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spatstat (version 1.23-3)

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

16,015

Version

1.23-3

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

August 12th, 2011

Functions in spatstat (1.23-3)

Extract.splitppp

Extract or Replace Sub-Patterns

K function of a model

Generic Pairwise Interaction model

Calculate four standard summary functions of a point pattern.

Diagnostics for random marking

The Fiksel Interaction

Multitype L-function (cross-type)

Convert a Window to a Polygonal Window

Convex Hull of Points

Centroid of a window

Colour Lookup Tables

Inhomogeneous K-function

Ord's Interaction model

Test Whether An Object Is A Fitted Point Process Model

Analysis of Deviance for Spatial Logistic Regression Models

Pairwise distances between two different three-dimensional point patterns

methods.distfun

Methods for Distance Functions

Extract Subset of Image

Function Value Table

Bounding Box of a Window or Point Pattern

Multitype K Function (Cross-type)

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Convert Function Value Table to Function

Identify Segments in a Line Segment Pattern

Convert Pixel Image from Numeric to Factor

Clark and Evans Aggregation Index

Artificial Data Point Pattern

Methods for Multi-Dimensional Box

ANOVA for Fitted Point Process Models

Convert Line Segment Pattern to Binary Pixel Mask

Extract Subset of Line Segment Pattern

Estimate the I-function

Methods for Fitted Point Process Models on a Linear Network

Classify Points in a Point Pattern

Estimate the empty space function F

Model Compensator of K Function

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Safely Convert Point Pattern Window to Binary Mask

Distance Map of Line Segment Pattern

Inhomogeneous Cross Type L Function

Multitype K Function (i-to-any)

Nearest neighbours in three dimensions

Determine Duplicated Points in a Spatial Point Pattern

Influenza Virus Proteins

Nearest Neighbours Between Two Patterns

Midpoints of Line Segment Pattern

Basis for Harmonic Functions

multiplicity.ppp

Count Multiplicity of Duplicate Points

Combine Function Value Tables

Locally Scaled K-function

Reduced Second Moment Measure

Pairwise distances between two different point patterns

Tropical rain forest trees

Scatterplot Matrix for Pixel Images

Extract Subset of Function Array

Rectangular grid of points

Simulation Envelopes of Summary Function

Reset Values in Subset of Image

Chicago Street Crime Data

Intersect Infinite Straight Lines with a Window

Apply Function to Image Broken Down by Factor

Model Compensator of Nearest Neighbour Function

The Lennard-Jones Potential

The Multitype Strauss Point Process Model

Envelope for Point Patterns on Linear Network

Plot a linear network

Chorley-Ribble Cancer Data

Test Whether A Point Pattern is Marked

Crossing Points of Two Line Segment Patterns

Foxall's Distance Functions

Hybrid Geyer Point Process Model

Inhomogeneous Multitype L Dot Function

The Area Interaction Point Process Model

Beadlet Anemones Data

Beta Ganglion Cells in Cat Retina, Old Version

Create Pixel Image on Linear Network

Diggle's Heather Data

Multitype J Function (i-to-any)

ANOVA for Fitted Point Process Models on Linear Network

Convert and Compare Colours in Different Formats

Residual K Function

plot a Spatial Line Segment Pattern

K-function using FFT

Kolmogorov-Smirnov Test for Point Process Model

Area of a Window

Mark Connection Function

Nearest Neighbour Distance Function G

Orientation Angles of Line Segments

Distance to Boundary of Window

Areas of Morphological Dilations

Determine Whether One Window is Contained In Another

Ponderosa Pine Tree Point Pattern

Convert Data to Three-Dimensional Box

Estimate the J-function

Dirichlet Tessellation of Point Pattern

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

spatstat-deprecated

Deprecated spatstat functions

Loglikelihood of Spatial Logistic Regression

Pair Correlation Function

Apply Affine Transformation To Point Pattern

Marked Nearest Neighbour Distance Function

Convert Polygonal Region into Different Format

Plot a Signed or Vector-Valued Measure

Create a Linear Network

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Inverse-distance weighted smoothing of observations at irregular points

Difference of Disc Areas

Poisson Point Process Model

Inhomogeneous Pair Correlation Function

Saturated Pairwise Interaction model

Print Progress Reports

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Create a Line Segment Pattern

Fitted Probabilities for Spatial Logistic Regression

Methods for Intensity Functions of Spatial Covariate

Plot a tessellation

Determine Initial State for Metropolis-Hastings Simulation.

