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spatstat (version 1.23-5)

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

16,015

Version

1.23-5

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

September 23rd, 2011

Functions in spatstat (1.23-5)

Apply Affine Transformation To Window

Multitype J Function (i-to-j)

Estimate the I-function

Saturated Pairwise Interaction model

Marked K-Function

Marked Nearest Neighbour Distance Function

Apply Affine Transformation

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Distance to Boundary of Window

Determine Duplicated Points in a Spatial Point Pattern

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Reset Values in Subset of Image

Methods for Three-Dimensional Box

Nearest Neighbour Distance Function G

Apply a Function to a Point Pattern Broken Down by Factor

Extract.splitppp

Extract or Replace Sub-Patterns

Pairwise distances between two different point patterns

bounding.box.xy

Convex Hull of Points

Test whether Object is Multitype

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

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

Stoyan's Rule of Thumb for Bandwidth Selection

Chorley-Ribble Cancer Data

Beta Ganglion Cells in Cat Retina

Pine saplings in Finland.

Influenza Virus Proteins

Cross Validated Bandwidth Selection for Spatial Smoothing

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Identify Segments in a Line Segment Pattern

crossdist.default

Pairwise distances between two different sets of points

Combine Function Value Tables

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

Exchange X and Y Coordinates

The Soft Core Point Process Model

Multitype L-function (cross-type)

Calculate four standard summary functions of a point pattern.

Function Value Table

Apply Function to Image Broken Down by Factor

pairdist.default

Pairwise distances

Artificial Data Point Pattern

Intersection of Two Tessellations

Compute Disc of Given Radius in Linear Network

Fitted Probabilities for Spatial Logistic Regression

Inhomogeneous Cross Type L Function

Collapse Several Function Tables into One

Exponential Energy Marks

Kolmogorov-Smirnov Test for Point Process Model

Endpoints of Line Segment Pattern

Linear Pair Correlation Function

Inverse-distance weighted smoothing of observations at irregular points

Convex Hull of Points

Bronze gradient filter data

Number of Points in a Point Pattern

Areas of Morphological Dilations

Inhomogeneous Cross K Function

Create Point Pattern on Linear Network

Bounding Box of a Window or Point Pattern

Pairwise distances

Evaluate Expression Involving Pixel Images

ANOVA for Fitted Point Process Models

Extract Dummy Points Used to Fit a Point Process Model

Loglikelihood of Spatial Logistic Regression

Pixel Image Approximation of a Window

Inhomogeneous Multitype L Dot Function

Morphological Closing

ANOVA for Fitted Point Process Models on Linear Network

Morphological Dilation

Identify Covariates Involved in each Model Term

Nearest neighbours in three dimensions

nearest.raster.point

Find Pixel Nearest to a Given Point

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Integral of a Pixel Image

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Distance to Boundary of Window

Kaplan-Meier Estimator using Histogram Data

Three-Dimensional Box

Mark Connection Function

Create a Line Segment Pattern

Ord's Interaction model

Analysis of Deviance for Spatial Logistic Regression Models

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

Apply Gaussian Blur to a Pixel Image

Diameter of a Window

Lansing Woods Point Pattern

Plot a Colour Map

Berman's Tests for Point Process Model

Divide Region into Quadrats

Convert Line Segment Pattern to Binary Pixel Mask

The Strauss Point Process Model

Dummy Function Returns Number of Points

Methods for Cluster Point Process Models

pairwise.family

Pairwise Interaction Process Family

Convert Data to Three-Dimensional Box

The Multitype Strauss Point Process Model

methods.distfun

Methods for Distance Functions

Residual G Function

Diagnostic Plots for Fitted Point Process Model

Fit Cluster or Cox Point Process Model

as.data.frame.im

Convert Pixel Image to Data Frame

Humberside Data on Childhood Leukaemia and Lymphoma

K-function using FFT

Inhomogeneous Linear Pair Correlation Function

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Estimate the empty space function F

