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spatstat (version 1.24-1)

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

17,668

Version

1.24-1

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

October 23rd, 2011

Functions in spatstat (1.24-1)

Model Compensator of Nearest Neighbour Function

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

Hughes' Amacrine Cell Data

ANOVA for Fitted Point Process Models

Circumradius and Diameter of a Linear Network

Extract Subset of Signed or Vector Measure

Estimate the J-function

Multitype J Function (i-to-j)

Convert Line Segment Pattern to Binary Pixel Mask

The Hard Core Point Process Model

Extract Subset of Line Segment Pattern

The Soft Core Point Process Model

Extract or Replace Subset of Point Pattern

Crossing Points of Two Line Segment Patterns

Apply Affine Transformation

Subset of Quadrature Scheme

Extract or Replace Subset of Tessellation

Apply Affine Transformation To Window

Bronze gradient filter data

Combine Function Value Tables

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

The Lennard-Jones Potential

Apply Affine Transformation To Line Segment Pattern

Multitype J Function (i-to-any)

Diagnostics for random marking

Contour plot of pixel image

Apply Function to Every Neighbourhood in a Point Pattern

Inhomogeneous Cross Type L Function

Inhomogeneous Cross K Function

Beta Ganglion Cells in Cat Retina

Residual G Function

Area of a Window

Berman's Tests for Point Process Model

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

Cross Validated Bandwidth Selection for Kernel Density

Apply Affine Transformation To Point Pattern

Plot a List of Things

Corners of a rectangle

Residual Diagnostics for Multiple Fitted Models

Envelope for Point Patterns on Linear Network

Nearest Neighbour Distance Function G

Berman-Huntington points and lines data

K function of a model

Generate a Default Pattern of Dummy Points

Colour Lookup Tables

Orientation Angles of Line Segments

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Apply a Function to a Point Pattern Broken Down by Factor

Convex Hull of Points

Summarise Marks in Every Neighbourhood in a Point Pattern

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

The Fiksel Interaction

Coefficients of Fitted Spatial Logistic Regression Model

Estimate the empty space function F

Clark and Evans Aggregation Index

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

Estimate the I-function

bounding.box.xy

Convex Hull of Points

Hybrid Geyer Point Process Model

Interactively Add Points

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Convert Data To Class ppp

Hutchings' Bramble Canes data

Multitype L-function (cross-type)

Border Region of a Window

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

Marked J Function

Pine saplings in Finland.

Reduced Second Moment Measure

Chorley-Ribble Cancer Data

Distance to Boundary of Window

Function Value Table

Foxall's Distance Functions

Convert Function Value Table to Function

Extract.splitppp

Extract or Replace Sub-Patterns

Apply Gaussian Blur to a Pixel Image

Distance to Boundary of Window

Extract or Replace Subset of a List of Things

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Inhomogeneous K-function

Centroid of a window

Intersection, Union or Set Subtraction of Two Windows

Influenza Virus Proteins

Generic Ord Interaction model

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Histogram of Pixel Values in an Image

Inhomogeneous Multitype L Dot Function

Apply Function to Image Broken Down by Factor

Residual K Function

Find Line Segment Nearest to Each Point

Distance Map of Point Pattern

Multitype K Function (Cross-type)

The Piecewise Constant Pairwise Interaction Point Process Model

Methods for Fitted Point Process Models on a Linear Network

Lansing Woods Point Pattern

Geometrical Calculations for Three-Dimensional Box

Simulation Envelopes of Summary Function

Pairwise distances between two different three-dimensional point patterns

as.data.frame.im

Convert Pixel Image to Data Frame

Distance Map of Window

Beadlet Anemones Data

Subdivide a Window or Tessellation using a Set of Lines

Multi-Dimensional Box

Lurking variable plot

Multitype L-function (i-to-any)

Marked Nearest Neighbour Distance Function

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Expand Window By Factor

Intersect Infinite Straight Lines with a Window

Pairwise distances between two different line segment patterns

ANOVA for Fitted Point Process Models on Linear Network

Delaunay Triangulation of Point Pattern

Inhomogeneous Multitype K Dot Function

Extract Interaction Structure

Weighted Empirical Cumulative Distribution Function

Beta Ganglion Cells in Cat Retina, Old Version

The Strauss / Hard Core Point Process Model

Analysis of Deviance for Spatial Logistic Regression Models

Nearest Neighbours Between Two Patterns

Marked K-Function

Model Compensator of K Function

Convert Data to Hyperframe

Inverse-distance weighted smoothing of observations at irregular points

Fitted Probabilities for Spatial Logistic Regression

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Distance Map of Line Segment Pattern

