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spatstat (version 1.23-6)

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. Also supports three-dimensional point patterns, and space-time point patterns in any number of dimensions. Contains over 1000 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 and tessellations. Exploratory methods include K-functions, 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 etc. Point process models can be fitted to point pattern data using functions ppm, kppm, slrm similar to glm. Models may include dependence on covariates, interpoint interaction, cluster formation 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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Install

install.packages('spatstat')

Monthly Downloads

17,668

Version

1.23-6

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

October 11th, 2011

Functions in spatstat (1.23-6)

Random Thinning

Simulate a Fitted Gibbs Point Process Model

Generate Poisson Point Pattern in Three Dimensions

Generate Poisson Point Pattern in Any Dimensions

Galaxies in the Shapley Supercluster

Extract List of Tiles in a Tessellation

Apply Vector Translation

Apply Smoothing to Function Values

Extract Unique Points from a Spatial Point Pattern

summary.splitppp

Summary of a Split Point Pattern

Update a Fitted Point Process Model

Compute Integral of Function Against Cumulative Distribution

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

Compute Quadratic Forms

Summary of a Point Pattern Dataset

Volume of an Object

Sufficient Statistic of Point Process Model

Generate N Uniform Random Points

Simulate systematic random point pattern

Update a Fitted Cluster Point Process Model

Spatial smoothing of observations at irregular points

Poisson Point Process on a Linear Network

Randomly Shift a Point Pattern

Divide Image Into Sub-images

Estimate Variance of Summary Statistic by Subdivision

Rounding of Pixel Values

rshift.splitppp

Randomly Shift a List of Point Patterns

spatstat-package

The Spatstat Package

Uniform Random Points on a Linear Network

Smooth a Signed or Vector-Valued Measure

Cut margins from rectangle

Identify Pixelwise Maximum of Several Pixel Images

Spokes pattern of dummy points

Generate N Uniform Random Points in Three Dimensions

Generate Poisson Point Pattern on Line Segments

Apply Vector Translation To Pixel Image

Union of Data and Dummy Points

Summary of a Line Segment Pattern Dataset

Compute Areas of Tiles in a Tessellation

Evaluate an Expression in a Function Table

Create a Tessellation

Spruces Point Pattern

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Summary of a Spatial Window

Generate Poisson Point Pattern

Swedish Pines Point Pattern

Generate N Uniform Random Points in a Disc

scaletointerval

Rescale Data to Lie Between Specified Limits

Name for Unit of Length

Weighted Histogram

Poisson Line Tessellation

Generate Poisson Random Line Process

Randomly Shift a Line Segment Pattern

Approximate a Polygon by a Simpler Polygon

Simulate Stratified Random Point Pattern

Apply Vector Translation To Point Pattern

The Area Interaction Point Process Model

Cross Validated Bandwidth Selection for Relative Risk Estimation

The Soft Core Point Process Model

Set Covariance of a Window

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Summary of a List of Things

Generate N Uniform Random Points in Any Dimensions

Residual Diagnostics for Multiple Fitted Models

Simulate a Fitted Cluster Point Process Model

Divide Point Pattern into Sub-patterns

Variance-Covariance Matrix for a Fitted Point Process Model

Collapse Several Function Tables into One

Marked Nearest Neighbour Distance Function

Safely Convert Point Pattern Window to Binary Mask

Simple Example of Linear Network

Calculate four standard summary functions of a point pattern.

Inhomogeneous Multitype K Dot Function

Diggle's Heather Data

Fitted Conditional Intensity for Point Process Model

Nearest Neighbour Distance Function G

Cross Validated Bandwidth Selection for Kernel Density

spatstat.options

Internal Options in Spatstat Package

Summarizing a Fitted Point Process Model

Multitype K Function (Cross-type)

Superimpose Several Geometric Patterns

Extract or Replace Subset of a List of Things

Bronze gradient filter data

Find Largest Circle Inside Window

Convert Pixel Image to Matrix or Array

inforder.family

Infinite Order Interaction Family

Connected components of an image or window

K-function using FFT

The Hard Core Point Process Model

Distance to Boundary of Window

Apply a Function to a Point Pattern Broken Down by Factor

Residual K Function

Corners of a rectangle

Convert to Pixel Image

Combine Function Value Tables

Distance Map of Point Pattern

Test Whether An Object Is Empty

Diagnostics for random marking

Ord's Interaction model

Estimate the I-function

Test Whether An Object Is A Pixel Image

Chorley-Ribble Cancer Data

Fit the Thomas Point Process by Minimum Contrast

Areas of Morphological Dilations

Multitype K Function (i-to-any)

Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern

Apply Affine Transformation

Recognise Stationary and Poisson Point Process Models

Pixel Image Approximation of a Window

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Saturated Pairwise Interaction model

Test whether Object is Multitype

Evaluate Expression Involving Pixel Images

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Extract Subset of Image

Distance to Boundary of Window

Aherne's hamster tumour data

Morishita Index Plot

ANOVA for Fitted Point Process Models on Linear Network

Nearest neighbour distances in three dimensions

Pairwise distances between two different point patterns

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Plot Function Values

spatstat-deprecated

Deprecated spatstat functions

Extract the Interaction from a Fitted Point Process Model

Extract Subset of Function Array

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Circumradius and Diameter of a Linear Network

Intersection, Union or Set Subtraction of Two Windows

Area of Part of Disc

pairdist.default

Pairwise distances

Identify Segments in a Line Segment Pattern

Divide Region into Quadrats

Kolmogorov-Smirnov Test for Point Process Model

The Piecewise Constant Pairwise Interaction Point Process Model

envelope.envelope

Recompute Envelopes

Delaunay Triangulation of Point Pattern

Create a Pixel Image Object

Poisson Point Process Model

Function Arrays for Spatial Patterns

Generate a Quadrature Scheme from a Point Pattern

Methods for three-dimensional point patterns

Fitted Probabilities for Spatial Logistic Regression

Generate a Default Pattern of Dummy Points

Extract Interaction Structure

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

The Lennard-Jones Potential

Diggle-Gratton model

Kaplan-Meier and Reduced Sample Estimator using Histograms

Hutchings' Bramble Canes data

Simulate point patterns using the Metropolis-Hastings algorithm.

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

model.matrix.ppm

Extract Design Matrix from Point Process Model

Diameter of an Object

project2segment

Move Point To Nearest Line

Plot a List of Things

crossdist.default

Pairwise distances between two different sets of points

Function Value Table

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Morphological Dilation

The Multitype Hard Core Point Process Model

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Extract Subset of Signed or Vector Measure

Crossing Points of Two Line Segment Patterns

Pairwise distances

Simulate Matern Model II

Plot a Fitted Spatial Logistic Regression

Fit Cluster or Cox Point Process Model

Marked K-Function

Mark Connection Function

Local pair correlation function

Apply Affine Transformation To Line Segment Pattern

Interaction Distance of a Point Process

Define Point Process Model for Metropolis-Hastings Simulation.

Coefficients of Fitted Spatial Logistic Regression Model

Compute Disc of Given Radius in Linear Network

Loglikelihood of Spatial Logistic Regression

Simulate Baddeley-Silverman Cell Process

Create a Window

Longleaf Pines Point Pattern

Create a Point Pattern

Extract Dummy Points Used to Fit a Point Process Model

Inhomogeneous Linear Pair Correlation Function

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Convert Data to Three-Dimensional Box

Foxall's Distance Functions

Simulate Neyman-Scott Process

Classify Points in a Point Pattern

Colour Lookup Tables

Estimate window from points alone

Create a Linear Network

Subset of Quadrature Scheme

Print Brief Details of a Spatial Window

Methods for Cluster Point Process Models

Create Pixel Image on Linear Network

Nearest neighbour distances between line segments

Extract or Replace Subset of Point Pattern

Lurking variable plot

Pairwise distances between line segments

Circular Window

Orientation Angles of Line Segments

Quadrat counting for a point pattern

Convert Point Pattern to Pixel Image

Dummy Function Returns Number of Points

Convert Data To Class psp

Geometrical Calculations for Three-Dimensional Box

as.data.frame.im

Convert Pixel Image to Data Frame

Japanese Pines Point Pattern

Areas of Morphological Erosions

Nearest Neighbour Distances in Any Dimensions

Endpoints of Line Segment Pattern

Generate grid of parallel lines with random displacement

Point and Click Interface for Displaying a Point Pattern

Print Brief Details of a Point Pattern Dataset

Test Whether An Object Is A Fitted Point Process Model

Model Compensator of Nearest Neighbour Function

Bounding Box of a Window or Point Pattern

Pairwise distances between two different three-dimensional point patterns

Beta Ganglion Cells in Cat Retina

Pairwise distances between two different line segment patterns

Convert Data To Class owin

Interactively Define a Polygon

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Methods for Linear Networks

Berman's Tests for Point Process Model

Number of Points in a Point Pattern

Hyper Data Frame

Geyer's Saturation Point Process Model

Pine saplings in Finland.

