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spatstat (version 1.23-0)

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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Version

Install

install.packages('spatstat')

Monthly Downloads

16,590

Version

1.23-0

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

July 24th, 2011

Functions in spatstat (1.23-0)

Generate Poisson Point Pattern

Generate N Uniform Random Points in Three Dimensions

Galaxies in the Shapley Supercluster

Random Thinning

Generate Poisson Point Pattern on Line Segments

Compute Integral of Function Against Cumulative Distribution

Apply Vector Translation To Window

Simulate systematic random point pattern

The Soft Core Point Process Model

Extract Subset of Line Segment Pattern

Generate N Uniform Random Points in a Disc

Orientation Angles of Line Segments

Distance to Boundary of Window

Beta Ganglion Cells in Cat Retina

spatstat-internal

Internal spatstat functions

Simulated Point Pattern

Summarizing a Quadrature Scheme

Urkiola Woods Point Pattern

Estimate Variance of Summary Statistic by Subdivision

Interpret Fitted Model for Metropolis-Hastings Simulation.

Weighted Histogram

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Summary of a Point Pattern Dataset

Area of a Window

The Area Interaction Point Process Model

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Contour plot of pixel image

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

Marked J Function

Nearest Neighbour Distance Function G

Generate N Random Points

Multitype J Function (i-to-any)

Randomly Shift a Point Pattern

Diagnostic Plots for Fitted Point Process Model

Multitype J Function (i-to-j)

Extract Unique Points from a Spatial Point Pattern

Test Whether Two Function Objects Are Compatible

Summarizing a Pixel Image

Distance Map of Window

Fit Cluster or Cox Point Process Model

Crossing Points of Two Line Segment Patterns

Approximate a Polygon by a Simpler Polygon

Spokes pattern of dummy points

Poisson Point Process on a Linear Network

Randomly Shift a Line Segment Pattern

Swedish Pines Point Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Set Covariance of a Window

Summary of a Spatial Window

Poisson Line Tessellation

Smooth a Signed or Vector-Valued Measure

The Piecewise Constant Pairwise Interaction Point Process Model

Variance-Covariance Matrix for a Fitted Point Process Model

ANOVA for Fitted Point Process Models

scaletointerval

Rescale Data to Lie Between Specified Limits

Longleaf Pines Point Pattern

Difference of Disc Areas

The Fiksel Interaction

Poisson Point Process Model

The Multitype Hard Core Point Process Model

Inhomogeneous K-function

Apply Affine Transformation

Foxall's Distance Functions

Extract List of Tiles in a Tessellation

Three-Dimensional Box

Extract.splitppp

Extract or Replace Sub-Patterns

Apply Vector Translation To Point Pattern

complement.owin

Take Complement of a Window

Convert a Window to a Polygonal Window

Spatial smoothing of observations at irregular points

Reduced Second Moment Measure

Analysis of Deviance for Spatial Logistic Regression Models

Apply Affine Transformation To Line Segment Pattern

Diggle-Gratton model

Corners of a rectangle

Multitype K Function (Cross-type)

Superimpose Several Geometric Patterns

crossdist.default

Pairwise distances between two different sets of points

Convert Data to Three-Dimensional Box

Extract or Replace Subset of Tessellation

Apply Gaussian Blur to a Pixel Image

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Methods for Multidimensional Space-Time Point Patterns

Geometrical Calculations for Multi-Dimensional Box

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Morphological Dilation

Rectangular grid of points

Pairwise distances between two different line segment patterns

Geyer's Saturation Point Process Model

The Lennard-Jones Potential

Histogram of Pixel Values in an Image

Summary of a List of Things

Convex Hull of Points

Bounding Box of a Window or Point Pattern

Convert Data To Class psp

Update a Fitted Point Process Model

Locally Scaled K-function

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

The Strauss Point Process Model

Signed or Vector-Valued Measure

Kernel Smoothed Intensity of Point Pattern

Ord Interaction Process Family

Determine Duplicated Points in a Spatial Point Pattern

Classify Points in a Point Pattern

Extract Interaction Structure

Apply Function to Image Broken Down by Factor

Summary of a Line Segment Pattern Dataset

Saturated Pairwise Interaction model

Dirichlet Tessellation of Point Pattern

Estimate the J-function

Test Whether An Object Is A Fitted Point Process Model

Plot a three-dimensional point pattern

Summarise Marks in Every Neighbourhood in a Point Pattern

Convert Point Pattern to Pixel Image

Extract Subset of Function Values

Calculate four standard summary functions of a point pattern.

