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spatstat (version 1.23-1)

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. 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

19,373

Version

1.23-1

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

August 1st, 2011

Functions in spatstat (1.23-1)

Extract.splitppp

Extract or Replace Sub-Patterns

Multitype J Function (i-to-any)

Residual G Function

K-function of a Three-Dimensional Point Pattern

K-function using FFT

Inhomogeneous Multitype K Dot Function

Subset of Quadrature Scheme

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

Multitype J Function (i-to-j)

Extract or Replace Subset of a List of Things

Generic Pairwise Interaction model

Foxall's Distance Functions

Convert Data to Three-Dimensional Box

Extract Subset of Line Segment Pattern

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Extract or Replace Subset of Point Pattern

Reduced Second Moment Measure

Multitype K Function (i-to-any)

Extract Interaction Structure

Multi-Dimensional Box

Convert Data To Class psp

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

Combine Function Value Tables

Apply Function to Every Neighbourhood in a Point Pattern

Spherical Contact Distribution Function

Beadlet Anemones Data

Locally Scaled K-function

Inhomogeneous K-function

The Hard Core Point Process Model

Apply Affine Transformation To Line Segment Pattern

Apply Function to Image Broken Down by Factor

Area of a Window

Apply Affine Transformation

Reset Values in Subset of Image

Saturated Pairwise Interaction model

The Lennard-Jones Potential

Test Whether Two Function Objects Are Compatible

Harkness-Isham ants' nests data

Cross Validated Bandwidth Selection for Relative Risk Estimation

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

Multitype K Function (Cross-type)

Difference of Disc Areas

ANOVA for Fitted Point Process Models on Linear Network

Calculate four standard summary functions of a point pattern.

bounding.box.xy

Convex Hull of Points

The Piecewise Constant Pairwise Interaction Point Process Model

Marked K-Function

Convert to Pixel Image

ANOVA for Fitted Point Process Models

Orientation Angles of Line Segments

Berman's Tests for Point Process Model

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Convert Data To Class ppp

Multitype L-function (i-to-any)

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

as.data.frame.im

Convert Pixel Image to Data Frame

Pixel Image Approximation of a Window

Pairwise distances between two different line segment patterns

Ord's Interaction model

Convex Hull of Points

Convert Data To Tessellation

Geometrical Calculations for Multi-Dimensional Box

Coefficients of Fitted Spatial Logistic Regression Model

The Strauss Point Process Model

Test Whether An Object Is A Point Pattern

Ord Interaction Process Family

Pairwise distances

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Model Compensator of Nearest Neighbour Function

Simulation Envelopes of Summary Function for 3D Point Pattern

Extract Original Data from a Fitted Point Process Model

Poisson Point Process Model

Connected components of an image or window

Geometrical Calculations for Three-Dimensional Box

Combine Two Line Segment Patterns

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Distance Map of Line Segment Pattern

Biological Cells Point Pattern

K function of a model

Convert Data To Class owin

Convert Pixel Image to Matrix or Array

Create a Function Value Table

compatible.fasp

Test Whether Two Function Arrays Are Compatible

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Evaluate Expression Involving Pixel Images

Centroid of a window

Endpoints of Line Segment Pattern

crossdist.default

Pairwise distances between two different sets of points

Convert Line Segment Pattern to Binary Pixel Mask

Model Formulae for Gibbs Point Process Models

Japanese Pines Point Pattern

Function Value Table

Distance to Boundary of Window

pairwise.family

Pairwise Interaction Process Family

Distance to Boundary of Window

Residual Diagnostics for Multiple Fitted Models

Border Region of a Window

Collapse Several Function Tables into One

Apply Gaussian Blur to a Pixel Image

Hyper Data Frame

Function Arrays for Spatial Patterns

The Strauss / Hard Core Point Process Model

model.frame.ppm

Extract the Environment of a Point Process Model

Kernel Smoothed Intensity of Point Pattern

New Zealand Trees Point Pattern

Inhomogeneous Linear K Function

Evaluate Expression Involving Functions

Diameter of a Window

Aherne's hamster tumour data

Interactively join vertices on a plot

Create a Pixel Image Object

Diagnostic Plots for Fitted Point Process Model

Place Points Evenly Along Specified Lines

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Print Progress Reports

Simulate point patterns using the Metropolis-Hastings algorithm.

