spatstat

swMATH4429CRANspatstatMaRDI QIDQ16605FDOQ16605

Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests

Adrian Baddeley, Rolf Turner, Ege Rubak

Last update: 30 October 2023

Copyright license: GNU General Public License, version 3.0, GNU General Public License, version 2.0

Software version identifier: 3.0-3, 3.0-5, 3.0-6, 1.0-1, 1.1-3, 1.2-1, 1.3-1, 1.3-2, 1.3-3, 1.3-4, 1.4-3, 1.4-4, 1.4-5, 1.4-6, 1.5-1, 1.5-3, 1.5-4, 1.5-5, 1.5-6, 1.5-7, 1.5-8, 1.5-9, 1.5-10, 1.6-1, 1.6-2, 1.6-3, 1.6-4, 1.6-5, 1.6-6, 1.6-7, 1.6-8, 1.6-9, 1.6-11, 1.6-12, 1.7-11, 1.7-12, 1.7-13, 1.8-1, 1.8-2, 1.8-3, 1.8-4, 1.8-5, 1.8-6, 1.8-7, 1.8-8, 1.8-9, 1.9-0, 1.9-1, 1.9-2, 1.9-3, 1.9-4, 1.9-5, 1.9-6, 1.10-1, 1.10-2, 1.10-3, 1.11-0, 1.11-1, 1.11-2, 1.11-3, 1.11-4, 1.11-5, 1.11-6, 1.11-7, 1.11-8, 1.12-0, 1.12-1, 1.12-2, 1.12-3, 1.12-4, 1.12-5, 1.12-6, 1.12-7, 1.12-8, 1.12-9, 1.13-0, 1.13-1, 1.13-2, 1.13-3, 1.13-4, 1.14-0, 1.14-1, 1.14-2, 1.14-3, 1.14-4, 1.14-5, 1.14-6, 1.14-7, 1.14-8, 1.14-9, 1.14-10, 1.15-0, 1.15-1, 1.15-2, 1.15-3, 1.15-4, 1.16-0, 1.16-1, 1.16-2, 1.16-3, 1.17-0, 1.17-1, 1.17-2, 1.17-4, 1.17-5, 1.17-6, 1.18-0, 1.18-1, 1.18-2, 1.18-3, 1.18-4, 1.19-0, 1.19-1, 1.19-2, 1.19-3, 1.20-1, 1.20-2, 1.20-3, 1.20-5, 1.21-0, 1.21-1, 1.21-2, 1.21-3, 1.21-4, 1.21-5.1, 1.21-5, 1.21-6, 1.22-0, 1.22-1, 1.22-2, 1.22-3, 1.23-0, 1.23-1, 1.23-2, 1.23-3, 1.23-4, 1.23-5, 1.23-6, 1.24-1, 1.24-2, 1.25-0, 1.25-1, 1.25-2, 1.25-3, 1.25-4, 1.25-5, 1.26-0, 1.26-1, 1.27-0, 1.28-0, 1.28-1, 1.28-2, 1.29-0, 1.30-0, 1.31-0, 1.31-1.1, 1.31-1, 1.31-2, 1.31-3, 1.32-0, 1.33-0, 1.34-0, 1.34-1, 1.35-0, 1.36-0, 1.37-0, 1.38-0, 1.38-1, 1.39-0, 1.39-1, 1.40-0, 1.41-1, 1.42-0, 1.42-1, 1.42-2, 1.43-0, 1.44-0, 1.44-1, 1.45-0, 1.45-2, 1.46-1, 1.47-0, 1.48-0, 1.49-0, 1.50-0, 1.51-0, 1.52-1, 1.53-2, 1.54-0, 1.55-0, 1.55-1, 1.56-0, 1.56-1, 1.57-1, 1.58-2, 1.59-0, 1.60-1, 1.61-0, 1.62-2, 1.63-0, 1.63-2, 1.63-3, 1.64-1, 2.0-1, 2.1-0, 2.2-0, 2.3-0, 2.3-3, 2.3-4, 3.0-2, 3.0-7

Source code repository: https://github.com/cran/spatstat

Description

Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images. Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks. Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.

Cited In (only showing first 100 items - show all)