Endpoints of Line Segment Pattern

Extract Original Data from a Fitted Point Process Model

Estimate the empty space function F

K-function of a Three-Dimensional Point Pattern

Pairwise distances

Hughes' Amacrine Cell Data

Apply Affine Transformation To Point Pattern

Circular Window

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

K-function using FFT

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

Rotate a Point Pattern

Expand Window By Factor

Function Value Table

Exponential Energy Marks

Marks of a Point Pattern

Geometrical Calculations for Three-Dimensional Box

Evaluate Expression Involving Functions

The Multitype Strauss Point Process Model

Convert to Pixel Image

Basis for Harmonic Functions

Concatenate x,y Coordinate Vectors

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

Intersection, Union or Set Subtraction of Two Windows

Intersection of Two Tessellations

Evaluate Expression Involving Function Arrays

Hyper Data Frame

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

Multi-Dimensional Box

Test Whether A Point Process Model is Marked

Tropical rain forest trees

Window in Shape of Letter R

Create a Point Pattern

Stoyan's Rule of Thumb for Bandwidth Selection

Ord's Interaction model

Biological Cells Point Pattern

Test Whether An Object Is A Point Pattern

Divide Point Pattern into Sub-patterns

Morphological Closing

Test Whether An Object Is A Window

Diameter of a Window

Point and Click Interface for Exploratory Analysis of Point Pattern

Lengths of Line Segments

Harkness-Isham ants' nests data

Marks of a Line Segment Pattern

Convert Pixel Image to Matrix or Array

model.matrix.ppm

Extract Design Matrix from Point Process Model

Japanese Pines Point Pattern

Inhomogeneous Linear K Function

Q-Q Plot of Residuals from Fitted Point Process Model

Recognise Stationary and Poisson Point Process Models

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

spatstat.options

Internal Options in Spatstat Package

Uniform Random Points on a Linear Network

Perspective Plot of Pixel Image

Distance to Boundary of Window

Rotate a Window

Diggle's Heather Data

Simple Example of Linear Network

California Redwoods Point Pattern (Entire Dataset)

