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spatstat (version 1.24-2)

Spatial Point Pattern analysis, model-fitting, simulation, tests

Description

A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, and space-time point patterns in any number of dimensions. Contains over 1000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images and tessellations. Exploratory methods include K-functions, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics etc. Point process models can be fitted to point pattern data using functions ppm, kppm, slrm similar to glm. Models may include dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Fitted models can be simulated automatically. Also provides facilities for formal inference (such as chi-squared tests) and model diagnostics (including simulation envelopes, residuals, residual plots and Q-Q plots).

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Version

Install

install.packages('spatstat')

Monthly Downloads

16,590

Version

1.24-2

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

November 11th, 2011

Functions in spatstat (1.24-2)

Extract Subset of Signed or Vector Measure

The Strauss Point Process Model

Hutchings' Bramble Canes data

Subdivide a Window or Tessellation using a Set of Lines

Stoyan's Rule of Thumb for Bandwidth Selection

Concatenate x,y Coordinate Vectors

Compute Quadrature Weights Based on Grid Counts

Diameter of a Window

Create a Pixel Image Object

Level Set of a Pixel Image

Window in Shape of Letter R

Morishita Index Plot

Ord Interaction Process Family

Pairwise Distances in Any Dimensions

Pair Correlation Function obtained from K Function

plot.bermantest

Plot Result of Berman Test

Class of Line Segment Patterns

Convert Window to Pixel Image

Divide Region into Quadrats

Random Perturbation of a Point Pattern

Extract or Replace Subset of Point Pattern

Interpret Fitted Model for Metropolis-Hastings Simulation.

Subset of Quadrature Scheme

Marked K-Function

Hughes' Amacrine Cell Data

The Triplet Point Process Model

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Difference of Disc Areas

Extract or Replace Subset of Tessellation

Convert Data To Tessellation

Distance Map of Line Segment Pattern

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

envelope.envelope

Recompute Envelopes

Convert Data to Hyperframe

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Extract Subset of Function Array

Morphological Closing

Geyer's Saturation Point Process Model

Apply Affine Transformation

Apply Function to Every Neighbourhood in a Point Pattern

Marks of a Line Segment Pattern

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

complement.owin

Take Complement of a Window

ANOVA for Fitted Point Process Models on Linear Network

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

Residual G Function

Ord's Interaction model

Fitted Conditional Intensity for Point Process Model

Bounding Box of a Window or Point Pattern

Inhomogeneous Multitype K Dot Function

Tropical rain forest trees

Apply Affine Transformation To Line Segment Pattern

Estimate the empty space function F

Extract Subset of Image

The Area Interaction Point Process Model

The Piecewise Constant Pairwise Interaction Point Process Model

Distance to Boundary of Window

Cross Validated Bandwidth Selection for Kernel Density

Analysis of Deviance for Spatial Logistic Regression Models

Methods for Fitted Point Process Models on a Linear Network

Interactively Define a Polygon

Test Whether Objects Are Compatible

Methods for Units

Plot a List of Things

Chorley-Ribble Cancer Data

Pair Correlation Function

Beta Ganglion Cells in Cat Retina

Cross Validated Bandwidth Selection for Relative Risk Estimation

Test Whether A Point Pattern is Marked

Inhomogeneous Multitype L Dot Function

Multitype J Function (i-to-j)

Artificial Data Point Pattern

Apply Affine Transformation To Point Pattern

Fit Cluster or Cox Point Process Model

Multitype K Function (Cross-type)

Create a Point Pattern

Morphological Dilation

Convert Data To Class ppp

Print Progress Reports

Interactively join vertices on a plot

Plot a Simulation Envelope

Centroid of a window

Envelope for Point Patterns on Linear Network

Influenza Virus Proteins

Multitype L-function (i-to-any)

Dirichlet Tessellation of Point Pattern

Safely Convert Point Pattern Window to Binary Mask

Determine Duplicated Points in a Spatial Point Pattern

Plot a Function Array

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Test Whether An Object Is A Fitted Point Process Model

Plot a Spatial Kolmogorov-Smirnov Test

Identify Points in a Point Pattern

Geometrical Calculations for Three-Dimensional Box

Intersection, Union or Set Subtraction of Two Windows

The Strauss / Hard Core Point Process Model

Three-Dimensional Box

Endpoints of Line Segment Pattern

Distance Map of Point Pattern

Berman's Tests for Point Process Model

Combine Function Value Tables

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Morphological Erosion

California Redwoods Point Pattern (Ripley's Subset)

