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spatstat (version 1.23-4)

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

16,590

Version

1.23-4

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

September 9th, 2011

Functions in spatstat (1.23-4)

spatstat.options

Internal Options in Spatstat Package

Fit the Thomas Point Process by Minimum Contrast

Evaluate an Expression in a Function Table

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

Spruces Point Pattern

Summary of a List of Things

Compute Quadratic Forms

Fit the Thomas Point Process by Minimum Contrast

Variance-Covariance Matrix for a Fitted Cluster Point Process Model

Smooth a Signed or Vector-Valued Measure

Variance-Covariance Matrix for a Fitted Point Process Model

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

spatstat-package

The Spatstat Package

Estimate Variance of Summary Statistic by Subdivision

The Hard Core Point Process Model

Hybrid Geyer Point Process Model

Summary of a Point Pattern Dataset

Estimate the J-function

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

Volume of an Object

Convert to Pixel Image

The Strauss / Hard Core Point Process Model

Divide Point Pattern into Sub-patterns

Convert Line Segment Pattern to Binary Pixel Mask

Empty Space Function of a Three-Dimensional Point Pattern

Simulate Baddeley-Silverman Cell Process

Interactively Add Points

Diggle-Gratton model

Model Compensator of K Function

Coefficients of Fitted Spatial Logistic Regression Model

Hutchings' Bramble Canes data

Superimpose Several Geometric Patterns

Poisson Point Process Model

Apply Affine Transformation To Point Pattern

Orientation Angles of Line Segments

Summarizing a Fitted Point Process Model

Morphological Dilation

K function of a model

Convert and Compare Colours in Different Formats

Diagnostics for random marking

Multitype K Function (i-to-any)

Inhomogeneous Multitype K Dot Function

Test Whether Two Function Objects Are Compatible

Chicago Street Crime Data

Convert Pixel Image to Matrix or Array

Hughes' Amacrine Cell Data

Distance Map of Line Segment Pattern

Envelope for Point Patterns on Linear Network

Apply Affine Transformation

Extract List of Tiles in a Tessellation

Pairwise distances between two different three-dimensional point patterns

Test Whether An Object Is A Pixel Image

Convert Function Value Table to Function

Harkness-Isham ants' nests data

Fitted Conditional Intensity for Point Process Model

Apply Function to Image Broken Down by Factor

Collapse Several Function Tables into One

Combine Function Value Tables

Pairwise distances between two different line segment patterns

Extract Original Data from a Fitted Point Process Model

Intersection, Union or Set Subtraction of Two Windows

Convert a Window to a Polygonal Window

Convert Data to Three-Dimensional Box

Convert Data To Tessellation

Diameter of an Object

Apply Affine Transformation To Window

Compute Disc of Given Radius in Linear Network

Locally Scaled K-function

Cut margins from rectangle

Centroid of a window

Inhomogeneous Multitype L Dot Function

Berman-Huntington points and lines data

Spatial smoothing of observations at irregular points

crossdist.default

Pairwise distances between two different sets of points

Lengths of Line Segments

Kolmogorov-Smirnov Test for Point Process Model

Urkiola Woods Point Pattern

Geyer's Saturation Point Process Model

Evaluate Expression Involving Function Arrays

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

Test Whether An Object Is A Point Pattern

Spokes pattern of dummy points

Estimate the empty space function F

Kaplan-Meier Estimator using Histogram Data

pairwise.family

Pairwise Interaction Process Family

Multitype J Function (i-to-any)

Apply Function to Every Neighbourhood in a Point Pattern

Sufficient Statistic of Point Process Model

Point Patterns of New Brunswick Forest Fires

Function Arrays for Spatial Patterns

Vertices of a Window

K-function of a Three-Dimensional Point Pattern

Methods for Intensity Functions of Spatial Covariate

Pairwise distances

Convex Hull of Points

Ord's Interaction model

Area of a Window

Create a Window

Kernel Smoothed Intensity of Point Pattern

Pairwise shortest-path distances between points on a linear network

spatstat-internal

Internal spatstat functions

Compute Integral of Function Against Cumulative Distribution

Diagnostic Plots for Fitted Point Process Model

Simulate Stratified Random Point Pattern

Convert Pixel Image from Numeric to Factor

Berman's Tests for Point Process Model

Test Whether Points Are Inside A Window

Test Whether An Object Is A Window

Exchange X and Y Coordinates

matclust.estpcf

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

Methods for Three-Dimensional Box

Infinite Straight Lines

Test Whether A Point Process Model is Marked

Scatterplot Matrix for Pixel Images

Delaunay Triangulation of Point Pattern

Identify Segments in a Line Segment Pattern

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Inverse-distance weighted smoothing of observations at irregular points

