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spatstat (version 1.11-4)

Spatial Point Pattern analysis, model-fitting, simulation, tests

Description

A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Contains functions for exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, and pixel images. Point process models can be fitted to point pattern data. Cluster type models are fitted by the method of minimum contrast. Very general Gibbs point process models can be fitted to point pattern data using a function ppm similar to lm or glm. Models may include dependence on covariates, interpoint interaction and dependence on marks. Fitted models can be simulated automatically. Also provides facilities for formal inference (such as chi-squared tests) and model diagnostics (including simulation envelopes, residuals, residual plots and Q-Q plots).

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Version

Install

install.packages('spatstat')

Monthly Downloads

14,637

Version

1.11-4

License

GPL version 2 or newer

Maintainer

Adrian Baddeley

Last Published

July 15th, 2024

Functions in spatstat (1.11-4)

ANOVA for Fitted Point Process Models

Area of a Window

K-function using FFT

The Lennard-Jones Potential

Mark Correlation Function

Convert Data To Class owin

Test Whether Two Pixel Images Are Compatible

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Extract Original Data from a Fitted Point Process Model

Orientation Angles of Line Segments

Dilate a Window

Berman-Huntington points and lines data

Combine Two Line Segment Patterns

Kaplan-Meier and Reduced Sample Estimator using Histograms

The Multitype Strauss Point Process Model

Geyer's Saturation Point Process Model

Prediction from a Fitted Point Process Model

Apply Affine Transformation

Evaluate Expression Involving Functions

Convert Point Pattern Marks from Numeric to Factor

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Variance-Covariance Matrix for a Fitted Point Process Model

subset.splitppp

Extract or Replace Sub-Patterns

Nearest neighbour distances

Fit the Thomas Point Process by Minimum Contrast

Multitype Nearest Neighbour Distance Function (i-to-j)

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Distance Map of Point Pattern

Marked Nearest Neighbour Distance Function

Histogram of Pixel Values in an Image

Determine Whether One Window is Contained In Another

Plot a List of Things

Create a Pixel Image Object

Simulate Stratified Random Point Pattern

Apply Vector Translation To Pixel Image

Summarise Marks in Every Neighbourhood in a Point Pattern

Estimate the empty space function F

Kernel Smoothed Intensity of Point Pattern

Ord's Interaction model

Plot a Function Array

Plot a Spatial Window

Pairwise distances

Sufficient Statistic of Point Process Model

Cartesian Coordinates for a Pixel Raster

Interpret Fitted Model for Metropolis-Hastings Simulation.

Simulate systematic random point pattern

Areas of Morphological Erosions

California Redwoods Point Pattern (Ripley's Subset)

Test Whether A Point Pattern is Marked

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Method of Minimum Contrast

spatstat-internal

Internal spatstat functions

Interactively Define a Polygon

Marked J Function

Plot a plotppm Object Created by plot.ppm

Beta Ganglion Cells in Cat Retina

New Zealand Trees Point Pattern

Compute Quadrature Weights Based on Grid Counts

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Mean Pixel Value in an Image

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Lansing Woods Point Pattern

Reduced Second Moment Measure

Kolmogorov-Smirnov Test for Point Process Model

Estimate the I-function

crossdist.default

Pairwise distances between two different sets of points

Apply Vector Translation To Window

Centroid of a window

Interactively Add Points

Marked K-Function

Nearest Neighbour in Another Point Pattern

bounding.box.xy

Convex Hull of Points

Intersection or Union of Two Windows

Hutchings' Bramble Canes data

Nearest neighbour

Set or Reset the Marks in a Point Pattern

Interaction Distance of a Point Process

Simulated Point Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Diagnostic Plots for Fitted Point Process Model