Determine Duplicated Points in a Spatial Point Pattern

Distance Map as a Function

Test Whether Two Pixel Images Are Compatible

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Pseudoscore Diagnostic For Fitted Model against Saturation Alternative

Artificial Data Point Pattern

Class of Images

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

California Redwoods Point Pattern (Ripley's Subset)

Pine saplings in Finland.

Convert Pixel Image from Numeric to Factor

complement.owin

Take Complement of a Window

Test Whether An Object Is A Window

Distance Map of Point Pattern

Recognise Stationary and Poisson Point Process Models

Loglikelihood of Spatial Logistic Regression

Compute Quadrature Weights Based on Grid Counts

Test Whether An Object Is Empty

Bronze gradient filter data

inforder.family

Infinite Order Interaction Family

Nonparametric Estimate of Spatially-Varying Relative Risk

Areas of Morphological Dilations

Methods for Linear Networks

Intersect Infinite Straight Lines with a Window

pppmatching.object

Class of Point Matchings

Hutchings' Bramble Canes data

Print Brief Details of a Point Pattern Dataset

Morphological Erosion

Weighted Empirical Cumulative Distribution Function

Test Whether Points Are Inside A Window

Pairwise distances between two different point patterns

Generate a Quadrature Scheme from a Point Pattern

Inhomogeneous Linear Pair Correlation Function

Volume of an Object

Compute Images of Constructed Covariates

Intersection of Two Tessellations

Subdivide a Window or Tessellation using a Set of Lines

Chorley-Ribble Cancer Data

Morphological Closing

Diggle-Gratton model

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

clarkevans.test

Clark and Evans Test

Expand Window By Factor

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Random Re-Labelling of Point Pattern

Interpolate a Pixel Image

Inverse-distance weighted smoothing of observations at irregular points

Print News About Latest Version of Package

Intersection, Union or Set Subtraction of Two Windows

Estimate window from points alone

Diggle's Heather Data

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Fitted Conditional Intensity for Point Process Model

Lengths of Line Segments

Fit the Matern Cluster Point Process by Minimum Contrast

Integral of a Pixel Image

Test Whether An Object Is A Pixel Image

Fit the Thomas Point Process by Minimum Contrast

Rectangular grid of points

Point and Click Interface for Displaying a Point Pattern

Extract Dummy Points Used to Fit a Point Process Model

Influenza Virus Proteins

Linear Pair Correlation Function

Generate N Uniform Random Points in Any Dimensions

Convert Point Pattern to Another Unit of Length

plot.hyperframe

Plot Entries in a Hyperframe

Determine Whether One Window is Contained In Another

Fit Point Process Model to Data

Beta Ganglion Cells in Cat Retina, Old Version

is.multitype.ppm

Test Whether A Point Process Model is Multitype

project2segment

Move Point To Nearest Line

Inhomogeneous Neighbourhood Density Function

Humberside Data on Childhood Leukaemia and Lymphoma

Nearest Neighbour Distances in Any Dimensions

Fry Plot of Point Pattern

Create a Window

Nearest neighbour distances

Nearest Neighbour Clutter Removal

model.matrix.ppm

Extract Design Matrix from Point Process Model

Nearest Neighbour Distance Function G

Methods for Point Patterns on a Linear Network

Create Point Pattern on Linear Network

Level Set of a Pixel Image

The Multitype Strauss Point Process Model

Fit Point Process Model to Point Pattern on Linear Network

Find Line Segment Nearest to Each Point

Plot a List of Point Patterns

The Multitype Hard Core Point Process Model

Spatial smoothing of observations at irregular points

Methods for Fitted Point Process Models on a Linear Network

Infinite Straight Lines

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Kolmogorov-Smirnov Test for Point Process Model

Perimeter Length of Window

Hughes' Amacrine Cell Data

Point Patterns of New Brunswick Forest Fires

Point and Click Interface for Exploratory Analysis of Point Pattern

Update a Fitted Cluster Point Process Model

Distance for a Point Pattern Matching

Kaplan-Meier Estimator using Histogram Data

spatstat-internal

Internal spatstat functions

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Saturated Pairwise Interaction Point Process Family