Identify Segments in a Line Segment Pattern

Lengths of Line Segments

Weighted Empirical Cumulative Distribution Function

Infinite Straight Lines

inforder.family

Infinite Order Interaction Family

Convert Pixel Image to Another Unit of Length

Signed or Vector-Valued Measure

Evaluate Expression Involving Pixel Images

Neighbourhood density function

as.data.frame.im

Convert Pixel Image to Data Frame

Data and Code From JRSS Discussion Paper on Residuals

Plot a three-dimensional point pattern

Distance to Boundary of Window

Print a Fitted Point Process Model

Convert Data to Three-Dimensional Box

Distance Map of Window

Generate Poisson Random Line Process

Berman-Huntington points and lines data

Create List of Plotting Layers

Distance for a Point Pattern Matching

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Test Whether a Window is Convex

Apply Vector Translation To Point Pattern

Convert Pixel Image from Numeric to Factor

Create a Linear Network

Marks of a Point Pattern

Plot a List of Things

Mark Correlation Integral

Fit Point Process Model to Data

Collapse Several Function Tables into One

Linear K Function

Pair Correlation Function of a Three-Dimensional Point Pattern

Plot Pixel Image on Linear Network

Randomly Shift a Line Segment Pattern

Diagnostics for random marking

Marked J Function

Reduced Sample Estimator using Histogram Data

Multitype pair correlation function (i-to-any)

Recognise Stationary and Poisson Point Process Models

Geometrical Calculations for Multi-Dimensional Box

Union of Data and Dummy Points

Methods for Multi-Dimensional Box

plot a Spatial Quadrature Scheme

Method of Minimum Contrast

Predict Point Process Model on Linear Network

Exchange X and Y Coordinates

Pool Data from Several Function Arrays

Multidimensional Space-Time Point Pattern

Mosaic Random Set

Extract Interaction Structure

Plot Function Values

Exponential Energy Marks

Place Points Evenly Along Specified Lines

bounding.box.xy

Convex Hull of Points

Saturated Pairwise Interaction Point Process Family

Inhomogeneous Linear Pair Correlation Function

Humberside Data on Childhood Leukaemia and Lymphoma

Simulate Matern Model II

Plot a List of Point Patterns

Perfect Simulation of the Strauss Process

Sample Quantiles of Pixel Image

Ponderosa Pine Tree Point Pattern

Plot a Pixel Image

Convert Line Segment Pattern to Another Unit of Length

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

California Redwoods Point Pattern (Entire Dataset)

Biological Cells Point Pattern

Create Pixel Image on Linear Network

Multi-Dimensional Box

Print Brief Details of a Line Segment Pattern Dataset

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Cartesian Coordinates for a Pixel Raster

Simulate Simple Sequential Inhibition

Methods for Intensity Functions of Spatial Covariate

Generate Poisson Point Pattern on Line Segments

Define Point Process Model for Metropolis-Hastings Simulation.

Apply Vector Translation To Pixel Image

Simulate systematic random point pattern

Convert Window to Another Unit of Length

Spokes pattern of dummy points

Update a Fitted Cluster Point Process Model

Evaluate Expression Involving Function Arrays

plot.hyperframe

Plot Entries in a Hyperframe

Fit the Thomas Point Process by Minimum Contrast

Simulate a Fitted Gibbs Point Process Model

Simulate a Fitted Cluster Point Process Model

Beta Ganglion Cells in Cat Retina, Old Version

Multitype L-function (cross-type)

Estimate window from points alone

rescue.rectangle

Convert Window Back To Rectangle

Multitype pair correlation function (cross-type)

Create a Function Value Table

Summary of a Spatial Window

Print a Quadrature Scheme

Test Whether An Object Is A Pixel Image

Simulate point patterns using the Metropolis-Hastings algorithm.