New Zealand Trees Point Pattern

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Interactively Add Points

Extract the Interaction from a Fitted Point Process Model

Areas of Morphological Erosions

inforder.family

Infinite Order Interaction Family

Test Whether Two Function Objects Are Compatible

Create a Point Matching

Aherne's hamster tumour data

multiplicity.ppp

Count Multiplicity of Duplicate Points

Nearest Neighbour Distances in Any Dimensions

Combine Two Line Segment Patterns

Fitted Conditional Intensity for Point Process Model

Find Line Segment Nearest to Each Point

Distance Map of Window

Multitype K Function (Cross-type)

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

Simulation Envelopes of Summary Function

Randomly Shift a Point Pattern

Contour plot of pixel image

Intersect Infinite Straight Lines with a Window

Recognise Stationary and Poisson Point Process Models

Residual Diagnostics for Multiple Fitted Models

Pair Correlation Function obtained from K Function

Extract Subset of Line Segment Pattern

Number of Line Segments in a Line Segment Pattern

Model Compensator of Nearest Neighbour Function

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

Pair Correlation Function of Point Pattern

Plot a List of Point Patterns

Japanese Pines Point Pattern

Evaluate Expression Involving Function Arrays

Print News About Latest Version of Package

Level Set of a Pixel Image

Q-Q Plot of Residuals from Fitted Point Process Model

Extract Original Data from a Fitted Point Process Model

Convert and Compare Colours in Different Formats

Methods for three-dimensional point patterns

Random Perturbation of a Point Pattern

Saturated Pairwise Interaction Point Process Family

Pair Correlation Function obtained from array of K functions

Compute Images of Constructed Covariates

K function of a model

Point and Click Interface for Exploratory Analysis of Point Pattern

Plot a Spatial Window

Interpolate a Pixel Image

Hyper Data Frame

Border Region of a Window

Berman-Huntington points and lines data

The Strauss / Hard Core Point Process Model

Interactively join vertices on a plot

Mosaic Random Set

Model Compensator of K Function

Plot a Fitted Spatial Logistic Regression

Place Points Evenly Along Specified Lines

Convert Data To Tessellation

Beadlet Anemones Data

Inhomogeneous Linear K Function

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

Simulate point patterns using the Metropolis-Hastings algorithm.

Convert dataset to another unit of length

Nearest Neighbours in Any Dimensions

Window in Shape of Letter R

Intersection, Union or Set Subtraction of Two Windows

Poisson Line Tessellation

Quadrat counting for a point pattern

Nonparametric Estimate of Spatially-Varying Relative Risk

Theoretical Distribution of Nearest Neighbour Distance

rshift.splitppp

Randomly Shift a List of Point Patterns

Apply Function to Every Neighbourhood in a Point Pattern

Test Whether Marks Are Present

Profile Maximum Pseudolikelihood

Tropical rain forest trees

Circular Window

Extract Subset of Image

Biological Cells Point Pattern

Empty Space Function of a Three-Dimensional Point Pattern

pppmatching.object

Class of Point Matchings

Pairwise distances

Plot a Simulation Envelope

Poisson Point Process on a Linear Network

California Redwoods Point Pattern (Ripley's Subset)

Print a Quadrature Scheme

Simulate Gauss-Poisson Process

Fit the Matern Cluster Point Process by Minimum Contrast

Pairwise distances between two different line segment patterns

Rotate a Window

Randomly Shift a Line Segment Pattern

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

quadratresample

Resample a Point Pattern by Resampling Quadrats

Class of Line Segment Patterns

Create Colour-Valued Pixel Image

Point and Click Interface for Displaying a Point Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

Reduced Second Moment Measure

Area of Part of Disc

Beta Ganglion Cells in Cat Retina, Old Version

Classify Points in a Point Pattern

Generic Pairwise Interaction model

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Extract Subset of Function Array

Hybrid Geyer Point Process Model

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Convert Window to Pixel Image

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Plot Function Values

Test Whether Two Pixel Images Are Compatible

Convert Data to Hyperframe

Simulate Stratified Random Point Pattern

Apply Vector Translation To Window

Class of Fitted Point Process Models

Simulate a Fitted Gibbs Point Process Model

Convert Point Pattern to Another Unit of Length

Create Pixel Image on Linear Network

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Read Point Pattern From Data File