Areas of Morphological Dilations

Perspective Plot of Pixel Image

Subdivide a Window or Tessellation using a Set of Lines

Uniform Random Points on a Linear Network

ANOVA for Fitted Point Process Models on Linear Network

Smoothing Estimate of Covariate Transformation

Pseudoscore Diagnostic For Fitted Model against General Alternative

Rounding of Pixel Values

Simulate a Fitted Gibbs Point Process Model

Set Control Parameters for Metropolis-Hastings Algorithm.

Test Whether Marks Are Present

Point and Click Interface for Exploratory Analysis of Point Pattern

Interpolate a Pixel Image

Nearest neighbour distances in three dimensions

bounding.box.xy

Convex Hull of Points

Fit Point Process Model to Data

Histogram of Pixel Values in an Image

Local pair correlation function

Geometrical Calculations for Multi-Dimensional Box

Morphological Erosion

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Extract Unique Points from a Spatial Point Pattern

Create a Point Pattern

Prediction from a Fitted Cluster Point Process Model

Apply Smoothing to Function Values

Create Pixel Image on Linear Network

The Lennard-Jones Potential

Create Point Pattern on Linear Network

Marked K-Function

Nearest Neighbour Distances in Any Dimensions

methods.distfun

Methods for Distance Functions

Randomly Shift a Point Pattern

Window in Shape of Letter R

Three Dimensional Point Pattern

Plot a tessellation

Convert Point Pattern to Pixel Image

Simulate Matern Model II

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Apply Affine Transformation To Line Segment Pattern

nearest.raster.point

Find Pixel Nearest to a Given Point

Number of Line Segments in a Line Segment Pattern

Level Set of a Pixel Image

Plot a Signed or Vector-Valued Measure

Simulate Gauss-Poisson Process

Define Point Process Model for Metropolis-Hastings Simulation.

Nearest neighbour distances

Prediction from a Fitted Point Process Model

Pair Correlation Function obtained from array of K functions

Extract Subset of Signed or Vector Measure

Fitted Probabilities for Spatial Logistic Regression

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Morphological Opening

Print Brief Details of a Spatial Window

Find Line Segment Nearest to Each Point

project2segment

Move Point To Nearest Line

Convert Data To Class ppp

Three-Dimensional Box

Profile Maximum Pseudolikelihood

Midpoints of Line Segment Pattern

quadratresample

Resample a Point Pattern by Resampling Quadrats

Simple Example of Linear Network

Spherical Contact Distribution Function

Approximate a Polygon by a Simpler Polygon

Generate N Uniform Random Points in a Disc

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Extract or Replace Subset of Point Pattern

Convert Data to Hyperframe

Simulated Point Pattern

Pixel Image Approximation of a Window

Morphological Closing

New Zealand Trees Point Pattern

Pair Correlation Function obtained from K Function

Cross Validated Bandwidth Selection for Spatial Smoothing

Summarizing a Quadrature Scheme

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Plot a linear network

Circumradius and Diameter of a Linear Network

Create a Function Value Table

plot a Spatial Point Pattern

Colour Lookup Tables

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Contour plot of pixel image

plot.bermantest

Plot Result of Berman Test

plot a Fitted Point Process Model

Make Periodic Copies of a Spatial Pattern

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

scaletointerval

Rescale Data to Lie Between Specified Limits

Expand Window By Factor

Bounding Box of a Window or Point Pattern

pppmatching.object

Class of Point Matchings

Interactively Define a Polygon

Weighted Empirical Cumulative Distribution Function

Biological Cells Point Pattern

complement.owin

Take Complement of a Window

Plot a three-dimensional point pattern

Convert Polygonal Region into Different Format

Fit Cluster or Cox Point Process Model

Simulate point patterns using the Metropolis-Hastings algorithm.