Print a Fitted Point Process Model

Lurking variable plot

Convert Line Segment Pattern to Pixel Image

Bounding Box of a Window or Point Pattern

plot a Fitted Point Process Model

Predict Point Process Model on Linear Network

Mark Correlation Integral

Marks of a Point Pattern

Murchison gold deposits

Pairwise distances

Methods for Intensity Functions of Spatial Covariate

Methods for three-dimensional point patterns

Plot a linear network

Pseudoscore Diagnostic For Fitted Model against General Alternative

Nearest Neighbours Between Two Patterns

Class of Point Patterns

matclust.estpcf

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

pairdist.default

Pairwise distances

Class of Fitted Point Process Models

Pairwise distances in Three Dimensions

Plot Pixel Image on Linear Network

Mosaic Random Set

Distance Between Two Point Patterns

Three Dimensional Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Local pair correlation function

Summary of a List of Things

Signed or Vector-Valued Measure

Generate Poisson Point Pattern in Three Dimensions

Generate N Random Points

Pair Correlation Function obtained from K Function

Multidimensional Space-Time Point Pattern

Quadrat counting for a point pattern

Summary of a Spatial Window

Make Periodic Copies of a Spatial Pattern

Class of Quadrature Schemes

Morphological Opening

Stoyan's Rule of Thumb for Bandwidth Selection

Concatenate x,y Coordinate Vectors

rshift.splitppp

Randomly Shift a List of Point Patterns

Name for Unit of Length

Plot a Signed or Vector-Valued Measure

Pairwise shortest-path distances between points on a linear network

Scatterplot Matrix for Pixel Images

Spatial Logistic Regression

Dummy Function Returns Number of Points

Method of Minimum Contrast

Ponderosa Pine Tree Point Pattern

Create a Point Pattern

Convert Window to Pixel Image

Plot a Spatial Kolmogorov-Smirnov Test

Print Brief Details of a Spatial Window

Corners of a rectangle

Class of Line Segment Patterns

Pair Correlation Function of Point Pattern

Distance to Boundary of Window

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Rotate a Line Segment Pattern

Methods for Multidimensional Space-Time Point Patterns

Uniform Random Points on a Linear Network

Diagnostics for random marking

Smooth a Signed or Vector-Valued Measure

Create a Point Matching

Convert Point Pattern to Pixel Image

Print Brief Details of an Image

Compute Areas of Tiles in a Tessellation

Mosaic Random Field

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Set Covariance of a Window

Extract Subset of Function Array

Simulate a Fitted Cluster Point Process Model

Simulate Matern Model I

Summary of a Point Pattern Dataset

Perfect Simulation of the Strauss Process

Sample Quantiles of Pixel Image

Simulate Baddeley-Silverman Cell Process

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Extract Subset of Function Values

Random Perturbation of a Point Pattern

Plot a Colour Map

Data and Code From JRSS Discussion Paper on Residuals

Simulate from a Fitted Point Process Model

Divide Image Into Sub-images

Urkiola Woods Point Pattern

Plot a Fitted Spatial Logistic Regression

Convert Spatial Object to Pixel Image

Estimate the I-function

rescue.rectangle

Convert Window Back To Rectangle

Randomly Shift a Point Pattern

Quadrature Scheme Based on Pixel Grid

Extract Subset of Image

Predicted or Fitted Values from Spatial Logistic Regression

methods.distfun

Methods for Distance Functions

spatstat.options

Internal Options in Spatstat Package

Circular Window

Plot a tessellation

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

Diameter of an Object

Extract Subset of Signed or Vector Measure

Generate Poisson Point Pattern in Any Dimensions

Superimpose Several Geometric Patterns

Convert dataset to another unit of length

Empty Space Function of a Three-Dimensional Point Pattern

Print a Quadrature Scheme

Simulate Neyman-Scott Process

Determine Initial State for Metropolis-Hastings Simulation.