Random Re-Labelling of Point Pattern

Create a Linear Network

Poisson Point Process Model

Identify Points in a Point Pattern

Weighted Histogram

Apply Vector Translation To Point Pattern

Signed or Vector-Valued Measure

The Multitype Hard Core Point Process Model

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

scaletointerval

Rescale Data to Lie Between Specified Limits

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Smooth a Signed or Vector-Valued Measure

Update a Fitted Cluster Point Process Model

Data Sharpening of Point Pattern

Extract Unique Points from a Spatial Point Pattern

Marked J Function

spatstat-internal

Internal spatstat functions

Hutchings' Bramble Canes data

Apply Vector Translation To Line Segment Pattern

model.frame.ppm

Extract the Environment of a Point Process Model

Method of Minimum Contrast

model.matrix.ppm

Extract Design Matrix from Point Process Model

Geometrical Calculations for Multi-Dimensional Box

Define Point Process Model for Metropolis-Hastings Simulation.

Nearest neighbour

Linear K Function

Urkiola Woods Point Pattern

Generate N Uniform Random Points in Three Dimensions

Nearest neighbour distances

Create List of Plotting Layers

Pairwise shortest-path distances between points on a linear network

complement.owin

Take Complement of a Window

Dirichlet Tessellation of Point Pattern

Convert Line Segment Pattern to Pixel Image

Spatial smoothing of observations at irregular points

Distance for a Point Pattern Matching

Morishita Index Plot

Multitype pair correlation function (i-to-any)

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Update a Fitted Point Process Model

Fit Point Process Model to Data

Predict Point Process Model on Linear Network

Spokes pattern of dummy points

Prediction from a Fitted Point Process Model

Prediction from a Fitted Cluster Point Process Model

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Test Whether A Point Pattern is Marked

Pairwise Distances in Any Dimensions

Test Whether a Window is Convex

Sufficient Statistic of Point Process Model

Methods for Multidimensional Space-Time Point Patterns

Lengths of Line Segments

Perspective Plot of Pixel Image

Rounding of Pixel Values

Nearest neighbour distances between line segments

Difference of Disc Areas

matclust.estpcf

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

Summary of a Point Pattern Dataset

Plot a Function Array

Methods for Multi-Dimensional Box

Convert Data To Class ppp

Multi-Dimensional Box

Hughes' Amacrine Cell Data

Diggle-Gratton model

Longleaf Pines Point Pattern

plot a Fitted Point Process Model

Methods for Intensity Functions of Spatial Covariate

Distance Map as a Function

The Fiksel Interaction

Foxall's Distance Functions

Convert Data To Class psp

Circumradius and Diameter of a Linear Network

Compute Quadrature Weights Based on Grid Counts

plot.bermantest

Plot Result of Berman Test

Multitype J Function (i-to-any)

Histogram of Pixel Values in an Image

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Pair Correlation Function of a Three-Dimensional Point Pattern

Simulate Matern Cluster Process

K-function of a Three-Dimensional Point Pattern

Methods for Point Patterns on a Linear Network

project2segment

Move Point To Nearest Line

Print Progress Reports

Quadrature Scheme Based on Pixel Grid

Create a Point Pattern

Convert Pixel Image to Another Unit of Length

plot a Spatial Line Segment Pattern

rescue.rectangle

Convert Window Back To Rectangle

Data and Code From JRSS Discussion Paper on Residuals

Generate grid of parallel lines with random displacement

Geyer's Saturation Point Process Model

Fry Plot of Point Pattern

Pseudoscore Diagnostic For Fitted Model against General Alternative

Extract or Replace Subset of Tessellation

Distance to Boundary of Window

Distance Map of Point Pattern

Plot a List of Things

envelope.envelope

Recompute Envelopes

Multitype L-function (i-to-any)

Uniform Random Points on a Linear Network

Print Brief Details of a Line Segment Pattern Dataset

Chicago Street Crime Data

Perfect Simulation of the Strauss Process

Plot a tessellation

Convert Pixel Image from Numeric to Factor

Convert a Window to a Polygonal Window

Inhomogeneous Pair Correlation Function

Area of a Window

Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative

Test Whether Points Are Inside A Window

plot a Spatial Point Pattern

Create a Window

Estimate the J-function

Plot a three-dimensional point pattern

Extract Quadrature Scheme Used to Fit a Point Process Model

Pseudoscore Diagnostic For Fitted Model against Saturation Alternative

Rotate a Line Segment Pattern

Simulate Neyman-Scott Process

Class of Point Patterns

Marks of a Line Segment Pattern

Plot a plotppm Object Created by plot.ppm

Simulate Thomas Process

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Union of Data and Dummy Points