Interactively join vertices on a plot

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Diggle-Gratton model

Artificial Data Point Pattern

Function Arrays for Spatial Patterns

Pair Correlation Function of Point Pattern

Generic Pairwise Interaction model

Dirichlet Tessellation of Point Pattern

Empty Space Function of a Three-Dimensional Point Pattern

Test Whether An Object Is A Point Pattern

Extract Subset of Function Array

Kernel Smoothing of Line Segment Pattern

Nearest neighbour distances between line segments

Pairwise distances between two different point patterns

Distance to Boundary of Window

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Log Likelihood and AIC for Point Process Model

Generate Poisson Point Pattern

Test Whether Objects Are Compatible

Convert and Compare Colours in Different Formats

Interactively Define a Polygon

Test Whether An Object Is A Fitted Point Process Model

Japanese Pines Point Pattern

Exchange X and Y Coordinates

Areas of Morphological Dilations

envelope.envelope

Recompute Envelopes

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

The Strauss Point Process Model

Geyer's Saturation Point Process Model

Multitype K Function (i-to-any)

Extract Dummy Points Used to Fit a Point Process Model

Morphological Closing

Ponderosa Pine Tree Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

Convert to Pixel Image

Convert a Window to a Polygonal Window

Randomly Shift a Point Pattern

Window in Shape of Letter R

Longleaf Pines Point Pattern

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Convert Spatial Object to Pixel Image

Fit Point Process Model to Data

Test Whether An Object Is A Pixel Image

Determine Initial State for Metropolis-Hastings Simulation.

Pseudoscore Diagnostic For Fitted Model against General Alternative

Class of Quadrature Schemes

Simulate Matern Model I

Safely Convert Point Pattern Window to Binary Mask

K-function using FFT

Distance Between Two Point Patterns

Compute Quadrature Weights Based on Grid Counts

Pairwise distances

Extract Subset of Image

Cross Validated Bandwidth Selection for Spatial Smoothing

Test Whether An Object Is A Window

Nearest neighbour distances in three dimensions

Fry Plot of Point Pattern

Interpolate a Pixel Image

Test Whether An Object Is Empty

Plot a Signed or Vector-Valued Measure

Determine Duplicated Points in a Spatial Point Pattern

Create List of Plotting Layers

Diameter of a Window

spatstat-deprecated

Deprecated spatstat functions

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

plot.hyperframe

Plot Entries in a Hyperframe

The Multitype Strauss Point Process Model

Nearest neighbour distances

Distance Map as a Function

Print a Fitted Point Process Model

Quadrature Scheme Based on Pixel Grid

Test Whether a Window is Convex

Collapse Several Function Tables into One

Biological Cells Point Pattern

Test Whether A Point Process Model is Marked

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

complement.owin

Take Complement of a Window

Plot a Function Array

Evaluate Expression Involving Functions

Tropical rain forest trees

Plot a linear network

Set Control Parameters for Metropolis-Hastings Algorithm.

Coefficients of Fitted Point Process Model

Linear K Function

Plot a Fitted Spatial Logistic Regression

Integral of a Pixel Image

Plot Pixel Image on Linear Network

Perimeter Length of Window

Method of Minimum Contrast

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Model Formulae for Gibbs Point Process Models

Test Whether Points Are Inside A Window

Print Progress Reports

Plot Function Values

Make Pixel Images Compatible

Linear Pair Correlation Function

Spatial smoothing of observations at irregular points

California Redwoods Point Pattern (Entire Dataset)

Plot a tessellation

Summary of a Point Pattern Dataset

Create a Point Matching

Plot a Colour Map

Pairwise distances in Three Dimensions

The Area Interaction Point Process Model

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

Fit Cluster or Cox Point Process Model

Profile Maximum Pseudolikelihood

Convert Data to Numeric Values by Constructing Dummy Variables

Compute Images of Constructed Covariates

Apply Vector Translation To Line Segment Pattern

Area of Part of Disc

Print Brief Details of a Line Segment Pattern Dataset

model.frame.ppm

Extract the Environment of a Point Process Model

Infinite Straight Lines

Create Colour-Valued Pixel Image

Weighted kernel smoother

Hyper Data Frame

Generate a Quadrature Scheme from a Point Pattern

Poisson Point Process on a Linear Network

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Distance for a Point Pattern Matching