Galaxies in the Shapley Supercluster

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Generate N Uniform Random Points in a Disc

Simulate Gauss-Poisson Process

Randomly Shift a Line Segment Pattern

Generate N Uniform Random Points

Fitted Probabilities for Spatial Logistic Regression

Extract List of Tiles in a Tessellation

Apply Vector Translation To Pixel Image

Interpret Fitted Model for Metropolis-Hastings Simulation.

The Fiksel Interaction

Swedish Pines Point Pattern

Simulated Point Pattern

Summarizing a Quadrature Scheme

Identify Points in a Point Pattern

Estimate the empty space function F

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

Cartesian Coordinates for a Pixel Raster

Rotate a Window

Variance-Covariance Matrix for a Fitted Cluster Point Process Model

Generate Poisson Point Pattern

Test whether Object is Multitype

Summarizing a Pixel Image

Fit the Thomas Point Process by Minimum Contrast

Convert Data to Hyperframe

summary.splitppp

Summary of a Split Point Pattern

The Soft Core Point Process Model

Plot a fitted cluster point process

Simulate Matern Model II

Rounding of Pixel Values

plot.bermantest

Plot Result of Berman Test

Theoretical Distribution of Nearest Neighbour Distance

Apply a Function to a Point Pattern Broken Down by Factor

Convert and Compare Colours in Different Formats

Test Whether Marks Are Present

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

The Area Interaction Point Process Model

Crossing Points of Two Line Segment Patterns

California Redwoods Point Pattern (Entire Dataset)

Estimate the J-function

Data Sharpening of Point Pattern

Marked J Function

Define Point Process Model for Metropolis-Hastings Simulation.

Residual K Function

Simulate Stratified Random Point Pattern

Three-Dimensional Box

Beta Ganglion Cells in Cat Retina

Apply Vector Translation To Window

Clark and Evans Aggregation Index

Inhomogeneous Cross K Function

Smoothing Estimate of Covariate Transformation

Multitype L-function (cross-type)

Methods for Multi-Dimensional Box

nearest.raster.point

Find Pixel Nearest to a Given Point

Simulate a Fitted Gibbs Point Process Model

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Nearest neighbour

Generate Poisson Point Pattern on Line Segments

Apply Smoothing to Function Values

Generate N Uniform Random Points in Three Dimensions

Circumradius and Diameter of a Linear Network

Nearest neighbour distances between line segments

Nearest neighbour distances in three dimensions

Evaluate an Expression in a Function Table

Perspective Plot of Pixel Image

Pair Correlation Function obtained from array of K functions

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Pairwise distances

Multitype pair correlation function (cross-type)

Interactively Define a Polygon

Identify Pixelwise Maximum of Several Pixel Images

Pairwise Distances in Any Dimensions

Delaunay Triangulation of Point Pattern

Simulation Envelopes of Summary Function

plot a Spatial Point Pattern

Colour Lookup Tables

Areas of Morphological Erosions

Exponential Energy Marks

Convert Polygonal Region into Different Format

Convert Pixel Image to Another Unit of Length

Apply Vector Translation To Line Segment Pattern

Plot a Pixel Image

Create a Line Segment Pattern

Reduced Sample Estimator using Histogram Data

Kernel Smoothing of Line Segment Pattern

Test Whether a Window is Convex

Summarizing a Fitted Point Process Model

Apply Vector Translation To Point Pattern

Log Likelihood and AIC for Point Process Model

Convert Window to Another Unit of Length

Mark Connection Function

Create Colour-Valued Pixel Image

Extract the Interaction from a Fitted Point Process Model

multiplicity.ppp

Count Multiplicity of Duplicate Points

Fit Cluster or Cox Point Process Model

Create Pixel Image on Linear Network

Multitype pair correlation function (i-to-any)

Number of Points in a Point Pattern

Set Control Parameters for Metropolis-Hastings Algorithm.