Nearest Neighbour Clutter Removal

Residuals for Fitted Point Process Model

Smoothing Estimate of Covariate Transformation

Summary of a Spatial Window

Generate Poisson Point Pattern

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Orientation Angles of Line Segments

Infinite Straight Lines

Approximate a Polygon by a Simpler Polygon

Set Control Parameters for Metropolis-Hastings Algorithm.

Name for Unit of Length

Morphological Erosion

Generate N Random Multitype Points

Locally Scaled K-function

Generate N Uniform Random Points in Any Dimensions

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

The Lennard-Jones Potential

Kernel Smoothing of Line Segment Pattern

Cartesian Coordinates for a Pixel Raster

Subset of Quadrature Scheme

Divide Point Pattern into Sub-patterns

Extract Subset of Function Values

Interpret Fitted Model for Metropolis-Hastings Simulation.

Pair Correlation Function

Harkness-Isham ants' nests data

Galaxies in the Shapley Supercluster

spatstat-deprecated

Deprecated spatstat functions

plot a Spatial Quadrature Scheme

Apply Smoothing to Function Values

Simulate Simple Sequential Inhibition

Generate Poisson Point Pattern on Line Segments

Test Whether A Point Process Model is Marked

Local pair correlation function

Simulate systematic random point pattern

Cut margins from rectangle

Convert to Pixel Image

Extract List of Tiles in a Tessellation

Estimate window from points alone

Pool Data from Several Envelopes

Ponderosa Pine Tree Point Pattern

Pairwise distances between line segments

Generate N Uniform Random Points in a Disc

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

Centroid of a window

Random Thinning

Delaunay Triangulation of Point Pattern

Vertices of a Window

Identify Pixelwise Maximum of Several Pixel Images

Divide Image Into Sub-images

plot.hyperframe

Plot Entries in a Hyperframe

Compute Areas of Tiles in a Tessellation

Envelope for Point Patterns on Linear Network

Apply Affine Transformation To Point Pattern

Pairwise distances in Three Dimensions

Simulate a Fitted Cluster Point Process Model

Nearest Neighbours Between Two Patterns

spatstat.options

Internal Options in Spatstat Package

Difference of Disc Areas

Evaluate Expression Involving Functions

Midpoints of Line Segment Pattern

Determine Whether One Window is Contained In Another

Log Likelihood and AIC for Point Process Model

Neighbourhood density function

Apply Vector Translation

Class of Images

Mark Correlation Integral

Summary of a List of Things

Distance Map of Line Segment Pattern

The Hard Core Point Process Model

Rectangular grid of points

Estimate Variance of Summary Statistic by Subdivision

Multitype pair correlation function (cross-type)

Interactively Define a Polygon

Superimpose Several Geometric Patterns

Subdivide a Window or Tessellation using a Set of Lines

Point Patterns of New Brunswick Forest Fires

Volume of an Object

Compute Quadratic Forms

Corners of a rectangle

Plot Pixel Image on Linear Network

Function Arrays for Spatial Patterns

Pool Data from Several Function Arrays

Plot a Pixel Image

Simulation Envelopes of Summary Function for 3D Point Pattern

Evaluate an Expression in a Function Table

Multidimensional Space-Time Point Pattern

Print Brief Details of an Image

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Make Periodic Copies of a Spatial Pattern

Plot a Spatial Kolmogorov-Smirnov Test

Simulate Matern Model I

Generate Poisson Point Pattern in Any Dimensions

Extract Interaction Structure

Simulate Log-Gaussian Cox Process

Generate Poisson Random Line Process

Mark Correlation Function

Summarizing a Pixel Image

Interaction Distance of a Point Process

Print Brief Details of a Point Pattern Dataset

Summarizing a Fitted Point Process Model

spatstat-package

The Spatstat Package

Connected components of an image or window

Determine Initial State for Metropolis-Hastings Simulation.