Compute Expansion Window for Simulation

Residual G Function

Generate N Random Multitype Points

Chorley-Ribble Cancer Data

Murchison gold deposits

Coefficients of Fitted Point Process Model

Rotate a Window

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Loglikelihood of Spatial Logistic Regression

Cross Validated Bandwidth Selection for Kernel Density

Clark and Evans Aggregation Index

Recognise Stationary and Poisson Point Process Models

Nearest Neighbour Distance Function G

Generic Ord Interaction model

Estimate window from points alone

Generate a Default Pattern of Dummy Points

Reset Values in Subset of Image

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Summary of a Spatial Window

Generate Poisson Point Pattern in Three Dimensions

Concatenate x,y Coordinate Vectors

Distance Map of Point Pattern

Log Likelihood and AIC for Point Process Model

Safely Convert Point Pattern Window to Binary Mask

Print a Quadrature Scheme

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Determine Whether One Window is Contained In Another

spatstat-deprecated

Deprecated spatstat functions

Rectangular grid of points

Perfect Simulation of the Strauss Process

Random Re-Labelling of Point Pattern

The Area Interaction Point Process Model

Aherne's hamster tumour data

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Plot a List of Things

The Fiksel Interaction

Identify Points in a Point Pattern

Areas of Morphological Erosions

Print Brief Details of an Image

Linear Pair Correlation Function

Pine saplings in Finland.

Extract Interaction Structure

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Simulate Neyman-Scott Process

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

Corners of a rectangle

Create a Linear Network

Simulate Matern Cluster Process

plot a Spatial Line Segment Pattern

Crossing Points of Two Line Segment Patterns

Circular Window

Mark Connection Function

Divide Image Into Sub-images

Hyper Data Frame

Distance to Boundary of Window

Create List of Plotting Layers

Poisson Point Process on a Linear Network

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Neighbourhood density function

Classify Points in a Point Pattern

Pairwise distances between two different point patterns

Residual Diagnostics for Multiple Fitted Models

Convert Point Pattern to Another Unit of Length

Methods for Linear Networks

Inhomogeneous Neighbourhood Density Function

Extract Subset of Function Array

Methods for Multi-Dimensional Box

Convert Window to Another Unit of Length

Reduced Second Moment Measure

Generate Poisson Random Line Process

Pairwise distances in Three Dimensions

Methods for Fitted Point Process Models on a Linear Network

Diggle's Heather Data

Set Covariance of a Window

Perimeter Length of Window

Apply Vector Translation To Window

Inhomogeneous Cross Type L Function

Japanese Pines Point Pattern

Inhomogeneous Cross K Function

Beta Ganglion Cells in Cat Retina

Pairwise distances

Simulation Envelopes of Summary Function

ANOVA for Fitted Point Process Models

plot.hyperframe

Plot Entries in a Hyperframe

Multitype K Function (Cross-type)

Plot a fitted cluster point process

Saturated Pairwise Interaction Point Process Family

Fit the Matern Cluster Point Process by Minimum Contrast

Distance Map of Window

Convert Data To Class owin

Ponderosa Pine Tree Point Pattern

as.data.frame.im

Convert Pixel Image to Data Frame

Simulate from a Fitted Point Process Model

Determine Duplicated Points in a Spatial Point Pattern

Print Progress Reports

Test whether Object is Multitype

Nearest Neighbour Clutter Removal

Pairwise Distances in Any Dimensions

Convert Line Segment Pattern to Another Unit of Length

multiplicity.ppp

Count Multiplicity of Duplicate Points

Place Points Evenly Along Specified Lines

Diameter of a Window

model.frame.ppm

Extract the Environment of a Point Process Model

Function Value Table

Analysis of Deviance for Spatial Logistic Regression Models

California Redwoods Point Pattern (Ripley's Subset)