Generate N Random Multitype Points

Summary of a Point Pattern Dataset

Generate N Uniform Random Points

Pairwise distances

Harkness-Isham ants' nests data

Rotate a Point Pattern

Nearest-Neighbour Correlation of Marked Point Pattern

Corners of a rectangle

Diameter of a Window

Summarizing a Fitted Point Process Model

Summary of a List of Things

Perspective Plot of Pixel Image

Print a Fitted Point Process Model

Reset Values in Subset of Image

rshift.splitppp

Randomly Shift a List of Point Patterns

Superimpose Several Point Patterns

Residuals for Fitted Point Process Model

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Random Thinning

Perfect Simulation of the Strauss Process

Quadrat counting for a point pattern

Plot a Pixel Image

Convert Point Pattern to Another Unit of Length

Update a Fitted Point Process Model

Summarizing a Quadrature Scheme

Simulate Baddeley-Silverman Cell Process

Summary of a Spatial Window

Window in Shape of Letter R

Convert dataset to another unit of length

Inhomogeneous Multitype K Dot Function

The Strauss Point Process Model

The Strauss / Hard Core Point Process Model

Point Patterns of New Brunswick Forest Fires

Extract the Interaction from a Fitted Point Process Model

Test whether Object is Multitype

Distance Map of Window

Apply Affine Transformation To Line Segment Pattern

plot a Spatial Line Segment Pattern

Circular Window

Remove Marks from a Marked Point Pattern

Determine Duplicated Points in a Spatial Point Pattern

Create a Line Segment Pattern

Tropical rain forest trees

Apply Function to Every Neighbourhood in a Point Pattern

pairdist.default

Pairwise distances

Test Whether Two Function Objects Are Compatible

Apply Affine Transformation To Point Pattern

Profile Maximum Pseudolikelihood

pairwise.family

Pairwise Interaction Process Family

Class of Quadrature Schemes

Class of Point Patterns

Spruces Point Pattern

Extract Subset of Function Array

Class of Line Segment Patterns

Aherne's hamster tumour data

Print Brief Details of an Image

Extract or Replace Subset of a List of Things

Midpoints of Line Segment Pattern

Fit Point Process Model to Data

Fit the Matern Cluster Point Process by Minimum Contrast

Read Point Pattern From Data File

Multitype J Function (i-to-j)

Simulate Neyman-Scott Process

Convert to Pixel Image

Evaluate Expression Involving Pixel Images

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Distance to Boundary of Window

Vertices of a Window

Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True

Convert Window to Another Unit of Length

Extract Subset of Line Segment Pattern

nearest.raster.point

Find Pixel Nearest to a Given Point

Extract or Replace Subset of Point Pattern

Generate Poisson Random Line Process

Expand Window By Factor

Summary of a Line Segment Pattern Dataset

California Redwoods Point Pattern (Entire Dataset)

Set Covariance of a Window

Diggle-Gratton model

Convert Data To Class psp

Biological Cells Point Pattern

Simulation envelopes of summary function

Calculate Statistic for All Types in a Multitype Point Pattern

Apply Vector Translation To Line Segment Pattern

Poisson Point Process Model

spatstat-deprecated

Deprecated spatstat functions

Pine saplings in Finland.

Test Whether Marks Are Present

Convert Line Segment Pattern to Another Unit of Length

Artificial Data Point Pattern

Simulate Matern Model II

Rectangular grid of points

Test Whether A Point Process Model is Marked

plot a Spatial Point Pattern

Reduced Sample Estimator using Histogram Data

Plot a List of Point Patterns

Japanese Pines Point Pattern

Rotate a Line Segment Pattern

Beadlet Anemones Data

plot a Spatial Quadrature Scheme

Simulate Simple Sequential Inhibition

Extract Dummy Points Used to Fit a Point Process Model

multiplicity.ppp

Count Multiplicity of Duplicate Points

Hughes' Amacrine Cell Data

Rotate a Window

Ord Interaction Process Family

Generate Poisson Point Pattern

summary.splitppp

Summary of a Split Point Pattern

Apply Affine Transformation To Window

Lengths of Line Segments

Basis for Harmonic Functions

Randomly Shift a Point Pattern

Saturated Pairwise Interaction model

Kaplan-Meier Estimator using Histogram Data

Generic Ord Interaction model

Pair Correlation Function

Print Brief Details of a Spatial Window

Create a Window

Randomly Shift a Line Segment Pattern

Class of Fitted Point Process Models

Print Brief Details of a Line Segment Pattern Dataset

Estimate window from points alone

Generate N Random Points

Generate N Uniform Random Points in a Disc

Extract Subset of Image

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Kernel Smoothing of Line Segment Pattern