Simulate from a Fitted Point Process Model

Generate Multitype Poisson Point Pattern

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Extract or Replace Subset of Point Pattern

Print Brief Details of a Spatial Window

Class of Quadrature Schemes

Generate N Random Points

Generate N Uniform Random Points

Spruces Point Pattern

Plot a Signed or Vector-Valued Measure

Rotate a Point Pattern

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Create a Tessellation

The Area Interaction Point Process Model

Summary of a Line Segment Pattern Dataset

Apply Affine Transformation To Line Segment Pattern

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

Colour Lookup Tables

Crossing Points of Two Line Segment Patterns

Find Largest Circle Inside Window

Kernel Smoothed Intensity of Point Pattern

Create a Pixel Image Object

Diggle's Heather Data

Extract Subset of Signed or Vector Measure

Multitype K Function (i-to-any)

Test Whether An Object Is A Fitted Point Process Model

Lurking variable plot

Expand Window By Factor

Geometrical Calculations for Three-Dimensional Box

Diagnostics for random marking

Coefficients of Fitted Spatial Logistic Regression Model

Compute Expansion Window for Simulation

Murchison gold deposits

Basis for Harmonic Functions

Summarise Marks in Every Neighbourhood in a Point Pattern

Scatterplot Matrix for Pixel Images

Clark and Evans Aggregation Index

Create a Function Value Table

Kaplan-Meier and Reduced Sample Estimator using Histograms

Morphological Opening

Fit Point Process Model to Point Pattern on Linear Network

Convert Data To Class owin

Convert Point Pattern to Pixel Image

Methods for Linear Networks

Generic Ord Interaction model

Convert Window to Another Unit of Length

Generate a Quadrature Scheme from a Point Pattern

Print a Fitted Point Process Model

Diameter of an Object

California Redwoods Point Pattern (Entire Dataset)

Perimeter Length of Window

Sample Quantiles of Pixel Image

Generate Poisson Point Pattern in Three Dimensions

Plot a fitted cluster point process

Distance Between Two Point Patterns

Summarizing a Quadrature Scheme

Set Covariance of a Window

Mosaic Random Field

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Spatial Logistic Regression

Fit the Thomas Point Process by Minimum Contrast

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Inhomogeneous K-function

The Piecewise Constant Pairwise Interaction Point Process Model

Spherical Contact Distribution Function

Cross Validated Bandwidth Selection for Relative Risk Estimation

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Pairwise distances between two different three-dimensional point patterns

Test Whether An Object Is Empty

Marks of a Point Pattern

Nearest neighbour distances in three dimensions

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Test Whether An Object Is A Point Pattern

Pairwise distances

Convert Function Value Table to Function

Safely Convert Point Pattern Window to Binary Mask

Plot a linear network

Define Point Process Model for Metropolis-Hastings Simulation.

Predicted or Fitted Values from Spatial Logistic Regression

Apply Vector Translation To Pixel Image

Simple Example of Linear Network

Compute Integral of Function Against Cumulative Distribution

Variance-Covariance Matrix for a Fitted Cluster Point Process Model

summary.splitppp

Summary of a Split Point Pattern

Extract or Replace Subset of a List of Things

Generate a Default Pattern of Dummy Points

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Model Formulae for Gibbs Point Process Models

Weighted Empirical Cumulative Distribution Function

Test Whether An Object Is A Pixel Image

Inhomogeneous Multitype K Dot Function

Cross Validated Bandwidth Selection for Kernel Density

Test Whether An Object Is A Window

Ord Interaction Process Family

Convert Pixel Image to Matrix or Array

Concatenate x,y Coordinate Vectors

clarkevans.test

Clark and Evans Test

Residual K Function

Methods for Fitted Point Process Models on a Linear Network

Coefficients of Fitted Point Process Model

Convert Polygonal Region into Different Format

Inhomogeneous Neighbourhood Density Function

Convert Spatial Object to Pixel Image

Three Dimensional Point Pattern

Simulate Matern Model II

Convert Line Segment Pattern to Another Unit of Length

Reduced Sample Estimator using Histogram Data

Simulate Baddeley-Silverman Cell Process

Simulated Point Pattern

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Swedish Pines Point Pattern

Fit the Thomas Point Process by Minimum Contrast