Compute Images of Constructed Covariates

Divide Region into Quadrats

Kernel Smoothing of Line Segment Pattern

Plot a Function Array

Pair Correlation Function of Point Pattern

Pairwise distances between line segments

Methods for three-dimensional point patterns

The Soft Core Point Process Model

Generate a Quadrature Scheme from a Point Pattern

Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative

Generic Pairwise Interaction model

Exponential Energy Marks

Basis for Harmonic Functions

Model Compensator of Nearest Neighbour Function

Convert Window to Pixel Image

Extract or Replace Subset of Tessellation

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

Morishita Index Plot

Generate Multitype Poisson Point Pattern

Distance Map as a Function

Test Whether An Object Is A Fitted Point Process Model

Extract or Replace Subset of a List of Things

Data and Code From JRSS Discussion Paper on Residuals

Model Formulae for Gibbs Point Process Models

Create Colour-Valued Pixel Image

Combine Two Line Segment Patterns

Marks of a Point Pattern

Marks of a Line Segment Pattern

Saturated Pairwise Interaction model

Apply a Function to a Point Pattern Broken Down by Factor

Simulate Thomas Process

Interactively join vertices on a plot

Print a Fitted Point Process Model

Apply Vector Translation To Point Pattern

Methods for Point Patterns on a Linear Network

Method of Minimum Contrast

Convert Data To Class psp

K-function using FFT

Nearest neighbour distances between line segments

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

is.multitype.ppp

Test Whether A Point Pattern is Multitype

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

Predict Point Process Model on Linear Network

Test Whether Two Pixel Images Are Compatible

Intersect Infinite Straight Lines with a Window

Class of Line Segment Patterns

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Q-Q Plot of Residuals from Fitted Point Process Model

Data Sharpening of Point Pattern

Influenza Virus Proteins

Number of Points in a Point Pattern

Methods for Multidimensional Space-Time Point Patterns

Distance Between Two Point Patterns

Extract the Interaction from a Fitted Point Process Model

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Multitype pair correlation function (cross-type)

Bronze gradient filter data

Artificial Data Point Pattern

Intersection of Two Tessellations

Convert Spatial Object to Pixel Image

Class of Fitted Point Process Models

Endpoints of Line Segment Pattern

California Redwoods Point Pattern (Entire Dataset)

pairdist.default

Pairwise distances

inforder.family

Infinite Order Interaction Family

Nonparametric Estimate of Spatially-Varying Relative Risk

Simulate systematic random point pattern

Plot a Spatial Window

Print Brief Details of a Line Segment Pattern Dataset

Ord Interaction Process Family

Test Whether A Point Pattern is Marked

Distance for a Point Pattern Matching

Interaction Distance of a Point Process

Inhomogeneous Linear Pair Correlation Function

Define Point Process Model for Metropolis-Hastings Simulation.

Inhomogeneous Pair Correlation Function

Simulate Simple Sequential Inhibition

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Multidimensional Space-Time Point Pattern

Plot a Simulation Envelope

Humberside Data on Childhood Leukaemia and Lymphoma

Multitype pair correlation function (i-to-any)

Find Largest Circle Inside Window

Fit Point Process Model to Point Pattern on Linear Network

Generate N Uniform Random Points in Any Dimensions

Nearest neighbours in three dimensions

Nearest Neighbours Between Two Patterns

Compute Areas of Tiles in a Tessellation

Print News About Latest Version of Package

summary.splitppp

Summary of a Split Point Pattern

Integral of a Pixel Image

Pseudoscore Diagnostic For Fitted Model against Saturation Alternative

Spatial Logistic Regression

Print Brief Details of a Point Pattern Dataset

Apply Vector Translation

Generate Poisson Point Pattern

Residuals for Fitted Point Process Model

Test Whether a Window is Convex

Generate N Uniform Random Points

Dummy Function Returns Number of Points

Generate N Uniform Random Points in Three Dimensions

Nearest neighbour

Update a Fitted Point Process Model

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Read Point Pattern From Data File

Mark Correlation Integral

Methods for Cluster Point Process Models

Identify Pixelwise Maximum of Several Pixel Images

Class of Point Patterns

plot a Spatial Quadrature Scheme

Simulate Log-Gaussian Cox Process

Determine Initial State for Metropolis-Hastings Simulation.