Nearest neighbour distances

Generate Poisson Random Line Process

Distance Between Two Point Patterns

Log Likelihood and AIC for Point Process Model

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Diameter of an Object

Test Whether An Object Is A Point Pattern

as.data.frame.im

Convert Pixel Image to Data Frame

plot.bermantest

Plot Result of Berman Test

Class of Images

Find Largest Circle Inside Window

Nearest neighbour distances between line segments

Kaplan-Meier and Reduced Sample Estimator using Histograms

Harkness-Isham ants' nests data

Simulate Thomas Process

Stoyan's Rule of Thumb for Bandwidth Selection

clarkevans.test

Clark and Evans Test

Pairwise distances in Three Dimensions

Diggle-Gratton model

Extract Interaction Structure

Distance to Boundary of Window

Number of Line Segments in a Line Segment Pattern

Three-Dimensional Box

Marked J Function

Kaplan-Meier Estimator using Histogram Data

Subdivide a Window or Tessellation using a Set of Lines

Pair Correlation Function of a Three-Dimensional Point Pattern

Convert Data To Tessellation

Pairwise shortest-path distances between points on a linear network

Pine saplings in Finland.

Predict Point Process Model on Linear Network

Biological Cells Point Pattern

Border Region of a Window

The Strauss Point Process Model

Distance to Boundary of Window

Hughes' Amacrine Cell Data

Data and Code From JRSS Discussion Paper on Residuals

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Berman's Tests for Point Process Model

Pairwise distances between two different line segment patterns

Compute Disc of Given Radius in Linear Network

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Apply a Function to a Point Pattern Broken Down by Factor

Q-Q Plot of Residuals from Fitted Point Process Model

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Interaction Distance of a Point Process

Inhomogeneous Cross K Function

Convert Data to Hyperframe

Infinite Straight Lines

Class of Point Patterns

Distance Map as a Function

Pairwise distances

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Convert Line Segment Pattern to Another Unit of Length

Pairwise distances

Set Covariance of a Window

Quadrature Scheme Based on Pixel Grid

Rotate a Window

Interactively join vertices on a plot

Compute Expansion Window for Simulation

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

Extract or Replace Subset of Tessellation

Fry Plot of Point Pattern

Convert Pixel Image to Another Unit of Length

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Coefficients of Fitted Point Process Model

Poisson Line Tessellation

Extract Dummy Points Used to Fit a Point Process Model

Create a Function Value Table

Class of Line Segment Patterns

California Redwoods Point Pattern (Entire Dataset)

Contour plot of pixel image

Estimate window from points alone

Plot a Colour Map

Plot a fitted cluster point process

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

Make Periodic Copies of a Spatial Pattern

Residuals for Fitted Point Process Model

Method of Minimum Contrast

Neighbourhood density function

Print a Fitted Point Process Model

Random Re-Labelling of Point Pattern

Generate N Uniform Random Points in a Disc

Residual Diagnostics for Multiple Fitted Models

Evaluate Expression Involving Function Arrays

Test Whether Marks Are Present

Distance for a Point Pattern Matching

Multitype L-function (i-to-any)

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

Simulate point patterns using the Metropolis-Hastings algorithm.

Print a Quadrature Scheme

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Concatenate x,y Coordinate Vectors

Profile Maximum Pseudolikelihood

Simulate from a Fitted Point Process Model

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Intersection of Two Tessellations

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Linear Pair Correlation Function

