# Welcome

This is the companion website for Spatial Point Patterns: Methodology and Applications with R.

Here you can download three sample chapters for free and find R code to reproduce all figures and output in the book.

PART I: BASICS

1. Introduction
Point patterns
Statistical methodology for point patterns

2. Software Essentials
Introduction to R
Packages for R
Introduction to spatstat
Getting started with spatstat
FAQ

3. Collecting and Handling Point Pattern Data (download pdf)
Surveys and experiments
Data handling
Entering point pattern data into spatstat
Data errors and quirks
Windows in spatstat
Pixel images in spatstat
Line segment patterns
Collections of objects
Interactive data entry in spatstat
Reading GIS file formats
FAQ

4. Inspecting and Exploring Data
Plotting
Manipulating point patterns and windows
Exploring images
Using line segment patterns
Tessellations
FAQ

5. Point Process Methods
Motivation
Basic definitions
Complete spatial randomness
Inhomogeneous Poisson process
A menagerie of models
Fundamental issues
Goals of analysis

PART II: EXPLORATORY DATA ANALYSIS

6. Intensity
Introduction
Estimating homogeneous intensity
Technical definition Quadrat counting
Smoothing estimation of intensity function
Investigating dependence of intensity on a covariate
Formal tests of (non-)dependence on a covariate
Hot spots, clusters, and local features
Kernel smoothing of marks
FAQ

Introduction
Manual methods
The K-function
Edge corrections for the K-function
Function objects in spatstat
The pair correlation function
Standard errors and confidence intervals
Testing whether a pattern is completely random
Detecting anisotropy
Local indicators of spatial association
Third- and higher-order summary statistics
Theory
FAQ

8. Spacing
Introduction
Basic methods
Nearest-neighbour function Gand empty-space function F
Confidence intervals and simulation envelopes
Empty-space hazard
J-function
Inhomogeneous F-, G- and J-functions
Anisotropy and the nearest-neighbour orientation
Empty-space distance for a spatial pattern
Distance from a point pattern to another spatial pattern
Theory for edge corrections
Palm distribution
FAQ

PART III: STATISTICAL INFERENCE

Introduction
Poisson point process models
Fitting Poisson models in spatstat
Statistical inference for Poisson models
Alternative fitting methods
More flexible models
Theory
Fine pixel approximation
Conditional logistic regression
Approximate Bayesian inference
Non-loglinear models
Local likelihood
FAQ

10. Hypothesis Tests and Simulation Envelopes
Introduction
Concepts and terminology
Testing for a covariate effect in a parametric model
Tests based on the cumulative distribution function
Monte Carlo tests
Monte Carlo tests based on summary functions
Envelopes in spatstat
Other presentations of envelope tests
Dao-Genton test and envelopes
Power of tests based on summary functions
FAQ

11. Model Validation
Overview of validation techniques
Relative intensity
Residuals for Poisson processes
Partial residual plots
Validating the independence assumption
Leverage and influence
Theory for leverage and influence
FAQ

12. Cluster and Cox Models
Introduction
Cox processes
Cluster processes
Fitting Cox and cluster models to data
Locally fitted models
Theory*
*FAQ

13. Gibbs Models
Introduction
Conditional intensity
Key concepts
Statistical insights
Fitting Gibbs models to data
Pairwise interaction models
Higher-order interactions
Hybrids of Gibbs models
Simulation
Goodness-of-fit and validation for fitted Gibbs models
Locally fitted models
Theory: Gibbs processes
Theory: Fitting Gibbs models
Determinantal point processes
FAQ

14. Patterns of Several Types of Points
Introduction
Methodological issues
Handling multitype point pattern data
Exploratory analysis of intensity
Multitype Poisson models
Correlation and spacing
Tests of randomness and independence
Multitype Gibbs models
Hierarchical interactions
Multitype Cox and cluster processes
Other multitype processes
Theory
FAQ

PART IV: ADDITIONAL STRUCTURE

15. Higher-Dimensional Spaces and Marks
Introduction
Point patterns with numerical or multidimensional marks
Three-dimensional point patterns
Point patterns with any kinds of marks and coordinates
FAQ

16. Replicated Point Patterns and Designed Experiments
Introduction
Methodology
Lists of objects
Hyperframes
Computing with hyperframes
Replicated point pattern datasets in spatstat
Exploratory data analysis
Analysing summary functions from replicated patterns
Poisson models
Gibbs models
Model validation
Theory
FAQ

17. Point Patterns on a Linear Network
Introduction
Network geometry
Data handling
Intensity
Poisson models
Intensity on a tree
Pair correlation function
K-function
FAQ