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spatstat (version 1.12-1)

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 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, 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

19,373

Version

1.12-1

License

GPL version 2 or newer

Maintainer

Adrian Baddeley

Last Published

September 22nd, 2024

Functions in spatstat (1.12-1)

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

Geyer's Saturation Point Process Model

Inhomogeneous K-function

Generic Pairwise Interaction model

Saturated Pairwise Interaction model

ANOVA for Fitted Point Process Models

Orientation Angles of Line Segments

Reduced Second Moment Measure

Ord's Interaction model

Berman-Huntington points and lines data

Tropical rain forest trees

Apply Function to Every Neighbourhood in a Point Pattern

Nearest Neighbour Distance Function G

The Strauss / Hard Core Point Process Model

Contour plot of pixel image

Calculate Statistic for All Types in a Multitype Point Pattern

crossdist.default

Pairwise distances between two different sets of points

Combine Two Line Segment Patterns

Corners of a rectangle

Test Whether Points Are Inside A Window

Marked K-Function

Convert Point Pattern Marks from Numeric to Factor

Test whether Object is Multitype

Biological Cells Point Pattern

Apply Affine Transformation To Point Pattern

Convert to Pixel Image

Generate a Default Pattern of Dummy Points

Dilate a Window

Harkness-Isham ants' nests data

Summarise Marks in Every Neighbourhood in a Point Pattern

Clark and Evans Aggregation Index

The Multitype Strauss Point Process Model

Simulation envelopes of summary function

Test Whether An Object Is A Window

Pairwise distances

Test Whether An Object Is A Point Pattern

Safely Convert Point Pattern Window to Binary Mask

Evaluate Expression Involving Functions

Distance to Boundary of Window

Optimal Match Between Two Point Patterns

Mark Correlation Function

Pairwise distances

Multitype J Function (i-to-any)

Expand Window By Factor

Endpoints of Line Segment Pattern

Convert Pixel Image from Numeric to Factor

Extract Dummy Points Used to Fit a Point Process Model

Extract the Interaction from a Fitted Point Process Model

Extract Original Data from a Fitted Point Process Model

Weighted Empirical Cumulative Distribution Function

Poisson Point Process Model

The Lennard-Jones Potential

Create a Pixel Image Object

Diggle-Gratton model

Midpoints of Line Segment Pattern

Circular Window

Hutchings' Bramble Canes data

Nearest neighbour distances between line segments

Estimate the J-function

Test Whether A Point Process Model is Marked

Kaplan-Meier and Reduced Sample Estimator using Histograms

Random Re-Labelling of Point Pattern

Neighbourhood density function

Print Brief Details of a Point Pattern Dataset

plot a Spatial Line Segment Pattern

plot.hyperframe

Plot Entries in a Hyperframe

Evaluate Expression Involving Pixel Images

Perfect Simulation of the Strauss Process

Coefficients of Fitted Point Process Model

Vertices of a Window

Humberside Data on Childhood Leukaemia and Lymphoma

bounding.box.xy

Convex Hull of Points

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

The Strauss Point Process Model

Nearest-Neighbour Correlation of Marked Point Pattern

Histogram of Pixel Values in an Image

Plot a Function Array

Nearest neighbour

Distance Map of Point Pattern

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Distance to Boundary of Window

Simulate Matern Model II

Print Brief Details of a Line Segment Pattern Dataset

Lurking variable plot

pairdist.default

Pairwise distances

Multitype J Function (i-to-j)

The Soft Core Point Process Model

spatstat-internal

Internal spatstat functions

Crossing Points of Two Line Segment Patterns

Apply Affine Transformation

Print Brief Details of an Image

Estimate the I-function

Print a Fitted Point Process Model

Q-Q Plot of Residuals from Fitted Point Process Model

nearest.raster.point

Find Pixel Nearest to a Given Point

Print Brief Details of a Spatial Window

Determine Duplicated Points in a Spatial Point Pattern

Calculate four standard summary functions of a point pattern.