Linear K Function

Perimeter Length of Window

Quadrat counting for a point pattern

Inhomogeneous Linear Pair Correlation Function

Subdivide a Window or Tessellation using a Set of Lines

Plot Function Values

Convert Pixel Image to Another Unit of Length

Berman-Huntington points and lines data

Convert Line Segment Pattern to Binary Pixel Mask

clarkevans.test

Clark and Evans Test

Plot a Signed or Vector-Valued Measure

Evaluate Expression Involving Pixel Images

Generate Poisson Random Line Process

Methods for Point Patterns on a Linear Network

Coefficients of Fitted Point Process Model

Union of Data and Dummy Points

Pairwise distances between two different point patterns

Hutchings' Bramble Canes data

Plot a Pixel Image

Generate N Uniform Random Points

Nearest neighbours in three dimensions

plot.bermantest

Plot Result of Berman Test

Morphological Erosion

Sufficient Statistic of Point Process Model

Extract the Interaction from a Fitted Point Process Model

Pairwise distances between line segments

Class of Images

Compute Disc of Given Radius in Linear Network

Plot a fitted cluster point process

Plot Pixel Image on Linear Network

Generate a Default Pattern of Dummy Points

Spatial Logistic Regression

Simulate Baddeley-Silverman Cell Process

Mark Connection Function

Point Patterns of New Brunswick Forest Fires

Find Largest Circle Inside Window

Cross Validated Bandwidth Selection for Relative Risk Estimation

Fit the Thomas Point Process by Minimum Contrast

Simulate a Fitted Gibbs Point Process Model

Residuals for Fitted Point Process Model

Nearest neighbour

Diameter of an Object

Methods for Intensity Functions of Spatial Covariate

Residual Diagnostics for Multiple Fitted Models

Compute Images of Constructed Covariates

plot a Spatial Quadrature Scheme

Plot a List of Things

inforder.family

Infinite Order Interaction Family

Convert Polygonal Region into Different Format

Pair Correlation Function obtained from array of K functions

Extract or Replace Subset of Point Pattern

Create Pixel Image on Linear Network

Create a Function Value Table

Variance-Covariance Matrix for a Fitted Cluster Point Process Model

Nearest Neighbours Between Two Patterns

Simulate Gauss-Poisson Process

pairwise.family

Pairwise Interaction Process Family

Number of Points in a Point Pattern

Test Whether A Point Pattern is Marked

Hybrid Geyer Point Process Model

Create Point Pattern on Linear Network

Safely Convert Point Pattern Window to Binary Mask

Midpoints of Line Segment Pattern

Scatterplot Matrix for Pixel Images

Empty Space Function of a Three-Dimensional Point Pattern

Murchison gold deposits

Inhomogeneous Pair Correlation Function

Predict Point Process Model on Linear Network

Inhomogeneous Cross Type L Function

Create a Linear Network

Subset of Quadrature Scheme

Nearest neighbour distances between line segments

Print News About Latest Version of Package

Pixel Image Approximation of a Window

pairdist.default

Pairwise distances

Pair Correlation Function

Simulate Log-Gaussian Cox Process

Print Progress Reports

Divide Region into Quadrats

Nearest Neighbour Distances in Any Dimensions

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Log Likelihood and AIC for Point Process Model

Create Colour-Valued Pixel Image

Methods for Cluster Point Process Models

Envelope for Point Patterns on Linear Network

Identify Pixelwise Maximum of Several Pixel Images

Convert Pixel Image from Numeric to Factor

Pair Correlation Function of a Three-Dimensional Point Pattern

Beta Ganglion Cells in Cat Retina, Old Version

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

quadratresample

Resample a Point Pattern by Resampling Quadrats

Mosaic Random Field

Plot a Function Array

Test Whether a Window is Convex

Model Compensator of K Function

Nearest neighbour distances

Pair Correlation Function of Point Pattern

Combine Function Value Tables

Point and Click Interface for Displaying a Point Pattern

Simulate Matern Model I

Beadlet Anemones Data

Three Dimensional Point Pattern

Simulate Matern Model II

rescue.rectangle

Convert Window Back To Rectangle

Test Whether An Object Is A Pixel Image

Test whether Object is Multitype

Identify Points in a Point Pattern

Generic Pairwise Interaction model

Bronze gradient filter data

Print a Quadrature Scheme

Print a Fitted Point Process Model

Convert Window to Pixel Image

Mosaic Random Set

Quadrature Scheme Based on Pixel Grid

Distance Map as a Function

Class of Fitted Point Process Models

Cartesian Coordinates for a Pixel Raster

Multitype pair correlation function (cross-type)

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Local pair correlation function

Clark and Evans Aggregation Index

Distance Between Two Point Patterns

Create a Pixel Image Object

Create a Line Segment Pattern

project2segment

Move Point To Nearest Line

Convert Point Pattern to Another Unit of Length

Make Periodic Copies of a Spatial Pattern

Estimate window from points alone

Simulate Simple Sequential Inhibition

Coefficients of Fitted Spatial Logistic Regression Model

Integral of a Pixel Image

Plot a plotppm Object Created by plot.ppm

Print Brief Details of a Spatial Window

Convert and Compare Colours in Different Formats

Set Control Parameters for Metropolis-Hastings Algorithm.