Extract Quadrature Scheme Used to Fit a Point Process Model

Expand Window By Factor

methods.distfun

Methods for Distance Functions

Kaplan-Meier Estimator using Histogram Data

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Mosaic Random Set

Diagnostic Plots for Fitted Point Process Model

Centroid of a window

Pair Correlation Function obtained from array of K functions

Pair Correlation Function of a Three-Dimensional Point Pattern

Simulation Envelopes of Summary Function for 3D Point Pattern

Multitype J Function (i-to-j)

Generate N Random Multitype Points

Identify Points in a Point Pattern

Class of Line Segment Patterns

Clark and Evans Aggregation Index

Estimate the empty space function F

Fry Plot of Point Pattern

K function of a model

compatible.fasp

Test Whether Two Function Arrays Are Compatible

plot a Spatial Line Segment Pattern

Sample Quantiles of Pixel Image

Analysis of Deviance for Spatial Logistic Regression Models

Interpret Fitted Model for Metropolis-Hastings Simulation.

Make Pixel Images Compatible

Histogram of Pixel Values in an Image

Plot a Function Array

Pair Correlation Function of Point Pattern

Test Whether a Window is Convex

New Zealand Trees Point Pattern

Inhomogeneous Cross Type L Function

Model Formulae for Gibbs Point Process Models

Convert dataset to another unit of length

Residuals for Fitted Point Process Model

Create List of Plotting Layers

Plot a fitted cluster point process

Inhomogeneous Linear K Function

Methods for Multidimensional Space-Time Point Patterns

plot a Spatial Point Pattern

K-function of a Three-Dimensional Point Pattern

Geometrical Calculations for Multi-Dimensional Box

Midpoints of Line Segment Pattern

Multitype J Function (i-to-any)

Summarise Marks in Every Neighbourhood in a Point Pattern

Fit Point Process Model to Point Pattern on Linear Network

Compute Images of Constructed Covariates

clarkevans.test

Clark and Evans Test

Extract Subset of Function Values

Neighbourhood density function

Simulation Envelopes of Summary Function

Point Patterns of New Brunswick Forest Fires

Pool Data from Several Envelopes

Pseudoscore Diagnostic For Fitted Model against General Alternative

Plot a List of Things

Inhomogeneous Cross K Function

Create a Function Value Table

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Marked J Function

Create a Line Segment Pattern

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Distance for a Point Pattern Matching

Murchison gold deposits

Pairwise distances in Three Dimensions

Apply Function to Image Broken Down by Factor

Test Whether Marks Are Present

Distance Map of Line Segment Pattern

Data and Code From JRSS Discussion Paper on Residuals

Convert Point Pattern to Another Unit of Length

Influenza Virus Proteins

Mark Correlation Integral

Test Whether A Point Pattern is Marked

Reduced Second Moment Measure

Apply Function to Every Neighbourhood in a Point Pattern

Hughes' Amacrine Cell Data

Methods for Three-Dimensional Box

Apply Affine Transformation To Window

Pairwise shortest-path distances between points on a linear network

Diameter of a Window

Scatterplot Matrix for Pixel Images

Extract Subset of Line Segment Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Theoretical Distribution of Nearest Neighbour Distance

nearest.raster.point

Find Pixel Nearest to a Given Point

Plot a linear network

Plot a Spatial Kolmogorov-Smirnov Test

Empty Space Function of a Three-Dimensional Point Pattern

Nearest neighbour

Multitype pair correlation function (cross-type)