Pair Correlation Function obtained from array of K functions

Pair Correlation Function obtained from K Function

Interpolate a Pixel Image

Marked J Function

Test Whether An Object Is A Pixel Image

Inhomogeneous Multitype K Dot Function

Beta Ganglion Cells in Cat Retina

Generate Multitype Poisson Point Pattern

rshift.splitppp

Randomly Shift a List of Point Patterns

Pair Correlation Function of Point Pattern

Generic Ord Interaction model

Generate a Quadrature Scheme from a Point Pattern

multiplicity.ppp

Count Multiplicity of Duplicate Points

Class of Line Segment Patterns

Rotate a Line Segment Pattern

Hughes' Amacrine Cell Data

Create a Point Pattern

Estimate the empty space function F

Apply Vector Translation To Point Pattern

Generate N Random Points

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Level Set of a Pixel Image

Randomly Shift a Point Pattern

Apply Affine Transformation To Window

Simulate Matern Model I

Reduced Sample Estimator using Histogram Data

Extract Quadrature Scheme Used to Fit a Point Process Model

Chorley-Ribble Cancer Data

Create a Line Segment Pattern

Set Covariance of a Window

complement.owin

Take Complement of a Window

Simulate point patterns using the Metropolis-Hastings algorithm.

Distance Map of Line Segment Pattern

Pixel Image Approximation of a Window

Read Point Pattern From Data File

Evaluate an Expression in Each Row of a Hyperframe

Convert Line Segment Pattern to Another Unit of Length

Sample Quantiles of Pixel Image

Convert Data To Class psp

Inhomogeneous Cross K Function

Convert Data To Class ppp

Apply Affine Transformation To Line Segment Pattern

Extract or Replace Subset of a List of Things

Exponential Energy Marks

Area of a Window

Convert Pixel Image to Matrix

Pairwise distances between two different line segment patterns

Bounding Box of a Window or Point Pattern

Beadlet Anemones Data

Simulate systematic random point pattern

Kernel Smoothing of Line Segment Pattern

Diagnostic Plots for Fitted Point Process Model

Beta Ganglion Cells in Cat Retina, Old Version

Summary of a Spatial Window

Pairwise distances between two different point patterns

Pine saplings in Finland.

Simulated Point Pattern

Areas of Morphological Erosions

subset.splitppp

Extract or Replace Sub-Patterns

Identify Points in a Point Pattern

Class of Images

Summarizing a Pixel Image

Extract Subset of Image

Log Likelihood for Poisson Point Process Model

Reset Values in Subset of Image

Convert Window to Another Unit of Length

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Generate Poisson Point Pattern

Create a Window

Test Whether Two Function Objects Are Compatible

Swedish Pines Point Pattern

Test Whether A Point Pattern is Marked

Generate N Random Multitype Points

Ord Interaction Process Family

Summary of a Line Segment Pattern Dataset

Test Whether An Object Is A Fitted Point Process Model

Generate N Uniform Random Points in a Disc

Plot a plotppm Object Created by plot.ppm

Interpret Fitted Model for Metropolis-Hastings Simulation.

Lansing Woods Point Pattern

spatstat-deprecated

Deprecated spatstat functions

Nearest Neighbour in Another Point Pattern

Convert dataset to another unit of length

Interactively Add Points

plot a Fitted Point Process Model

Artificial Data Point Pattern

Multitype K Function (i-to-any)

Test Whether Two Pixel Images Are Compatible

Multitype K Function (Cross-type)

Convex Hull of Points

Diameter of a Window

Fit the Matern Cluster Point Process by Minimum Contrast

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Divide Point Pattern into Sub-patterns

Hyper Data Frame

Saturated Pairwise Interaction Point Process Family

Fit Point Process Model to Data

Spatial smoothing of observations at irregular points

plot a Spatial Point Pattern

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Pairwise distances

Determine Initial State for Metropolis-Hastings Simulation.

