Roger S. Bivand Edzer J. Pebesma Virgilio Gömez-Rubio. Applied Spatial Data Analysis with R. 4:1 Springer

Transcription

1 Roger S. Bivand Edzer J. Pebesma Virgilio Gömez-Rubio Applied Spatial Data Analysis with R 4:1 Springer

2 Contents Preface VII 1 Hello World: Introducing Spatial Data Applied Spatial Data Analysis Why Do We Use R In General? for Spatial Data Analysis? R and GIS What is GIS? Service-Oriented Architectures Further Reading an GIS Types of Spatial Data Storage and Display Applied Spatial Data Analysis R Spatial Resources Online Resources Layout of the Book 14 Part I Handling Spatial Data in R 2 Classes for Spatial Data in R Introduction Classes and Methods in R Spat ial Objects Spat ia1p o int s Methods Data Frames for Spatial Point Data Spat ianines 38

3 X Contents 2.6 Spat lallpolygons SpatialPolygonsDataFrame Objects Holes and Ring Direction Spat ialgr id and Spat ialpixel Objects 47 3 Visualising Spatial Data The Traditional Plot System Plotting Points, Lines, Polygons, and Grids Axes and Layout Elements Degrees in Axes Labels and Reference Grid Plot Size, Plotting Area, Map Scale, and Multiple Plots Plotting Attributes and Map Legends Trellis/Lattice Plots with spplot A Straight Trellis Example Plotting Points, Lines, Polygons, and Grids Adding Reference and Layout Elements to Plots Arranging Panel Layout Interacting with Plots Interacting with Base Graphics Interacting with spplot and Lattice Plots Colour Palettes and Class Intervals Colour Palettes Class Intervals 77 4 Spatial Data Import and Export Coordinate Reference Systems Using the EPSG List PROJ.4 CRS Specification Projection and Transformation Degrees, Minutes, and Seconds Vector File Formats Using OGR Drivers in rgdal Other Import/Export Functions Raster File Formats Using GDAL Drivers in rgdal Writing a Google Earthrm Image Overlay Other Import/Export Functions Grass Broad Street Cholera Data Other Import/Export Interfaces Analysis and Visualisation Applications TerraLib and art Other GIS and Web Mapping Systems Installing rgdal 111

4 Contents XI 5 Further Methods for Handling Spatial Data Support Overlay Spatial Sampling Checking Topologies Dissolving Polygons Checking Hole Status Combining Spatial Data Combining Positional Data Combining Attribute Data Auxiliary Functions Customising Spatial Data Classes and Methods Programming with Classes and Methods S3-Style Classes and Methods Style Classes and Methods Animal Track Data in Package Trip Generic and Constructor Functions Methods for Trip Objects Multi-Point Data: Spat ia1multipoint s Hexagonal Grids Spatio-Temporal Grids Analysing Spatial Monte Carlo Simulations Processing Massive Grids 146 Part II Analysing Spatial Data 7 Spatial Point Pattern Analysis Introduction Packages for the Analysis of Spatial Point Patterns Preliminary Analysis of a Point Pattern Complete Spatial Randomness G Function: Distance to the Nearest Event F Function: Distance from a Point to the Nearest Event Statistical Analysis of Spatial Point Processes Homogeneous Poisson Processes Inhomogeneous Poisson Processes Estimation of the Intensity Likelihood of an Inhomogeneous Poisson Process Second-Order Properties Some Applications in Spatial Epidemiology Case Control Studies Binary Regression Estimator 178

5 XII Contents Binary Regression Using Generalised Additive Models Point Source Pollution Accounting for Confounding and Covariates Further Methods for the Analysis of Point Patterns Interpolation and Geostatistics Introduction Exploratory Data Analysis Non-Geostatistical Interpolation Methods Inverse Distance Weighted Interpolation Linear Regression Estimating Spatial Correlation: The Variogram Exploratory Variogram Analysis Cutoff, Lag Width, Direction Dependence Variogram Modelling Anisotropy Multivariable Variogram Modelling Residual Variogram Modelling Spatial Prediction Universal, Ordinary, and Simple Kriging Multivariable Prediction: Cokriging Collocated Cokriging Cokriging Contrasts Kriging in a Local Neighbourhood Change of Support: Block Kriging Stratifying the Domain Trend Functions and their Coefficients Non-Linear Transforms of the Response Variable Singular Matrix Errors Model Diagnostics Cross Validation Residuals Cross Validation z-scores Multivariable Cross Validation Limit ations to Cross Validation Geostatistical Simulation Sequential Simulation Non-Linear Spatial Aggregation and Block Averages Multivariable and Indicator Simulation Model-Based Geostatistics and Bayesian Approaches Monitoring Network Optimization Other R Packages for Interpolation and Geostatistics Non-Geostatistical Interpolation spatial RandomFields geor and georglm fields 235

6 Contents XIII 9 Areal Data and Spatial Autocorrelation Introduction Spatial Neighbours Neighbour Objects Creating Contiguity Neighbours Creating Graph-Based Neighbours Distance-Based Neighbours Higher-Order Neighbours Grid Neighbours Spatial Weights Spatial Weights Styles General Spatial Weights Importing, Converting, and Exporting Spatial Neighbours and Weights Using Weights to Simulate Spatial Autocorrelation Manipulating Spatial Weights Spatial Autocorrelation: Tests Global Tests Local Tests Modelling Areal Data Introduction Spatial Statistics Approaches Simultaneous Autoregressive Models Conditional Autoregressive Models Fitting Spatial Regression Models Mixed-Effects Models Spatial Econometrics Approaches Other Methods GAM, GEE, GLMM Moran Eigenvectors Geographically Weighted Regression Disease Mapping Introduction Statistical Models Poisson-Gamma Model Log-Normal Model Marshall's Global EB Estimator Spatially Structured Statistical Models Bayesian Hierarchical Models The Poisson-Gamma Model Revisited Spatial Models Detection of Clusters of Disease Testing the Homogeneity of the Relative Risks Moran's I Test of Spatial Autocorrelation 335

7 XIV Contents Tango's Test of General Clustering Detection of the Location of a Cluster Geographical Analysis Machine Kulldorff's Statistic Stone's Test for Localised Clusters Other Topics in Disease Mapping 341 Afterword 343 R and Package Versions Used 344 Data Sets Used 344 References 347 Subject Index 361 Functions Index 371