Combine Two Line Segment Patterns

Apply Vector Translation To Window

Generic Ord Interaction model

Compute Integral of Function Against Cumulative Distribution

Nearest Neighbour Clutter Removal

Test Whether An Object Is A Window

Apply Affine Transformation To Window

Area of Part of Disc

Mosaic Random Set

K-function of a Three-Dimensional Point Pattern

Distance Map of Window

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

New Zealand Trees Point Pattern

Convert Point Pattern to Pixel Image

Summarizing a Pixel Image

Kernel Smoothing of Line Segment Pattern

spatstat-internal

Internal spatstat functions

Longleaf Pines Point Pattern

The Strauss / Hard Core Point Process Model

Spruces Point Pattern

Function Arrays for Spatial Patterns

Exponential Energy Marks

Expand Window By Factor

Pixel Image Approximation of a Window

summary.splitppp

Summary of a Split Point Pattern

Plot a Function Array

Exchange X and Y Coordinates

Read Point Pattern From Data File

Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative

Generate Poisson Point Pattern in Any Dimensions

Perimeter Length of Window

Extract the Interaction from a Fitted Point Process Model

Summarise Marks in Every Neighbourhood in a Point Pattern

Extract Subset of Signed or Vector Measure

Union of Data and Dummy Points

Create a Pixel Image Object

Place Points Evenly Along Specified Lines

Prediction from a Fitted Cluster Point Process Model

Convert Window to Another Unit of Length

Compute Areas of Tiles in a Tessellation

quadratresample

Resample a Point Pattern by Resampling Quadrats

Morishita Index Plot

Point and Click Interface for Displaying a Point Pattern

Lengths of Line Segments

Marked K-Function

Simulate Log-Gaussian Cox Process

Subset of Quadrature Scheme

Swedish Pines Point Pattern

Residual G Function

Summarizing a Fitted Point Process Model

Histogram of Pixel Values in an Image

Generate N Random Multitype Points

model.frame.ppm

Extract the Environment of a Point Process Model

Simulate Gauss-Poisson Process

Poisson Point Process on a Linear Network

Lurking variable plot

plot a Spatial Point Pattern

Apply Affine Transformation To Line Segment Pattern

Plot a Pixel Image

Nearest neighbour

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Simulate Baddeley-Silverman Cell Process

Simulate Matern Cluster Process

Nearest Neighbours in Any Dimensions

spatstat.options

Internal Options in Spatstat Package

Convert Pixel Image to Matrix or Array

Point Patterns of New Brunswick Forest Fires

Identify Pixelwise Maximum of Several Pixel Images

Summary of a Line Segment Pattern Dataset

Theoretical Distribution of Nearest Neighbour Distance

Plot Function Values

Convert Spatial Object to Pixel Image

Plot a three-dimensional point pattern

Simulated Point Pattern

Multi-Dimensional Box

Print Brief Details of a Point Pattern Dataset

Extract List of Tiles in a Tessellation

Cross Validated Bandwidth Selection for Relative Risk Estimation

Circumradius and Diameter of a Linear Network

Morphological Closing

Extract Unique Points from a Spatial Point Pattern

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Apply Function to Every Neighbourhood in a Point Pattern

Divide Image Into Sub-images

Beta Ganglion Cells in Cat Retina

Plot a List of Point Patterns

Perfect Simulation of the Strauss Process

Interpret Fitted Model for Metropolis-Hastings Simulation.

matclust.estpcf

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

Divide Point Pattern into Sub-patterns

Collapse Several Function Tables into One

Plot a plotppm Object Created by plot.ppm

Coefficients of Fitted Spatial Logistic Regression Model

Test Whether Points Are Inside A Window

Delaunay Triangulation of Point Pattern

Generate grid of parallel lines with random displacement

Extract or Replace Subset of Point Pattern

Recognise Stationary and Poisson Point Process Models

Methods for three-dimensional point patterns

Number of Points in a Point Pattern

Convert to Pixel Image

Estimate Variance of Summary Statistic by Subdivision

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Methods for Three-Dimensional Box