Class of Quadrature Schemes

Create a Line Segment Pattern

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Create a Tessellation

Random Perturbation of a Point Pattern

rescue.rectangle

Convert Window Back To Rectangle

Reduced Sample Estimator using Histogram Data

Update a Fitted Cluster Point Process Model

Rotate a Point Pattern

Poisson Line Tessellation

Test Whether An Object Is Empty

Summarizing a Pixel Image

Union of Data and Dummy Points

Extract Subset of Image

Estimate the I-function

Inhomogeneous K-function

Extract Subset of Line Segment Pattern

Residual K Function

Subset of Quadrature Scheme

Multitype L-function (cross-type)

Calculate four standard summary functions of a point pattern.

Extract Subset of Function Values

Distance to Boundary of Window

Multitype J Function (i-to-j)

Tropical rain forest trees

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Distance to Boundary of Window

Multitype L-function (i-to-any)

Border Region of a Window

Swedish Pines Point Pattern

Connected components of an image or window

Extract Dummy Points Used to Fit a Point Process Model

Difference of Disc Areas

Evaluate Expression Involving Functions

Difference of Disc Areas

Geometrical Calculations for Three-Dimensional Box

Point and Click Interface for Displaying a Point Pattern

Pair Correlation Function of a Three-Dimensional Point Pattern

Plot a Fitted Spatial Logistic Regression

Beta Ganglion Cells in Cat Retina, Old Version

Class of Images

Evaluate Expression Involving Pixel Images

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Plot Function Values

Create a Pixel Image Object

Predicted or Fitted Values from Spatial Logistic Regression

Convert Pixel Image to Another Unit of Length

Mosaic Random Set

Lurking variable plot

Kaplan-Meier and Reduced Sample Estimator using Histograms

Linear K Function

Generate N Random Points

Longleaf Pines Point Pattern

Weighted Histogram

Convert Line Segment Pattern to Pixel Image

Plot a List of Point Patterns

Randomly Shift a Line Segment Pattern

Cartesian Coordinates for a Pixel Raster

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Plot a Pixel Image

Interpret Fitted Model for Metropolis-Hastings Simulation.

Pairwise distances

Summary of a Line Segment Pattern Dataset

Extract Quadrature Scheme Used to Fit a Point Process Model

Random Thinning

Plot Pixel Image on Linear Network

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Generate Poisson Point Pattern on Line Segments

Generate Poisson Point Pattern in Any Dimensions

Extract.splitppp

Extract or Replace Sub-Patterns

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Foxall's Distance Functions

Beadlet Anemones Data

The Multitype Strauss Point Process Model

clarkevans.test

Clark and Evans Test

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Inhomogeneous Linear K Function

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

Fry Plot of Point Pattern

Signed or Vector-Valued Measure

Mark Correlation Function

Create a Point Matching

Plot a Spatial Kolmogorov-Smirnov Test

Pair Correlation Function

Generate grid of parallel lines with random displacement

Simulate Matern Model I

Apply Vector Translation To Pixel Image

Rotate a Line Segment Pattern

Name for Unit of Length

The Piecewise Constant Pairwise Interaction Point Process Model

The Strauss Point Process Model

Marked J Function

Cross Validated Bandwidth Selection for Relative Risk Estimation

The Multitype Hard Core Point Process Model

Marked Nearest Neighbour Distance Function

Stoyan's Rule of Thumb for Bandwidth Selection

Apply Gaussian Blur to a Pixel Image

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Compute Quadrature Weights Based on Grid Counts

Simulation Envelopes of Summary Function for 3D Point Pattern

Multi-Dimensional Box

Dirichlet Tessellation of Point Pattern

Area of Part of Disc

Summarise Marks in Every Neighbourhood in a Point Pattern

Lansing Woods Point Pattern

Identify Covariates Involved in each Model Term

model.matrix.ppm

Extract Design Matrix from Point Process Model

Plot a plotppm Object Created by plot.ppm

Plot a Colour Map

Nearest Neighbours in Any Dimensions

Sample Quantiles of Pixel Image

Quadrature Scheme Based on Pixel Grid

Quadrat counting for a point pattern

Mosaic Random Field

rshift.splitppp

Randomly Shift a List of Point Patterns

Convert dataset to another unit of length

Theoretical Distribution of Nearest Neighbour Distance

Galaxies in the Shapley Supercluster

Apply Vector Translation To Line Segment Pattern

Simulate a Fitted Cluster Point Process Model