Generate Poisson Random Line Process

Update a Fitted Point Process Model

Plot Function Values

Mark Correlation Function

Plot a Simulation Envelope

Plot a List of Things

plot a Spatial Line Segment Pattern

Methods for Three-Dimensional Box

Pair Correlation Function

Vertices of a Window

Spokes pattern of dummy points

Morishita Index Plot

Simulate Thomas Process

Residuals for Fitted Point Process Model

Simulate Simple Sequential Inhibition

Generate Multitype Poisson Point Pattern

Simulate Matern Cluster Process

Rotate a Point Pattern

Read Point Pattern From Data File

Generate N Random Multitype Points

Extract Unique Points from a Spatial Point Pattern

Poisson Point Process on a Linear Network

Summary of a Line Segment Pattern Dataset

spatstat-package

The Spatstat Package

Create a Tessellation

Cut margins from rectangle

Estimate Variance of Summary Statistic by Subdivision

Inhomogeneous Multitype L Dot Function

Inhomogeneous Cross Type L Function

Classify Points in a Point Pattern

Generate a Default Pattern of Dummy Points

Safely Convert Point Pattern Window to Binary Mask

Evaluate Expression Involving Function Arrays

Identify Segments in a Line Segment Pattern

Create a Linear Network

Number of Line Segments in a Line Segment Pattern

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Pairwise distances between line segments

Pair Correlation Function of a Three-Dimensional Point Pattern

Nearest Neighbours in Any Dimensions

plot a Spatial Quadrature Scheme

Simulate Log-Gaussian Cox Process

Simulate systematic random point pattern

Apply Vector Translation

Simple Example of Linear Network

Approximate a Polygon by a Simpler Polygon

Compute Integral of Function Against Cumulative Distribution

Sufficient Statistic of Point Process Model

Marked Nearest Neighbour Distance Function

Geyer's Saturation Point Process Model

Difference of Disc Areas

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Convert a Window to a Polygonal Window

Tropical rain forest trees

Chicago Street Crime Data

Interactively Add Points

Contour plot of pixel image

Berman-Huntington points and lines data

spatstat-deprecated

Deprecated spatstat functions

Dirichlet Tessellation of Point Pattern

Distance Map of Window

Test Whether A Point Process Model is Marked

Neighbourhood density function

Longleaf Pines Point Pattern

Marks of a Line Segment Pattern

Summarise Marks in Every Neighbourhood in a Point Pattern

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Nearest neighbours in three dimensions

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Plot a plotppm Object Created by plot.ppm

Plot a three-dimensional point pattern

Divide Region into Quadrats

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

scaletointerval

Rescale Data to Lie Between Specified Limits

Weighted Histogram

Extract Quadrature Scheme Used to Fit a Point Process Model

Variance-Covariance Matrix for a Fitted Point Process Model

Model Compensator of K Function

Generic Ord Interaction model

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Convert Function Value Table to Function

Coefficients of Fitted Point Process Model

Compute Expansion Window for Simulation

Morphological Dilation

Area of Part of Disc

Envelope for Point Patterns on Linear Network

Histogram of Pixel Values in an Image

Basis for Harmonic Functions

Find Largest Circle Inside Window

Kaplan-Meier and Reduced Sample Estimator using Histograms

Lansing Woods Point Pattern

Midpoints of Line Segment Pattern

Methods for Cluster Point Process Models

Inhomogeneous Pair Correlation Function

Plot a Spatial Window

Prediction from a Fitted Cluster Point Process Model

Profile Maximum Pseudolikelihood

quadratresample

Resample a Point Pattern by Resampling Quadrats

Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative

Convert Line Segment Pattern to Another Unit of Length

Random Thinning

Divide Point Pattern into Sub-patterns

Spruces Point Pattern

Plot a Function Array

Analysis of Deviance for Spatial Logistic Regression Models

Linear K Function

Extract or Replace Subset of Tessellation

Apply Affine Transformation To Point Pattern

Pairwise distances between two different three-dimensional point patterns

Hybrid Geyer Point Process Model

Interaction Distance of a Point Process

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

Window in Shape of Letter R

Print Brief Details of a Line Segment Pattern Dataset

Test Whether An Object Is A Fitted Point Process Model

Generate grid of parallel lines with random displacement

Test Whether A Point Pattern is Marked

Poisson Line Tessellation

Q-Q Plot of Residuals from Fitted Point Process Model

Union of Data and Dummy Points

Apply Affine Transformation To Window

Prediction from a Fitted Point Process Model

Compute Disc of Given Radius in Linear Network