Convert Data To Class psp

Methods for Point Patterns on a Linear Network

Apply Vector Translation To Line Segment Pattern

Nearest Neighbour Distances in Any Dimensions

Three Dimensional Point Pattern

Apply Smoothing to Function Values

Convert dataset to another unit of length

Intersection, Union or Set Subtraction of Two Windows

Signed or Vector-Valued Measure

Convert Data To Class ppp

Randomly Shift a Point Pattern

Extract Subset of Function Values

Sufficient Statistic of Point Process Model

Test Whether An Object Is A Pixel Image

Print Brief Details of an Image

Simulate Stratified Random Point Pattern

Create Point Pattern on Linear Network

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

Multitype pair correlation function (cross-type)

rshift.splitppp

Randomly Shift a List of Point Patterns

The Soft Core Point Process Model

pppmatching.object

Class of Point Matchings

Urkiola Woods Point Pattern

Simulate a Fitted Cluster Point Process Model

scaletointerval

Rescale Data to Lie Between Specified Limits

Class of Quadrature Schemes

Data Sharpening of Point Pattern

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Difference of Disc Areas

nearest.raster.point

Find Pixel Nearest to a Given Point

Circular Window

Superimpose Several Geometric Patterns

Morphological Erosion

Aherne's hamster tumour data

Connected components of an image or window

spatstat-package

The Spatstat Package

Simulate Simple Sequential Inhibition

Distance Map of Point Pattern

Morphological Opening

complement.owin

Take Complement of a Window

Find Line Segment Nearest to Each Point

inforder.family

Infinite Order Interaction Family

Convert Line Segment Pattern to Pixel Image

Diagnostic Plots for Fitted Point Process Model

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Generate a Default Pattern of Dummy Points

Geometrical Calculations for Three-Dimensional Box

Plot Pixel Image on Linear Network

Rotate a Point Pattern

Evaluate an Expression in a Function Table

Simulate a Fitted Gibbs Point Process Model

crossdist.default

Pairwise distances between two different sets of points

Humberside Data on Childhood Leukaemia and Lymphoma

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Plot a List of Things

plot.hyperframe

Plot Entries in a Hyperframe

Murchison gold deposits

Smooth a Signed or Vector-Valued Measure

Integral of a Pixel Image

Inhomogeneous Linear K Function

Pair Correlation Function of Point Pattern

Perspective Plot of Pixel Image

Simulation Envelopes of Summary Function for 3D Point Pattern

Weighted Empirical Cumulative Distribution Function

Point and Click Interface for Exploratory Analysis of Point Pattern

Quadrat counting for a point pattern

Evaluate Expression Involving Pixel Images

Plot a Spatial Kolmogorov-Smirnov Test

Convert Data To Class owin

Fit the Matern Cluster Point Process by Minimum Contrast

Generate N Uniform Random Points

Model Formulae for Gibbs Point Process Models

Random Perturbation of a Point Pattern

Saturated Pairwise Interaction Point Process Family

is.multitype.ppp

Test Whether A Point Pattern is Multitype

plot a Fitted Point Process Model

Print Brief Details of a Spatial Window

Mosaic Random Field

Pair Correlation Function obtained from K Function

Hyper Data Frame

Extract Quadrature Scheme Used to Fit a Point Process Model

Define Point Process Model for Metropolis-Hastings Simulation.

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Generate Poisson Point Pattern

Mark Correlation Function

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Dummy Function Returns Number of Points

Create a Point Matching

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

project2segment

Move Point To Nearest Line

Generate Poisson Point Pattern on Line Segments

Random Thinning

Linear K Function

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Divide Region into Quadrats

pairdist.default

Pairwise distances

Uniform Random Points on a Linear Network

Apply Vector Translation To Point Pattern

Methods for Linear Networks

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

Multidimensional Space-Time Point Pattern

Create a Window

Randomly Shift a Line Segment Pattern

Fit the Thomas Point Process by Minimum Contrast

Methods for Cluster Point Process Models

Compute Quadratic Forms

Spatial Logistic Regression

Reduced Sample Estimator using Histogram Data

Summary of a Point Pattern Dataset

Nearest neighbour distances in three dimensions

Sample Quantiles of Pixel Image

Generate Multitype Poisson Point Pattern

Spokes pattern of dummy points

rescue.rectangle

Convert Window Back To Rectangle

Fit the Thomas Point Process by Minimum Contrast

Endpoints of Line Segment Pattern

Summary of a Spatial Window

Update a Fitted Point Process Model

Summary of a List of Things

Prediction from a Fitted Point Process Model

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Pairwise Distances in Any Dimensions

pairwise.family

Pairwise Interaction Process Family

Smoothing Estimate of Covariate Transformation

Rounding of Pixel Values

Update a Fitted Cluster Point Process Model

Variance-Covariance Matrix for a Fitted Point Process Model

Plot a Fitted Spatial Logistic Regression

Print Brief Details of a Line Segment Pattern Dataset

Pseudoscore Diagnostic For Fitted Model against General Alternative

Generate a Quadrature Scheme from a Point Pattern

Simulate Neyman-Scott Process

Set Control Parameters for Metropolis-Hastings Algorithm.