Apply Affine Transformation To Window

Compute Areas of Tiles in a Tessellation

Triplet Interaction Family

Variance-Covariance Matrix for a Fitted Cluster Point Process Model

Class of Point Patterns

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Test Whether An Object Is Empty

Generate N Uniform Random Points in a Disc

Superimpose Several Geometric Patterns

Fit the Matern Cluster Point Process by Minimum Contrast

Divide Point Pattern into Sub-patterns

Circumradius and Diameter of a Linear Network

Cut margins from rectangle

Estimate the I-function

Rotate a Line Segment Pattern

Random Thinning

Apply Function to Image Broken Down by Factor

Divide Image Into Sub-images

Extract Subset of Line Segment Pattern

pairdist.default

Pairwise distances

spatstat.options

Internal Options in Spatstat Package

Extract Unique Points from a Spatial Point Pattern

Methods for Point Patterns on a Linear Network

Nearest Neighbour Distance Function G

Convert and Compare Colours in Different Formats

The Lennard-Jones Potential

model.matrix.ppm

Extract Design Matrix from Point Process Model

Area of Part of Disc

Classify Points in a Point Pattern

K-function of a Three-Dimensional Point Pattern

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Plot a Signed or Vector-Valued Measure

K-function using FFT

New Zealand Trees Point Pattern

Vertices of a Window

Class of Images

The Multitype Hard Core Point Process Model

Generic Pairwise Interaction model

Saturated Pairwise Interaction model

Create a Line Segment Pattern

Pseudoscore Diagnostic For Fitted Model against General Alternative

Area of a Window

spatstat-internal

Internal spatstat functions

Determine Whether One Window is Contained In Another

Apply a Function to a Point Pattern Broken Down by Factor

Test Whether An Object Is A Window

Convert to Pixel Image

Convert Data To Class psp

Data Sharpening of Point Pattern

Intersect Infinite Straight Lines with a Window

Local pair correlation function

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Nearest neighbour

Nearest neighbours in three dimensions

Cross Validated Bandwidth Selection for Spatial Smoothing

Evaluate Expression Involving Functions

Weighted Histogram

Weighted kernel smoother

compatible.fasp

Test Whether Function Arrays Are Compatible

Model Compensator of K Function

Estimate Variance of Summary Statistic by Subdivision

Number of Points in a Point Pattern

Distance Map as a Function

Beadlet Anemones Data

Print News About Latest Version of Package

Hyper Data Frame

Random Re-Labelling of Point Pattern

Convert Pixel Image to Matrix or Array

Urkiola Woods Point Pattern

Reduced Second Moment Measure

Rectangular grid of points

Convert Point Pattern to Pixel Image

Basis for Harmonic Functions

Uniform Random Points on a Linear Network

Scatterplot Matrix for Pixel Images

Pixel Image Approximation of a Window

Convert Polygonal Region into Different Format

clarkevans.test

Clark and Evans Test

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

Loglikelihood of Spatial Logistic Regression

Summarise Marks in Every Neighbourhood in a Point Pattern

Multitype J Function (i-to-any)

The Multitype Strauss Point Process Model

Plot a Fitted Spatial Logistic Regression

Test Whether Marks Are Present

Profile Maximum Pseudolikelihood

Interpolate a Pixel Image

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

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Diagnostic Plots for Fitted Point Process Model

Plot a Colour Map

Simulate Matern Cluster Process

Circular Window

Interaction Distance of a Point Process

Apply Gaussian Blur to a Pixel Image

Smoothing Estimate of Covariate Transformation

Function Value Table

Generate N Random Points

Pairwise distances between two different three-dimensional point patterns

nearest.raster.point

Find Pixel Nearest to a Given Point

crossdist.default

Pairwise distances between two different sets of points

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Generate Poisson Point Pattern in Three Dimensions

Inverse-distance weighted smoothing of observations at irregular points

Print Brief Details of a Spatial Window

Kolmogorov-Smirnov Test for Point Process Model

scaletointerval

Rescale Data to Lie Between Specified Limits

Volume of an Object

Theoretical Distribution of Nearest Neighbour Distance

Class of Quadrature Schemes

Create Colour-Valued Pixel Image

Log Likelihood and AIC for Point Process Model

Test Whether A Point Process Model is Marked

Residuals for Fitted Point Process Model

Japanese Pines Point Pattern

Approximate a Polygon by a Simpler Polygon

Integral of a Pixel Image

Longleaf Pines Point Pattern

Poisson Line Tessellation

Nearest Neighbour Clutter Removal

Create Point Pattern on Linear Network

Pairwise distances

Convert Spatial Object to Pixel Image

Morphological Opening

Randomly Shift a Point Pattern

Pairwise distances between line segments

rshift.splitppp

Randomly Shift a List of Point Patterns

Apply Vector Translation

Generate Poisson Point Pattern in Any Dimensions

Distance Between Two Point Patterns

Apply Vector Translation To Line Segment Pattern

Estimate the J-function

Apply Smoothing to Function Values

Create a Point Matching

Residual K Function

Print Brief Details of an Image

Perimeter Length of Window

Summarizing a Fitted Point Process Model

project2segment

Move Point To Nearest Line

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Convert dataset to another unit of length

Clark and Evans Aggregation Index

Convert a Window to a Polygonal Window

Compute Quadratic Forms

Pairwise distances

Mosaic Random Field

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Contour plot of pixel image

Determine Initial State for Metropolis-Hastings Simulation.