Apply a Function to a Point Pattern Broken Down by Factor

Multidimensional Space-Time Point Pattern

Distance to Boundary of Window

New Zealand Trees Point Pattern

pppmatching.object

Class of Point Matchings

Distance for a Point Pattern Matching

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Sample Quantiles of Pixel Image

Data Sharpening of Point Pattern

Generate Poisson Point Pattern in Any Dimensions

Simulate Thomas Process

Extract Quadrature Scheme Used to Fit a Point Process Model

Morishita Index Plot

Apply Vector Translation To Line Segment Pattern

Name for Unit of Length

Chorley-Ribble Cancer Data

Nearest Neighbour Clutter Removal

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Convert Line Segment Pattern to Another Unit of Length

Interaction Distance of a Point Process

California Redwoods Point Pattern (Ripley's Subset)

Print Brief Details of a Point Pattern Dataset

Delaunay Triangulation of Point Pattern

Fry Plot of Point Pattern

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

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Pairwise distances

rshift.splitppp

Randomly Shift a List of Point Patterns

Theoretical Distribution of Nearest Neighbour Distance

Area of Part of Disc

Methods for Linear Networks

Plot a Spatial Kolmogorov-Smirnov Test

Volume of an Object

Pine saplings in Finland.

Class of Point Patterns

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Apply Vector Translation

Apply Vector Translation To Pixel Image

Ponderosa Pine Tree Point Pattern

Convert Function Value Table to Function

Prediction from a Fitted Point Process Model

Identify Segments in a Line Segment Pattern

Generate grid of parallel lines with random displacement

Compute Quadrature Weights Based on Grid Counts

Convert Spatial Object to Pixel Image

Plot a Colour Map

Spherical Contact Distribution Function

Extract or Replace Subset of a List of Things

Level Set of a Pixel Image

Saturated Pairwise Interaction Point Process Family

Test Whether Marks Are Present

Model Compensator of Nearest Neighbour Function

Plot a linear network

spatstat-deprecated

Deprecated spatstat functions

Vertices of a Window

methods.distfun

Methods for Distance Functions

Fit Point Process Model to Data

Nearest neighbour distances in three dimensions

Inhomogeneous Cross K Function

Residual G Function

Class of Line Segment Patterns

Lurking variable plot

Residual K Function

Pairwise distances

Plot a List of Point Patterns

Place Points Evenly Along Specified Lines

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Spruces Point Pattern

Apply Function to Every Neighbourhood in a Point Pattern

Inhomogeneous Multitype K Dot Function

Define Point Process Model for Metropolis-Hastings Simulation.

plot a Spatial Point Pattern

Evaluate an Expression in a Function Table

Prediction from a Fitted Cluster Point Process Model

Apply Smoothing to Function Values

Generate a Quadrature Scheme from a Point Pattern

Multitype K Function (i-to-any)

Interactively join vertices on a plot

Berman's Tests for Point Process Model

Pseudoscore Diagnostic For Fitted Model against General Alternative

Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative

Marked Nearest Neighbour Distance Function

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

Nonparametric Estimate of Spatially-Varying Relative Risk

Colour Lookup Tables

Inhomogeneous Multitype L Dot Function

The Strauss / Hard Core Point Process Model

Intersect Infinite Straight Lines with a Window

Apply Affine Transformation To Window

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

model.frame.ppm

Extract the Environment of a Point Process Model

Circumradius and Diameter of a Linear Network

Pairwise distances between two different three-dimensional point patterns

Random Re-Labelling of Point Pattern

Simulate point patterns using the Metropolis-Hastings algorithm.

K function of a model

Distance Map of Line Segment Pattern

Convert Data To Tessellation

Fitted Probabilities for Spatial Logistic Regression

Connected components of an image or window

Model Formulae for Gibbs Point Process Models

Distance Map of Point Pattern

Test Whether Two Pixel Images Are Compatible

Compute Expansion Window for Simulation

Determine Whether One Window is Contained In Another

Areas of Morphological Erosions

Areas of Morphological Dilations

Aherne's hamster tumour data

Infinite Straight Lines

Loglikelihood of Spatial Logistic Regression

Fitted Conditional Intensity for Point Process Model

Method of Minimum Contrast

Find Line Segment Nearest to Each Point

Pairwise shortest-path distances between points on a linear network

Methods for Multi-Dimensional Box

Mark Correlation Integral

matclust.estpcf

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

Pairwise Distances in Any Dimensions

Pair Correlation Function obtained from K Function

Plot a Simulation Envelope

Pairwise distances in Three Dimensions

Dummy Function Returns Number of Points

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Plot a Spatial Window

Random Perturbation of a Point Pattern

Perfect Simulation of the Strauss Process

Define Point Process Model for Metropolis-Hastings Simulation.