• Modeling partially surveyed point process data: inferring spatial point intensity of geomagnetic anomalies
• A bound of the \(\beta\)-mixing coefficient for point processes in terms of their intensity functions
• Estimation of summary characteristics from replicated spatial point processes
• Reach of repulsion for determinantal point processes in high dimensions
• Local spatial log-Gaussian Cox processes for seismic data
• Normal approximation for associated point processes via Stein's method with applications to determinantal point processes
• Exact sampling of determinantal point processes without eigendecomposition
• Title not available (Why is that?)
• Spatio-temporal improvised explosive device monitoring: improving detection to minimise attacks
• Spatial Point Patterns: Models and Statistics
• Territorial behaviour of buzzards versus random matrix spacing distributions
• The Accumulated Persistence Function, a New Useful Functional Summary Statistic for Topological Data Analysis, With a View to Brain Artery Trees and Spatial Point Process Applications
• On the zeros of the spectrogram of white noise
• Consistent smooth bootstrap kernel intensity estimation for inhomogeneous spatial Poisson point processes
• Convex and non-convex regularization methods for spatial point processes intensity estimation
• Time-frequency transforms of white noises and Gaussian analytic functions
• Polynomial ensembles and recurrence coefficients
• Optimal transport between determinantal point processes and application to fast simulation
• Computation of coverage probabilities in a spherical germ-grain model
• Structured space-sphere point processes and \(K\)-functions
• Thinning spatial point processes into Poisson processes
• Testing goodness of fit for point processes via topological data analysis
• A note on the simulation of the Ginibre point process
• Novel concave hull-based heuristic algorithm for TSP
• Adjusted composite likelihood ratio test for spatial Gibbs point processes
• Intensity estimation on geometric networks with penalized splines
• Leverage and Influence Diagnostics for Spatial Point Processes
• The multipoint Morisita index for the analysis of spatial patterns
• Inhomogeneous higher-order summary statistics for point processes on linear networks
• Incorporating big microdata in life table construction: A hypothesis-free estimator
• Stochastic Quasi-Likelihood for Case-Control Point Pattern Data
• How to asses, visualize and compare the anisotropy of linear structures reconstructed from optical sections -- a study based on histopathological quantification of human brain microvessels
• Prey density, value, and spatial distribution affect the efficiency of area-concentrated search
• Cardinality estimation for random stopping sets based on Poisson point processes
• Pair correlation functions and limiting distributions of iterated cluster point processes
• Cauchy cluster process
• Estimating functions for inhomogeneous spatial point processes with incomplete covariate data
• Perfect sampling for Gibbs point processes using partial rejection sampling
• On proportional volume sampling for experimental design in general spaces
• On a few statistical applications of determinantal point processes
• The Poisson binomial distribution -- old \& new
• Determinantal point process mixtures via spectral density approach
• Monte Carlo integration of non-differentiable functions on \([0,1]^\iota\), \(\iota =1,\ldots, d\), using a single determinantal point pattern defined on \([0,1]^d\)
• Effect of endothelial glycocalyx layer redistribution upon microvessel poroelastohydrodynamics
• Determinantal point processes
• Computation of lacunarity from covariance of spatial binary maps
• Contrast Estimation for Parametric Stationary Determinantal Point Processes
• Modelling aggregation on the large scale and regularity on the small scale in spatial point pattern datasets
• Assessing implicit hypotheses in life table construction
• Incomplete determinantal processes: from random matrix to Poisson statistics
• Fast approximation of the intensity of Gibbs point processes
• Spatial logistic regression and change-of-support in Poisson point processes
• Two-step estimation procedures for inhomogeneous shot-noise Cox processes
• Variational approach for spatial point process intensity estimation
• Identifying radon-prone building typologies by marginal modelling
• Monte Carlo with determinantal point processes
• Approximate methods in Bayesian point process spatial models
• Residual Analysis for Spatial Point Processes (with Discussion)
• Spatial point process models for location-allocation problems
• Parameter estimation for inhomogeneous space-time shot-noise Cox point processes
• Correction note: Poisson point process models solve the ``pseudo-absence problem for presence-only data in ecology
• Intensity approximation for pairwise interaction Gibbs point processes using determinantal point processes
• Sliced inverse regression and independence in random marked sets with covariates
• Determinantal sampling designs
• Modelling Spatial Point Patterns in R
• PARAMETER ESTIMATION IN NON-HOMOGENEOUS BOOLEAN MODELS: AN APPLICATION TO PLANT DEFENSE RESPONSE
• Structured Spatio-Temporal Shot-Noise Cox Point Process Models, with a View to Modelling Forest Fires
• The stochastic geometry of unconstrained one-bit data compression
• Modelling and classification of species abundance: a case study in the Barro Colorado Island plot
• Improving the usability of spatial point process methodology: an interdisciplinary dialogue between statistics and ecology
• Variable selection for inhomogeneous spatial point process models
• Self-exciting point processes: infections and implementations
• Circulant L-ensembles in the thermodynamic limit
• Investigations of the effects of random sampling schemes on the stability of generalized sampling
• Fast computation of spatially adaptive kernel estimates
• A Model-Based Approach for Making Ecological Inference from Distance Sampling Data
• Title not available (Why is that?)
• Symmetric adaptive smoothing regimens for estimation of the spatial relative risk function
• Estimating inter-group interaction radius for point processes with nested spatial structures
• An extension of Monte Carlo hypothesis tests
• Spatiotemporal point processes: regression, model specifications and future directions
• Comparison of relative density of two random geometric digraph families in testing spatial clustering
• A multivariate uniformity test for the case of unknown support
• Estimating second order characteristics of point processes with known independent noise
• Score, pseudo-score and residual diagnostics for spatial point process models
• Quasi-systematic sampling from a continuous population
• Bounds for the Probability Generating Functional of a Gibbs Point Process
• Title not available (Why is that?)
• Covariance of empirical functionals for inhomogeneous spatial point processes when the intensity has a parametric form
• Estimating abundance from counts in large data sets of irregularly spaced plots using spatial basis functions
• Comparing spatial counts characterizing human mobility using ratio maps
• On the Bayesian estimation for the stationary Neyman-Scott point processes.
• Unbiased estimation of the volume of a convex body
• Patchy patterns due to group dispersal
• Statistics for inhomogeneous space-time shot-noise Cox processes
• Testing spatial symmetry using contingency tables based on nearest neighbor relations
• Diffraction theory of point processes: systems with clumping and repulsion
• Testing multivariate uniformity based on random geometric graphs
• Bias correction for parameter estimates of spatial point process models
• A Kolmogorov-Smirnov type test for independence between marks and points of marked point processes

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