Generate N Random Multitype Points

Poisson Point Process on a Linear Network

Empty Space Function of a Three-Dimensional Point Pattern

The Fiksel Interaction

Inhomogeneous Cross K Function

Delaunay Triangulation of Point Pattern

Pairwise distances between two different line segment patterns

Generate Poisson Point Pattern

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Galaxies in the Shapley Supercluster

Summary of a List of Things

Spruces Point Pattern

Name for Unit of Length

Convert Data to Numeric Values by Constructing Dummy Variables

Identify Pixelwise Maximum of Several Pixel Images

Model Formulae for Gibbs Point Process Models

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Spherical Contact Distribution Function

Locally Scaled K-function

edges2triangles

List Triangles in a Graph

Generic Ord Interaction model

The Soft Core Point Process Model

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Convert Line Segment Pattern to Binary Pixel Mask

Simulation Envelopes of Summary Function for 3D Point Pattern

Point and Click Interface for Displaying a Point Pattern

Intersection of Two Tessellations

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

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Diggle's Heather Data

Create a Tessellation

Compute Disc of Given Radius in Linear Network

model.frame.ppm

Extract the Environment of a Point Process Model

pairwise.family

Pairwise Interaction Process Family

Convert Function Value Table to Function

Pairwise shortest-path distances between points on a linear network

Border Region of a Window

Function Arrays for Spatial Patterns

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Bronze gradient filter data

methods.distfun

Methods for Distance Functions

Crossing Points of Two Line Segment Patterns

Pool Data from Several Envelopes

Pairwise distances

Diameter of an Object

Methods for Three-Dimensional Box

Number of Line Segments in a Line Segment Pattern

quadratresample

Resample a Point Pattern by Resampling Quadrats

Generate N Uniform Random Points in Any Dimensions

Evaluate an Expression in a Function Table

Pairwise distances between two different point patterns

Spatial Covariance of a Pixel Image

Generate N Uniform Random Points in Three Dimensions

Dummy Function Returns Number of Points

Point and Click Interface for Exploratory Analysis of Point Pattern

Inhomogeneous Linear K Function

Prediction from a Fitted Point Process Model

Quadrat counting for a point pattern

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Simulate Baddeley-Silverman Cell Process

Simulate from a Fitted Point Process Model

Methods for Linear Networks

Nearest neighbour distances

Simulated Point Pattern

Methods for three-dimensional point patterns

Perspective Plot of Pixel Image

Spatial Scan Test

Convert Line Segment Pattern to Pixel Image

Sufficient Statistic of Point Process Model

Fit the Thomas Point Process by Minimum Contrast

plot a Spatial Point Pattern

Pool Data from Several Ratio Objects

Extract List of Tiles in a Tessellation

pppmatching.object

Class of Point Matchings

Print Brief Details of a Point Pattern Dataset

Set Control Parameters for Metropolis-Hastings Algorithm.

Pseudoscore Diagnostic For Fitted Model against Saturation Alternative

Simulate Thomas Process

Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative

Convert Point Pattern to Another Unit of Length

Read Point Pattern From Data File

Model Compensator of Nearest Neighbour Function

The Hard Core Point Process Model

Set Covariance of a Window

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Test Whether Function Objects Are Compatible

Simple Example of Linear Network

spatstat-deprecated

Deprecated spatstat functions

Compute Integral of Function Against Cumulative Distribution

Hybrid Geyer Point Process Model

Summarizing a Quadrature Scheme

Summary of a Line Segment Pattern Dataset

Extract or Replace Subset of a List of Things

Pine saplings in Finland.