Murchison gold deposits

crossdist.default

Pairwise distances between two different sets of points

Concatenate x,y Coordinate Vectors

Circular Window

Smooth a Signed or Vector-Valued Measure

Poisson Line Tessellation

Humberside Data on Childhood Leukaemia and Lymphoma

Methods for Point Patterns on a Linear Network

Level Set of a Pixel Image

Determine Whether One Window is Contained In Another

Morphological Opening

Simulate Matern Model II

Difference of Disc Areas

Apply Vector Translation

Plot a Pixel Image

Identify Points in a Point Pattern

Pair Correlation Function obtained from array of K functions

Superimpose Several Geometric Patterns

Summary of a List of Things

Find Largest Circle Inside Window

Multitype pair correlation function (cross-type)

Generate N Uniform Random Points in a Disc

Lengths of Line Segments

Number of Points in a Point Pattern

project2segment

Move Point To Nearest Line

Classify Points in a Point Pattern

Perspective Plot of Pixel Image

Sample Quantiles of Pixel Image

Prediction from a Fitted Point Process Model

Pairwise distances between line segments

Simulate a Fitted Cluster Point Process Model

pairdist.default

Pairwise distances

Print Brief Details of an Image

Marks of a Point Pattern

Update a Fitted Cluster Point Process Model

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Extract Quadrature Scheme Used to Fit a Point Process Model

Point and Click Interface for Displaying a Point Pattern

Nearest-Neighbour Correlation Indices of Marked Point Pattern

methods.distfun

Methods for Distance Functions

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Spokes pattern of dummy points

Nearest Neighbour Distances in Any Dimensions

Point Patterns of New Brunswick Forest Fires

Plot a Spatial Window

Print a Quadrature Scheme

Theoretical Distribution of Nearest Neighbour Distance

Simulate Thomas Process

Simulate Log-Gaussian Cox Process

Define Point Process Model for Metropolis-Hastings Simulation.