Biological Cells Point Pattern

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

Reset Values in Subset of Image

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Plot a List of Point Patterns

pairwise.family

Pairwise Interaction Process Family

Inhomogeneous K-function

Methods for Multi-Dimensional Box

Maximum, Minimum, Mean, Median, Range or Sum of Pixel Values in an Image

Methods for Fitted Point Process Models on a Linear Network

Plot a Pixel Image

Residual G Function

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

Subdivide a Window or Tessellation using a Set of Lines

Prediction from a Fitted Cluster Point Process Model

Locally Scaled K-function

Generate N Random Points

Humberside Data on Childhood Leukaemia and Lymphoma

Ponderosa Pine Tree Point Pattern

Methods for Point Patterns on a Linear Network

Interactively Add Points

Ord Interaction Process Family

Generic Ord Interaction model

Pairwise distances

Convert Data To Class ppp

Method of Minimum Contrast

Cross Validated Bandwidth Selection for Spatial Smoothing

Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative

Artificial Data Point Pattern

Pseudoscore Diagnostic For Fitted Model against Saturation Alternative

Pair Correlation Function obtained from K Function

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Inhomogeneous Pair Correlation Function

Perimeter Length of Window

Distance Map of Window

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Interactively join vertices on a plot

Prediction from a Fitted Point Process Model

Chicago Street Crime Data

Convert Spatial Object to Pixel Image

Plot Pixel Image on Linear Network

Fit Point Process Model to Data

plot.bermantest

Plot Result of Berman Test

Multitype L-function (cross-type)

Create Colour-Valued Pixel Image

The Strauss Point Process Model

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Compute Expansion Window for Simulation

Three-Dimensional Box

The Strauss / Hard Core Point Process Model

Evaluate Expression Involving Functions

Concatenate x,y Coordinate Vectors

Intersection of Two Tessellations

Combine Two Line Segment Patterns

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Plot a three-dimensional point pattern

Kernel Smoothed Intensity of Point Pattern

Convert Line Segment Pattern to Pixel Image

Multi-Dimensional Box

Apply Vector Translation To Line Segment Pattern

Perfect Simulation of the Strauss Process

Saturated Pairwise Interaction Point Process Family

Rotate a Line Segment Pattern

plot a Fitted Point Process Model

Print a Fitted Point Process Model

Predict Point Process Model on Linear Network

Reduced Sample Estimator using Histogram Data

Border Region of a Window

Simulate Gauss-Poisson Process

Class of Fitted Point Process Models

Smoothing Estimate of Covariate Transformation

Create a Point Matching

Simulate Log-Gaussian Cox Process

Convert Pixel Image from Numeric to Factor

Print Progress Reports

Spatial Covariance of a Pixel Image

California Redwoods Point Pattern (Ripley's Subset)

ANOVA for Fitted Point Process Models

Print a Quadrature Scheme

Point and Click Interface for Exploratory Analysis of Point Pattern

Exponential Energy Marks

Intersect Infinite Straight Lines with a Window

Lengths of Line Segments

Tropical rain forest trees

Harkness-Isham ants' nests data

Envelope for Point Patterns on Linear Network

Data Sharpening of Point Pattern

Extract.splitppp

Extract or Replace Sub-Patterns

complement.owin

Take Complement of a Window

Summarizing a Quadrature Scheme

California Redwoods Point Pattern (Entire Dataset)

Morphological Closing

Dirichlet Tessellation of Point Pattern

Extract or Replace Subset of Tessellation

Convert Window to Another Unit of Length

Beta Ganglion Cells in Cat Retina, Old Version

Convert Pixel Image to Another Unit of Length

Log Likelihood and AIC for Point Process Model

Vertices of a Window

Weighted Empirical Cumulative Distribution Function

Nonparametric Estimate of Spatially-Varying Relative Risk

Random Re-Labelling of Point Pattern

Nearest Neighbour Clutter Removal

Print News About Latest Version of Package

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Quadrature Scheme Based on Pixel Grid

Window in Shape of Letter R

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Lansing Woods Point Pattern

Marks of a Point Pattern

Simulate Simple Sequential Inhibition

matclust.estpcf

Fit the Matern Cluster Point Process by Minimum Contrast Using Pair Correlation

Generic Pairwise Interaction model

Methods for Intensity Functions of Spatial Covariate

Identify Covariates Involved in each Model Term

Set Control Parameters for Metropolis-Hastings Algorithm.