Convert dataset to another unit of length

plot.hyperframe

Plot Entries in a Hyperframe

plot a Fitted Point Process Model

Predicted or Fitted Values from Spatial Logistic Regression

Neighbourhood density function

Simulate Matern Cluster Process

Convert Window to Another Unit of Length

Pseudoscore Diagnostic For Fitted Model against Saturation Alternative

Simulate from a Fitted Point Process Model

Generate Multitype Poisson Point Pattern

Generate Poisson Point Pattern in Three Dimensions

Simulate Stratified Random Point Pattern

Read Point Pattern From Data File

Summarizing a Fitted Point Process Model

Update a Fitted Cluster Point Process Model

Cut margins from rectangle

Create a Tessellation

Extract Subset of Image

Multitype L-function (cross-type)

Generic Ord Interaction model

Interactively Define a Polygon

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Interpolate a Pixel Image

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Mark Correlation Function

Linear Pair Correlation Function

nearest.raster.point

Find Pixel Nearest to a Given Point

Create a Window

Reduced Sample Estimator using Histogram Data

Smoothing Estimate of Covariate Transformation

plot a Spatial Line Segment Pattern

Generate N Random Multitype Points

spatstat-package

The Spatstat Package

Rounding of Pixel Values

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

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Reset Values in Subset of Image

ANOVA for Fitted Point Process Models on Linear Network

Calculate Summary Statistic for All Types in a Multitype Point Pattern

bounding.box.xy

Convex Hull of Points

Centroid of a window

The Hard Core Point Process Model

Interactively Add Points

Combine Two Line Segment Patterns

Simulation Envelopes of Summary Function for 3D Point Pattern

Function Arrays for Spatial Patterns

Humberside Data on Childhood Leukaemia and Lymphoma

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Kaplan-Meier Estimator using Histogram Data

Lansing Woods Point Pattern

Methods for Fitted Point Process Models on a Linear Network

Nearest Neighbours in Any Dimensions

Number of Line Segments in a Line Segment Pattern

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Create a Point Matching

Print Brief Details of an Image

Profile Maximum Pseudolikelihood

Test Whether An Object Is Empty

Fit Point Process Model to Point Pattern on Linear Network

Generate N Uniform Random Points in Any Dimensions

Simulate a Fitted Cluster Point Process Model

Divide Image Into Sub-images

summary.splitppp

Summary of a Split Point Pattern

Extract Subset of Signed or Vector Measure

Marked K-Function

Extract Subset of Function Array

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Difference of Disc Areas

Convert Data to Hyperframe

as.data.frame.im

Convert Pixel Image to Data Frame

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Convert Data To Class ppp

Border Region of a Window

Chicago Street Crime Data

Weighted Empirical Cumulative Distribution Function

Influenza Virus Proteins

Kaplan-Meier and Reduced Sample Estimator using Histograms

Kolmogorov-Smirnov Test for Point Process Model

Artificial Data Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

Methods for Three-Dimensional Box

Methods for three-dimensional point patterns

multiplicity.ppp

Count Multiplicity of Duplicate Points

Morphological Opening

Simulation Envelopes of Summary Function

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Plot a tessellation

Print Brief Details of a Line Segment Pattern Dataset

Class of Quadrature Schemes

Simulate Neyman-Scott Process

Data and Code From JRSS Discussion Paper on Residuals

Convert Data To Class owin

Diagnostics for random marking

Multitype L-function (i-to-any)

Estimate the I-function

Collapse Several Function Tables into One

Extract Dummy Points Used to Fit a Point Process Model

Kernel Smoothing of Line Segment Pattern

Test Whether Points Are Inside A Window

Plot a Fitted Spatial Logistic Regression

Multitype pair correlation function (i-to-any)

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Convert Line Segment Pattern to Pixel Image

Rotate a Line Segment Pattern

Compute Areas of Tiles in a Tessellation

Fit the Thomas Point Process by Minimum Contrast