pairwise.family

Pairwise Interaction Process Family

Create Pixel Image on Linear Network

Divide Point Pattern into Sub-patterns

Uniform Random Points on a Linear Network

Mosaic Random Field

Interaction Distance of a Point Process

Pool Data from Several Function Arrays

Summarizing a Fitted Point Process Model

Compute Disc of Given Radius in Linear Network

Q-Q Plot of Residuals from Fitted Point Process Model

Simulate from a Fitted Point Process Model

Convert Point Pattern to Pixel Image

Generate grid of parallel lines with random displacement

Extract Subset of Function Values

Name for Unit of Length

Rectangular grid of points

Three Dimensional Point Pattern

Rotate a Window

multiplicity.ppp

Count Multiplicity of Duplicate Points

Simulation Envelopes of Summary Function for 3D Point Pattern

Apply Vector Translation To Pixel Image

Spatial Scan Test

spatstat.options

Internal Options in Spatstat Package

Aherne's hamster tumour data

Extract Original Data from a Fitted Point Process Model

Urkiola Woods Point Pattern

Vertices of a Window

Neighbourhood density function

Evaluate Expression Involving Function Arrays

Generate N Random Multitype Points

Compute Quadratic Forms

Generate Poisson Point Pattern on Line Segments

Simulate a Fitted Gibbs Point Process Model

Methods for three-dimensional point patterns

Saturated Pairwise Interaction Point Process Family

Pairwise distances

Signed or Vector-Valued Measure

scaletointerval

Rescale Data to Lie Between Specified Limits

Create a Linear Network

Marks of a Line Segment Pattern

rshift.splitppp

Randomly Shift a List of Point Patterns

Spatial Logistic Regression

Methods for Multidimensional Space-Time Point Patterns

Inhomogeneous Linear Pair Correlation Function

Smoothing Estimate of Covariate Transformation

Test Whether Function Objects Are Compatible

Basis for Harmonic Functions

runifpointOnLines

Generate N Uniform Random Points On Line Segments

pppmatching.object

Class of Point Matchings

plot a Spatial Point Pattern

Print Brief Details of a Point Pattern Dataset

Areas of Morphological Erosions

Create Point Pattern on Linear Network

Convert Line Segment Pattern to Another Unit of Length

Convert Pixel Image to Another Unit of Length

Generate N Random Points

plot a Fitted Point Process Model

Divide Image Into Sub-images

Weighted Histogram

Galaxies in the Shapley Supercluster

Scatterplot Matrix for Pixel Images

quadratresample

Resample a Point Pattern by Resampling Quadrats

Identify Pixelwise Maximum of Several Pixel Images

Test Whether Marks Are Present

Evaluate Expression Involving Pixel Images

Divide Region into Quadrats

Create a Tessellation

Plot a Spatial Kolmogorov-Smirnov Test

Interpret Fitted Model for Metropolis-Hastings Simulation.

Print Brief Details of a Spatial Window

Pool Data from Several Ratio Objects

Cut margins from rectangle

Create a Point Pattern

Plot a List of Things

Pairwise shortest-path distances between points on a linear network

Spatial Covariance of a Pixel Image

Read Point Pattern From Data File

Perfect Simulation of the Strauss Process

Generate N Uniform Random Points

Generate Poisson Random Line Process

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Extract List of Tiles in a Tessellation

Ord Interaction Process Family

Union of Data and Dummy Points

Compute Expansion Window for Simulation

Pool Data from Several Envelopes

Sufficient Statistic of Point Process Model

Pseudoscore Diagnostic For Fitted Model against Saturation Alternative

Nearest Neighbours in Any Dimensions

Apply Smoothing to Function Values

Summarizing a Pixel Image

Kernel Smoothed Intensity of Point Pattern

Prediction from a Fitted Cluster Point Process Model

Identify Segments in a Line Segment Pattern

Simulate Baddeley-Silverman Cell Process

Residuals for Fitted Point Process Model

Simulated Point Pattern

Methods for Units

Summary of a Line Segment Pattern Dataset

Swedish Pines Point Pattern

Nearest neighbours in three dimensions

Simulate Matern Cluster Process

Define Point Process Model for Metropolis-Hastings Simulation.

Methods for Three-Dimensional Box

New Zealand Trees Point Pattern

Create a Window

Apply Vector Translation To Window

Pair Correlation Function of a Three-Dimensional Point Pattern

Summary of a Spatial Window

Methods for Linear Networks

Extract Unique Points from a Spatial Point Pattern

Estimate Variance of Summary Statistic by Subdivision

plot.bermantest

Plot Result of Berman Test

Variance-Covariance Matrix for a Fitted Point Process Model

Diagnostic Plots for Fitted Point Process Model

Plot a three-dimensional point pattern

Simulate Stratified Random Point Pattern

Simulate point patterns using the Metropolis-Hastings algorithm.

Intersection of Two Tessellations

Plot a Simulation Envelope

Place Points Evenly Along Specified Lines

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Morphological Dilation

nearest.raster.point

Find Pixel Nearest to a Given Point

Diameter of an Object

Convert Data to Three-Dimensional Box

Random Thinning

Estimate window from points alone

Generate Poisson Point Pattern in Three Dimensions

plot a Spatial Line Segment Pattern

Generate Poisson Point Pattern in Any Dimensions

Simple Example of Linear Network

Variance-Covariance Matrix for a Fitted Cluster Point Process Model

Convert Data To Class owin

Convert Line Segment Pattern to Pixel Image

Randomly Shift a Line Segment Pattern

Plot a fitted cluster point process

Inhomogeneous Neighbourhood Density Function

Class of Fitted Point Process Models

summary.splitppp

Summary of a Split Point Pattern

Compute Areas of Tiles in a Tessellation

Random Perturbation of a Point Pattern

Print News About Latest Version of Package

Spruces Point Pattern

Loglikelihood of Spatial Logistic Regression

plot a Spatial Quadrature Scheme

Methods for Intensity Functions of Spatial Covariate

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Approximate a Polygon by a Simpler Polygon