Exchange X and Y Coordinates

Multitype pair correlation function (i-to-any)

Beadlet Anemones Data

Make Periodic Copies of a Spatial Pattern

Nearest Neighbours Between Two Patterns

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Convert Line Segment Pattern to Binary Pixel Mask

Place Points Evenly Along Specified Lines

Rectangular grid of points

Convert Window to Pixel Image

Integral of a Pixel Image

Plot a tessellation

Determine Whether One Window is Contained In Another

Predicted or Fitted Values from Spatial Logistic Regression

Distance Between Two Point Patterns

Interpolate a Pixel Image

pppmatching.object

Class of Point Matchings

Kernel Smoothing of Line Segment Pattern

quadratresample

Resample a Point Pattern by Resampling Quadrats

Cartesian Coordinates for a Pixel Raster

Simulate Matern Cluster Process

Multidimensional Space-Time Point Pattern

Mosaic Random Field

Simulate Thomas Process

Define Point Process Model for Metropolis-Hastings Simulation.

Print Brief Details of an Image

Rotate a Window

Print Brief Details of a Line Segment Pattern Dataset

Simulate Matern Model I

Convert Line Segment Pattern to Another Unit of Length

Convert Data to Hyperframe

Find Line Segment Nearest to Each Point

Generate Multitype Poisson Point Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Plot a Spatial Window

Class of Images

Compute Fitted Effect of a Spatial Covariate in a Point Process Model

Distance to Boundary of Window

Signed or Vector-Valued Measure

multiplicity.ppp

Count Multiplicity of Duplicate Points

Simulate from a Fitted Point Process Model

Test Whether Two Function Objects Are Compatible

Coefficients of Fitted Point Process Model

Urkiola Woods Point Pattern

Nearest Neighbours in Any Dimensions

Class of Quadrature Schemes

Variance-Covariance Matrix for a Fitted Cluster Point Process Model

spatstat-internal

Internal spatstat functions

Model Compensator of K Function

Spherical Contact Distribution Function

Difference of Disc Areas

Test Whether Two Pixel Images Are Compatible

Pairwise distances

Morphological Erosion

Test Whether A Point Process Model is Marked

Test Whether An Object Is A Point Pattern

Level Set of a Pixel Image

Three Dimensional Point Pattern

Hybrid Geyer Point Process Model

rescue.rectangle

Convert Window Back To Rectangle

Multitype L-function (i-to-any)

Random Perturbation of a Point Pattern

Extract Original Data from a Fitted Point Process Model

Pairwise Distances in Any Dimensions

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Inverse-distance weighted smoothing of observations at irregular points

Inhomogeneous Neighbourhood Density Function

Linear K Function

Infinite Straight Lines

Pair Correlation Function

Class of Point Patterns

Pool Data from Several Function Arrays

Profile Maximum Pseudolikelihood

Q-Q Plot of Residuals from Fitted Point Process Model

Rotate a Point Pattern

Difference of Disc Areas

Read Point Pattern From Data File

Fit the Thomas Point Process by Minimum Contrast

Estimate the J-function

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Apply Affine Transformation To Point Pattern

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Berman-Huntington points and lines data

Evaluate Expression Involving Function Arrays

Test Whether Points Are Inside A Window

Test Whether An Object Is A Window

Nearest neighbour distances

Morphological Opening

Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)

Perspective Plot of Pixel Image

Plot a plotppm Object Created by plot.ppm

Number of Line Segments in a Line Segment Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

The Multitype Strauss Point Process Model

plot.hyperframe

Plot Entries in a Hyperframe

Convert Data to Numeric Values by Constructing Dummy Variables

Apply Gaussian Blur to a Pixel Image

Apply Vector Translation To Window

Simulated Point Pattern

Spatial Logistic Regression

Summarizing a Pixel Image

The Fiksel Interaction

Inhomogeneous Multitype L Dot Function

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Area of a Window

Convert Function Value Table to Function

Convert a Window to a Polygonal Window

Convert Data To Tessellation

Contour plot of pixel image

Convex Hull of Points

Convert and Compare Colours in Different Formats

Determine Duplicated Points in a Spatial Point Pattern

Compute Quadrature Weights Based on Grid Counts

Basis for Harmonic Functions

Linear Pair Correlation Function

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Create Point Pattern on Linear Network

Marks of a Line Segment Pattern

Mark Correlation Function

model.frame.ppm

Extract the Environment of a Point Process Model

Nearest neighbours in three dimensions

Plot a Colour Map

Plot a Simulation Envelope

Plot a Signed or Vector-Valued Measure

plot a Spatial Quadrature Scheme

Stoyan's Rule of Thumb for Bandwidth Selection

Convert Polygonal Region into Different Format

bounding.box.xy

Convex Hull of Points

Distance Map as a Function