spatstat
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.
- gfilmm
- siplab
- dixon
- gfilogisreg
- latticeDensity
- BEMLIB
- CalSim
- RImageJROI
- ppmData
- spatialreg
- stlnpp
- lsirm12pl
- binspp
- tictoc
- concaveman
- noisyCE2
- sphereplot
- stars
- lwgeom
- bestNormalize
- kernelTDA
- Surveillance
- Hypothesis testing for topological data analysis
- Intensity approximation for pairwise interaction Gibbs point processes using determinantal point processes
- Improving the usability of spatial point process methodology: an interdisciplinary dialogue between statistics and ecology
- A common goodness-of-fit framework for neural population models using marked point process time-rescaling
- Self-exciting point processes: infections and implementations
- BRATIO
- On two-stage Monte Carlo tests of composite hypotheses
- Quasi-systematic sampling from a continuous population
- Symmetric adaptive smoothing regimens for estimation of the spatial relative risk function
- Algorithm 840
- geoR
- GRASS GIS
- spatial
- Patchy patterns due to group dispersal
- KernSmooth
- Fast computation of spatially adaptive kernel estimates
- A bound of the \(\beta\)-mixing coefficient for point processes in terms of their intensity functions
- sppmix: Poisson point process modeling using normal mixture models
- Simulating Coulomb and log-gases with hybrid Monte Carlo algorithms
- MCQueue
- Convex and non-convex regularization methods for spatial point processes intensity estimation
- JTS Topology Suite
- The multipoint Morisita index for the analysis of spatial patterns
- 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
- R-Geo
- Toolbox Fast Marching
- smacof
- A toolbox for fitting complex spatial point process models using integrated nested Laplace approximation (INLA)
- Optimal obstacle placement with disambiguations
- Fast approximation of the intensity of Gibbs point processes
- Spatial logistic regression and change-of-support in Poisson point processes
- SPAGEDi
- INLA
- alphahull
- Principal component analysis of persistent homology rank functions with case studies of spatial point patterns, sphere packing and colloids
- maptools
- ks
- Robust clustering around regression lines with high density regions
- fields
- RandomFields
- BARD
- adehabitat
- RArcInfo
- raster
- S+SpatialStats
- splm
- spacetime
- gstat
- Splancs
- Pysal
- DCluster
- Monte Carlo integration of non-differentiable functions on \([0,1]^\iota\), \(\iota =1,\ldots, d\), using a single determinantal point pattern defined on \([0,1]^d\)
- Estimating animal utilization distributions from multiple data types: a joint spatiotemporal point process framework
- Local spatial log-Gaussian Cox processes for seismic data
- Novel concave hull-based heuristic algorithm for TSP
- Traceis
- Intensity estimation on geometric networks with penalized splines
- Perfect sampling for Gibbs point processes using partial rejection sampling
- Testing goodness of fit for point processes via topological data analysis
- Monte Carlo with determinantal point processes
- geometry
- rgl
- Inhomogeneous higher-order summary statistics for point processes on linear networks
- Modeling partially surveyed point process data: inferring spatial point intensity of geomagnetic anomalies
- Testing multivariate uniformity based on random geometric graphs
- Territorial behaviour of buzzards versus random matrix spacing distributions
- 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
- Incorporating big microdata in life table construction: A hypothesis-free estimator
- The stochastic geometry of unconstrained one-bit data compression
- Determinantal point process mixtures via spectral density approach
- EnviroStat
- On the zeros of the spectrogram of white noise
- Determinantal sampling designs
- Normal approximation for associated point processes via Stein's method with applications to determinantal point processes
- Incomplete determinantal processes: from random matrix to Poisson statistics
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