Create a Function Value Table

Fit the Thomas Point Process by Minimum Contrast

Rounding of Pixel Values

Class of Point Patterns

Simulate systematic random point pattern

Evaluate an Expression in a Function Table

Identify Covariates Involved in each Model Term

matclust.estpcf

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

Fit Point Process Model to Point Pattern on Linear Network

Apply Vector Translation To Point Pattern

Compute Integral of Function Against Cumulative Distribution

Fitted Conditional Intensity for Point Process Model

model.matrix.ppm

Extract Design Matrix from Point Process Model

Diggle's Heather Data

Point and Click Interface for Exploratory Analysis of Point Pattern

Test Whether Pixel Images Are Compatible

Class of Line Segment Patterns

Pair Correlation Function

Mosaic Random Set

Cartesian Coordinates for a Pixel Raster

Morishita Index Plot

Test whether Object is Multitype

Rotate a Point Pattern

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Make Periodic Copies of a Spatial Pattern

Reduced Sample Estimator using Histogram Data

Inhomogeneous Pair Correlation Function

Reset Values in Subset of Image

Convert Window to Another Unit of Length

Rotate a Line Segment Pattern

Spherical Contact Distribution Function

Locally Scaled K-function

Predicted or Fitted Values from Spatial Logistic Regression

Convert Data To Class psp

Multitype pair correlation function (i-to-any)

Calculate four standard summary functions of a point pattern.

Geometrical Calculations for Multi-Dimensional Box

Extract the Interaction from a Fitted Point Process Model

Mark Connection Function

Mark Correlation Function

Recognise Stationary and Poisson Point Process Models

Methods for Multi-Dimensional Box

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

Quadrat counting for a point pattern

Convert Point Pattern to Another Unit of Length

Simulate Neyman-Scott Process

Nearest neighbour

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

Kolmogorov-Smirnov Test for Point Process Model

rescue.rectangle

Convert Window Back To Rectangle

spatstat-package

The Spatstat Package

Create a Line Segment Pattern

Kaplan-Meier Estimator using Histogram Data

Convert Data To Tessellation

Update a Fitted Point Process Model

Saturated Pairwise Interaction model

Cross Validated Bandwidth Selection for Relative Risk Estimation

The Multitype Hard Core Point Process Model

compatible.fasp

Test Whether Function Arrays Are Compatible

Stoyan's Rule of Thumb for Bandwidth Selection

K-function of a Three-Dimensional Point Pattern

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Convert Polygonal Region into Different Format

Nearest Neighbour Clutter Removal

California Redwoods Point Pattern (Ripley's Subset)

Convert Window to Pixel Image

Nonparametric Estimate of Spatially-Varying Relative Risk

Data Sharpening of Point Pattern

clarkevans.test

Clark and Evans Test

Poisson Point Process Model

Dummy Function Returns Number of Points

Simulate Gauss-Poisson Process

Harkness-Isham ants' nests data

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Three-Dimensional Box

Difference of Disc Areas

Convert Pixel Image from Numeric to Factor

Chicago Street Crime Data

Pixel Image Approximation of a Window

Exponential Energy Marks

Morphological Erosion

Bounding Box of a Window or Point Pattern

Combine Two Line Segment Patterns

Class of Images

Local pair correlation function

Pairwise Distances in Any Dimensions

Kaplan-Meier and Reduced Sample Estimator using Histograms

Midpoints of Line Segment Pattern

Plot a plotppm Object Created by plot.ppm

Data and Code From JRSS Discussion Paper on Residuals

Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative

Simulate Simple Sequential Inhibition

spatstat-internal

Internal spatstat functions

Pair Correlation Function obtained from K Function

Plot a List of Point Patterns

Multidimensional Space-Time Point Pattern

Fit the Thomas Point Process by Minimum Contrast

Create a Pixel Image Object

Random Re-Labelling of Point Pattern

Pairwise distances

Connected components of an image or window

Ord's Interaction model

inforder.family

Infinite Order Interaction Family

Number of Line Segments in a Line Segment Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Mark Correlation Integral

Inhomogeneous Linear K Function

Convert dataset to another unit of length

Predict Point Process Model on Linear Network

Test Whether A Point Pattern is Marked

Endpoints of Line Segment Pattern

Generate N Uniform Random Points in Three Dimensions

Methods for Cluster Point Process Models

Generate Multitype Poisson Point Pattern

Set Covariance of a Window

Volume of an Object

Summarizing a Quadrature Scheme

Convert Pixel Image to Matrix or Array

Generate N Uniform Random Points in Any Dimensions