Fitted Conditional Intensity for Point Process Model

Define Point Process Model for Metropolis-Hastings Simulation.

Generate N Uniform Random Points in Any Dimensions

Morphological Dilation

Name for Unit of Length

Generate N Random Points

Multitype J Function (i-to-j)

Spherical Contact Distribution Function

Approximate a Polygon by a Simpler Polygon

Generate N Uniform Random Points in Three Dimensions

Inhomogeneous Multitype K Dot Function

Apply Affine Transformation

Cartesian Coordinates for a Pixel Raster

Apply Gaussian Blur to a Pixel Image

Hutchings' Bramble Canes data

Bronze gradient filter data

Pseudoscore Diagnostic For Fitted Model against Saturation Alternative

Fit Cluster or Cox Point Process Model

Interactively Define a Polygon

Test Whether Two Function Objects Are Compatible

Berman-Huntington points and lines data

Diameter of a Window

Identify Points in a Point Pattern

Test Whether Two Pixel Images Are Compatible

Simulate Matern Model I

Plot a Simulation Envelope

California Redwoods Point Pattern (Ripley's Subset)

Methods for Multidimensional Space-Time Point Patterns

Test Whether A Point Process Model is Marked

Japanese Pines Point Pattern

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

Lansing Woods Point Pattern

The Hard Core Point Process Model

Inhomogeneous Linear Pair Correlation Function

Level Set of a Pixel Image

Marks of a Point Pattern

Pair Correlation Function obtained from array of K functions

Convert Window to Pixel Image

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Convert Point Pattern to Another Unit of Length

Class of Fitted Point Process Models

Interactively Add Points

Corners of a rectangle

Areas of Morphological Erosions

Create a Tessellation

Test whether Object is Multitype

Print News About Latest Version of Package

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Ord Interaction Process Family

Multitype pair correlation function (i-to-any)

Predicted or Fitted Values from Spatial Logistic Regression

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Simulate systematic random point pattern

Apply Vector Translation To Pixel Image

Apply Vector Translation

Weighted Histogram

Vertices of a Window

Inhomogeneous Neighbourhood Density Function

Compute Images of Constructed Covariates

Empty Space Function of a Three-Dimensional Point Pattern

Geyer's Saturation Point Process Model

The Piecewise Constant Pairwise Interaction Point Process Model

compatible.fasp

Test Whether Two Function Arrays Are Compatible

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Test Whether An Object Is Empty

Test Whether a Window is Convex

Interpolate a Pixel Image

Fit Point Process Model to Point Pattern on Linear Network

Pairwise distances

Create a Point Pattern

Rotate a Line Segment Pattern

Galaxies in the Shapley Supercluster

Simple Example of Linear Network

Spatial smoothing of observations at irregular points

Summarizing a Quadrature Scheme

Extract or Replace Subset of a List of Things

The Multitype Hard Core Point Process Model

Extract Original Data from a Fitted Point Process Model

bounding.box.xy

Convex Hull of Points

Kernel Smoothed Intensity of Point Pattern

Geometrical Calculations for Multi-Dimensional Box

Compute Quadrature Weights Based on Grid Counts

Evaluate Expression Involving Functions

Window in Shape of Letter R

Local pair correlation function

Mark Correlation Integral

Marks of a Line Segment Pattern

model.matrix.ppm

Extract Design Matrix from Point Process Model

Pairwise distances between line segments

Plot a Spatial Window

plot a Spatial Quadrature Scheme

Simulate Matern Model II

Nonparametric Estimate of Spatially-Varying Relative Risk

Create Colour-Valued Pixel Image

Cut margins from rectangle

Variance-Covariance Matrix for a Fitted Cluster Point Process Model

Volume of an Object

Fit Point Process Model to Data

Generate Poisson Point Pattern in Three Dimensions