Level Set of a Pixel Image

Bounding Box of a Window or Point Pattern

Create a Point Pattern

Beta Ganglion Cells in Cat Retina, Old Version

Name for Unit of Length

Spokes pattern of dummy points

Pairwise distances between two different line segment patterns

Interpolate a Pixel Image

Calculate four standard summary functions of a point pattern.

Pair Correlation Function obtained from array of K functions

Estimate the J-function

Crossing Points of Two Line Segment Patterns

Coefficients of Fitted Point Process Model

Multitype Nearest Neighbour Distance Function (i-to-any)

Plot Function Valuesn

Generic Pairwise Interaction model

Lurking variable plot

Pairwise distances between line segments

Class of Images

Chorley-Ribble Cancer Data

Extract Unique Points from a Spatial Point Pattern

Multitype K Function (Cross-type)

Test Whether An Object Is A Fitted Point Process Model

Generate Multitype Poisson Point Pattern

Q-Q Plot of Residuals from Fitted Point Process Model

spatstat.options

Internal Options in Spatstat Package

Swedish Pines Point Pattern

Union of Data and Dummy Points

Longleaf Pines Point Pattern

Summarizing a Pixel Image

Simulate Matern Model I

Apply Vector Translation To Point Pattern

The Piecewise Constant Pairwise Interaction Point Process Model

Distance to Boundary of Window

Test Whether An Object Is A Pixel Image

Test Whether Points Are Inside A Window

Test Whether An Object Is A Point Pattern

Distance Map of Line Segment Pattern

complement.owin

Take Complement of a Window

Endpoints of Line Segment Pattern

Pairwise distances between two different point patterns

Humberside Data on Childhood Leukaemia and Lymphoma

Pixel Image Approximation of a Window

Data and Code From JRSS Discussion Paper on Residuals

Optimal Match Between Two Point Patterns

Simulate point patterns using the Metropolis-Hastings algorithm.

Simulate Thomas Process

The Soft Core Point Process Model

The Spatstat Package

Inhomogeneous K-function

Inhomogeneous Cross K Function

Weighted Empirical Cumulative Distribution Function

Convert Data To Class ppp

Data Frames of Function Values

Exponential Energy Marks

Nearest Neighbour Distance Function G

Pairwise distances

Sample Quantiles of Pixel Image

Nearest neighbour distances between line segments

Simulate from a Fitted Point Process Model

Simulate Matern Cluster Process

Convex Hull of Points

Saturated Pairwise Interaction Point Process Family

Multitype J Function (i-to-any)

Generate a Default Pattern of Dummy Points

Contour plot of pixel image

Function Arrays for Spatial Patterns

Multitype K Function (i-to-any)

Test Whether An Object Is A Window

Pair Correlation Function obtained from K Function

Convert Pixel Image from Numeric to Factor

Generate a Quadrature Scheme from a Point Pattern

Print Progress Reports

rescue.rectangle

Convert Window Back To Rectangle

Random Re-Labelling of Point Pattern

Extract Subset of Function Values

Define Point Process Model for Metropolis-Hastings Simulation.

Cut margins from rectangle

Apply Vector Translation

Pair Correlation Function of Point Pattern

Concatenate x,y Coordinate Vectors

Convert Pixel Image to Matrix

Identify Points in a Point Pattern

Print a Quadrature Scheme

Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts

plot a Fitted Point Process Model

Define Point Process Model for Metropolis-Hastings Simulation.

Fitted Conditional Intensity for Point Process Model

Divide Point Pattern into Sub-patterns

Extract Quadrature Scheme Used to Fit a Point Process Model

Print Brief Details of a Point Pattern Dataset

Set Control Parameters for Metropolis-Hastings Algorithm.