sampling
5.4 Methods for Variogram Estimation
5.5 Estimating the Sample Size
5.6 Sampling for Thematic Mapping
5.7 Design-Based and Model-Based Sampling
5.8 Further Reading
Preparing Spatial Data for Analysis
6.1 Introduction
6.2 Quality of Attribute Data
6.2.1 Dealing with Outliers and Contaminants
6.2.2 Quality of Ecological Survey Data
6.2.3 Quality of Automatically Recorded Data
6.3 Spatial Interpolation Procedures
6.3.1 Inverse Weighted Distance Interpolation
6.3.2 Kriging Interpolation
6.3.3 Cokriging Interpolation
6.4 Spatial Rectification and Alignment of Data
6.4.1 Definitions of Scale-Related Processes
6.4.2 Change of Coverage
6.4.3 Change of Support
6.5 Further Reading
Preliminary Exploration of Spatial Data
7.1 Introduction
7.2 Data Set 1
7.3 Data Set 2
7.4 Data Set 3
7.5 Data Set 4
8.2.1 Introduction to Principal Components Analysis
8.2.2 Principal Components Analysis of Data Set 2
8.2.3 Application to Data Set 4, Field 1
8.3 Classification and Regression Trees (a.k.a. Recursive Partitioning)
8.3.1 Introduction to the Method
8.3.2 Mathematics of Recursive Partitioning
8.3.3 Exploratory Analysis of Data Set 2 with Regression Trees
8.3.4 Exploratory Analysis of Data Set 3 with Recursive Partitioning
8.3.5 Exploratory Analysis of Field 4.1 with Recursive Partitioning
8.4 Random Forest
8.4.1 Introduction to Random Forest
8.4.2 Application to Data Set 2
8.5 Further Reading
9.2.2.1 Added Variable Plots
9.2.2.2 Partial Residual Plots
9.2.3 Cautious Approach to Model Selection as an Exploratory Tool
9.3 Building a Multiple Regression Model for Field 4.1
9.4 Generalized Linear Models
9.4.1 Introduction to Generalized Linear Models
9.4.2 Multiple Logistic Regression Model for Data Set 2
9.4.3 Logistic Regression Model of Count Data for Data Set 1
9.4.4 Analysis of the Counts of Data Set 1: Zero-Inflated Poisson Data
9.5 Further Reading
Variance Estimation, the Effective Sample Size, and the Bootstrap
10.1 Introduction
10.2 Bootstrap Estimation of the Standard Error
10.3 Bootstrapping Time Series Data
10.3.1 Problem with Correlated Data
10.3.2 Block Bootstrap
10.3.3 Parametric Bootstrap
10.4 Bootstrapping Spatial Data
10.4.1 Spatial Block Bootstrap
10.4.2 Parametric Spatial Bootstrap
10.4.3 Power of the Tests
10.5 Application to the EM38 Data
10.6 Further Reading
Measures of Bivariate Association between Two Spatial Variables
11.1 Introduction
11.2 Estimating and Testing the Correlation Coefficient
11.2.1 Correlation Coefficient
11.2.2 Clifford et al. Correction
11.2.3 Bootstrap Variance Estimate
11.2.4 Application to the Example Problem
11.3 Contingency Tables
11.3.1 Large Sample Size Contingency Tables
11.3.2 Small Sample Size Contingency Tables
11.4 Mantel and Partial Mantel Statistics
11.4.1 Mantel Statistic
11.4.2 Partial Mantel Test
11.5 Modifiable Areal Unit Problem and Ecological Fallacy
11.5.1 Modifiable Areal Unit Problem
11.5.2 Ecological Fallacy
11.6 Further Reading
12.1 Introduction
12.2 Basic Properties of the Mixed Model
12.3 Application to Data Set 3
12.4 Incorporating Spatial Autocorrelation
12.5 Generalized Least Squares
12.6 Spatial Logistic Regression
12.6.1 Upscaling Data Set 2 in the Coast Range
12.6.2 Incorporation of Spatial Autocorrelation
12.7 Further Reading
Regression Models for Spatially Autocorrelated Data
13.1 Introduction
13.2 Detecting Spatial Autocorrelation in a Regression Model
13.3 Models for Spatial Processes
13.3.1 Spatial Lag Model
13.3.2 Spatial Error Model
13.4 Determining the Appropriate Regression Model
13.4.1 Formulation of the Problem
13.4.2 Lagrange Multiplier Test
13.5 Fitting the Spatial Lag and Spatial Error Models
13.6 Conditional Autoregressive Model
13.7 Application of SAR and CAR Models to Field Data
13.7.1 Fitting the Data
13.7.2 Comparison of the Mixed and Autoregressive Models
13.8 Autologistic Model for Binary Data
13.9 Further Reading
Bayesian Analysis of Spatially Autocorrelated Data
14.1 Introduction
14.2 Markov Chain Monte Carlo Methods
14.3 Introduction to WinBUGS
14.3.1 WinBUGS Basics
14.3.2 WinBUGS Diagnostics
14.3.3 Introduction to R2WinBUGS
14.5.1 Spatial Effects in the Linear Model
14.5.2 Application to Data Set 3
14.6 Further Reading
Analysis of Spatiotemporal Data
15.1 Introduction
15.2 Spatiotemporal Cluster Analysis
15.3 Factors Underlying Spatiotemporal Yield Clusters
15.4.2 Application of Bayesian Updating to Data Set 3
15.5 Other Approaches to Spatiotemporal Modeling
15.5.1 Models for Dispersing Populations
15.5.2 State and Transition Models
15.6 Further Reading
Analysis of Data from Controlled Experiments
16.1 Introduction
16.2 Classical Analysis of Variance
16.3 Comparison of Methods
16.3.1 Comparison Statistics
16.3.2 Papadakis Nearest Neighbor Method
16.3.3 Trend Method
16.3.4 “Correlated Errors” Method
16.3.5 Published Comparisons of the Methods
16.4 Pseudoreplicated Data and the Effective Sample Size
16.4.1 Pseudoreplicated Comparisons
16.4.2 Calculation of the Effective Sample Size
16.4.3 Application to Field Data
16.5 Further Reading
Assembling Conclusions
17.1 Introduction
17.2 Data Set 1
17.3 Data Set 2
17.4 Data Set 3
17.5 Data Set 4
17.6 Conclusions
Appendix A: Review of Mathematical Concepts
Appendix B: The Data Sets
Appendix C: An R Thesaurus
References
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Spatial.data.Analysis.in.Ecology.and.Agriculture.using.R.by.Richard.E..Plant

Spatial.data.Analysis.in.Ecology.and.Agriculture.using.R.by.Richard.E..Plant

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