Simulation Envelopes of Summary Function

Extract Subset of Function Values

spatstat-package

The Spatstat Package

Extract.splitppp

Extract or Replace Sub-Patterns

Lansing Woods Point Pattern

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Linear Pair Correlation Function

Fit Point Process Model to Point Pattern on Linear Network

ANOVA for Fitted Point Process Models

Chicago Street Crime Data

Areas of Morphological Dilations

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Inhomogeneous Neighbourhood Density Function

Midpoints of Line Segment Pattern

Mark Correlation Function

multiplicity.ppp

Count Multiplicity of Duplicate Points

Compute Images of Constructed Covariates

matclust.estpcf

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

Find Line Segment Nearest to Each Point

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Nearest Neighbour Distances in Any Dimensions

Nearest neighbour distances in three dimensions

Nearest Neighbours in Any Dimensions

Create a Window

Plot a Spatial Window

Inhomogeneous Pair Correlation Function

Plot a tessellation

Simulate Gauss-Poisson Process

Q-Q Plot of Residuals from Fitted Point Process Model

Three Dimensional Point Pattern

Prediction from a Fitted Cluster Point Process Model

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

Predicted or Fitted Values from Spatial Logistic Regression

Generate a Quadrature Scheme from a Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Simulate Matern Model I

Simulate Neyman-Scott Process

Rotate a Window

Nonparametric Estimate of Spatially-Varying Relative Risk

Summarizing a Pixel Image

Generate Multitype Poisson Point Pattern

Diggle-Gratton model

Spatial Logistic Regression

Apply Vector Translation To Window

Swedish Pines Point Pattern

Marked Nearest Neighbour Distance Function

Combine Two Line Segment Patterns

Difference of Disc Areas

Extract Original Data from a Fitted Point Process Model

Reset Values in Subset of Image

Generate a Default Pattern of Dummy Points

Make Pixel Images Compatible

Test Whether Points Are Inside A Window

Methods for Multidimensional Space-Time Point Patterns

Kaplan-Meier Estimator using Histogram Data

Identify Covariates Involved in each Model Term

Nearest Neighbours Between Two Patterns

Lurking variable plot

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Pairwise distances in Three Dimensions

Pair Correlation Function obtained from array of K functions

Quadrature Scheme Based on Pixel Grid

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Plot a fitted cluster point process

Plot a linear network

Class of Fitted Point Process Models

plot a Fitted Point Process Model

Generate N Uniform Random Points

summary.splitppp

Summary of a Split Point Pattern

Rounding of Pixel Values

Summary of a Point Pattern Dataset

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Smooth a Signed or Vector-Valued Measure

Variance-Covariance Matrix for a Fitted Point Process Model

Inhomogeneous Cross Type L Function

Inhomogeneous K-function

Coefficients of Fitted Point Process Model

Convex Hull of Points

Test Whether Pixel Images Are Compatible

Connected components of an image or window

Interactively Add Points

Poisson Point Process Model

Multitype K Function (i-to-any)

Fitted Probabilities for Spatial Logistic Regression

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

Residual Diagnostics for Multiple Fitted Models

Test whether Object is Multitype

Distance to Boundary of Window

Convert Data To Class owin

Fry Plot of Point Pattern

Kernel Smoothed Intensity of Point Pattern

Methods for Cluster Point Process Models

Find Largest Circle Inside Window

Expand Window By Factor

Colour Lookup Tables

Extract Dummy Points Used to Fit a Point Process Model

Corners of a rectangle

Make Periodic Copies of a Spatial Pattern

Kaplan-Meier and Reduced Sample Estimator using Histograms

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

Histogram of Pixel Values in an Image

Orientation Angles of Line Segments

Test Whether An Object Is A Point Pattern

Plot a plotppm Object Created by plot.ppm

Mark Connection Function

Areas of Morphological Erosions

Point Patterns of New Brunswick Forest Fires

Simulate Log-Gaussian Cox Process

Spatial smoothing of observations at irregular points

Nearest neighbour distances between line segments

Update a Fitted Point Process Model

Aherne's hamster tumour data

plot a Spatial Line Segment Pattern

Extract Quadrature Scheme Used to Fit a Point Process Model

Kernel Smoothing of Line Segment Pattern

Generate grid of parallel lines with random displacement

Simulate Stratified Random Point Pattern

Calculate four standard summary functions of a point pattern.

Harkness-Isham ants' nests data

Coefficients of Fitted Spatial Logistic Regression Model

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Pair Correlation Function of Point Pattern

Rotate a Point Pattern

Foxall's Distance Functions

Murchison gold deposits

K function of a model

Compute Expansion Window for Simulation

Extract the Interaction from a Fitted Point Process Model