Convert Data To Class owin

Distance Map of Window

Mean Pixel Value in an Image

Intersection or Union of Two Windows

Aherne's hamster tumour data

Point Patterns of New Brunswick Forest Fires

Plot a Pixel Image

Class of Point Patterns

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Rotate a Point Pattern

Data Frames of Function Values

Rectangular grid of points

Plot a List of Point Patterns

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

Basis for Harmonic Functions

Kolmogorov-Smirnov Test for Point Process Model

Print Progress Reports

Pair Correlation Function

Function Arrays for Spatial Patterns

California Redwoods Point Pattern (Ripley's Subset)

Spruces Point Pattern

Test Whether Marks Are Present

Determine Whether One Window is Contained In Another

Perspective Plot of Pixel Image

Profile Maximum Pseudolikelihood

Plot Function Valuesn

Define Point Process Model for Metropolis-Hastings Simulation.

New Zealand Trees Point Pattern

Remove Marks from a Marked Point Pattern

Simulate Thomas Process

Estimate window from points alone

Simulate Baddeley-Silverman Cell Process

Class of Fitted Point Process Models

Method of Minimum Contrast

Quadrat counting for a point pattern

Pairwise distances between line segments

Kernel Smoothed Intensity of Point Pattern

pairwise.family

Pairwise Interaction Process Family

Update a Fitted Point Process Model

Interaction Distance of a Point Process

Lengths of Line Segments

Define Point Process Model for Metropolis-Hastings Simulation.

Simulate Neyman-Scott Process

Plot a List of Things

Randomly Shift a Line Segment Pattern

Summary of a Point Pattern Dataset

Set or Reset the Marks in a Point Pattern

Marked Nearest Neighbour Distance Function

Kaplan-Meier Estimator using Histogram Data

Summary of a List of Things

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Summarizing a Fitted Point Process Model

Fit the Thomas Point Process by Minimum Contrast

Extract Unique Points from a Spatial Point Pattern

Apply Vector Translation To Window

Interactively Define a Polygon

Prediction from a Fitted Point Process Model

summary.splitppp

Summary of a Split Point Pattern

Window in Shape of Letter R

Variance-Covariance Matrix for a Fitted Point Process Model

Simulate Matern Cluster Process

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Cartesian Coordinates for a Pixel Raster

Nearest neighbour distances

Centroid of a window

Simulate from a Fitted Point Process Model

Compute Quadrature Weights Based on Grid Counts

plot a Spatial Quadrature Scheme

The Spatstat Package

Residuals for Fitted Point Process Model

K-function using FFT

Set Control Parameters for Metropolis-Hastings Algorithm.

Apply Vector Translation To Pixel Image

The Piecewise Constant Pairwise Interaction Point Process Model

Concatenate x,y Coordinate Vectors

Rotate a Window

Name for Unit of Length

Longleaf Pines Point Pattern

Simulate Stratified Random Point Pattern

Fitted Conditional Intensity for Point Process Model

Plot a Spatial Window

California Redwoods Point Pattern (Entire Dataset)

rescue.rectangle

Convert Window Back To Rectangle

Spokes pattern of dummy points

Ponderosa Pine Tree Point Pattern

Print a Quadrature Scheme

Convert Point Pattern to Another Unit of Length

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Japanese Pines Point Pattern

Class of Quadrature Schemes

Extract or Replace Subset of Point Pattern

Data and Code From JRSS Discussion Paper on Residuals

Generate grid of parallel lines with random displacement

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Generate Poisson Random Line Process

Summarizing a Quadrature Scheme

Generate N Uniform Random Points

Superimpose Several Point Patterns

Apply Vector Translation To Line Segment Pattern

Random Thinning

Extract Subset of Line Segment Pattern

Simulate Simple Sequential Inhibition

Sufficient Statistic of Point Process Model

Union of Data and Dummy Points

Apply Vector Translation

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

Extract Subset of Function Array

spatstat.options

Internal Options in Spatstat Package

Extract Subset of Function Values

Cut margins from rectangle