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spatstat (version 1.22-2)

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

1.22-2

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

June 15th, 2011

Functions in spatstat (1.22-2)

Geyer's Saturation Point Process Model

Extract Subset of Signed or Vector Measure

The Lennard-Jones Potential

Extract or Replace Subset of a List of Things

The Hard Core Point Process Model

Extract or Replace Subset of Tessellation

Extract or Replace Subset of Point Pattern

Apply Affine Transformation To Line Segment Pattern

Hybrid Geyer Point Process Model

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Pairwise distances between two different point patterns

Marked Nearest Neighbour Distance Function

Multitype K Function (i-to-any)

Distance to Boundary of Window

Extract Subset of Function Values

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Estimate the J-function

Convert to Pixel Image

Inhomogeneous Multitype K Dot Function

Multitype J Function (i-to-j)

Three-Dimensional Box

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Orientation Angles of Line Segments

The Strauss / Hard Core Point Process Model

Convert Data To Tessellation

Inhomogeneous Cross K Function

K-function using FFT

Inhomogeneous K-function

Extract Original Data from a Fitted Point Process Model

Empty Space Function of a Three-Dimensional Point Pattern

Marked J Function

Generic Ord Interaction model

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Saturated Pairwise Interaction model

Analysis of Deviance for Spatial Logistic Regression Models

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Convert a Window to a Polygonal Window

Difference of Disc Areas

Marked K-Function

Foxall's Distance Functions

The Area Interaction Point Process Model

bounding.box.xy

Convex Hull of Points

Coefficients of Fitted Spatial Logistic Regression Model

Extract Subset of Image

Convert Data to Hyperframe

as.data.frame.im

Convert Pixel Image to Data Frame

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Extract Subset of Line Segment Pattern

Locally Scaled K-function

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Apply Affine Transformation

Artificial Data Point Pattern

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Multitype L-function (i-to-any)

Convert Line Segment Pattern to Binary Pixel Mask

Kernel Smoothed Intensity of Point Pattern

Reset Values in Subset of Image

Diagnostics for random marking

Concatenate x,y Coordinate Vectors

Multitype L-function (cross-type)

Inhomogeneous Cross Type L Function

Apply Affine Transformation To Point Pattern

Poisson Point Process Model

Estimate the I-function

Apply Function to Every Neighbourhood in a Point Pattern

Multitype K Function (Cross-type)

Tropical rain forest trees

K-function of a Three-Dimensional Point Pattern

Combine Two Line Segment Patterns

Convert Polygonal Region into Different Format

Subdivide a Window or Tessellation using a Set of Lines

Combine Function Value Tables

Pairwise distances between two different three-dimensional point patterns

Estimate the empty space function F

The Fiksel Interaction

The Strauss Point Process Model

Spherical Contact Distribution Function

Subset of Quadrature Scheme

The Piecewise Constant Pairwise Interaction Point Process Model

Point and Click Interface for Exploratory Analysis of Point Pattern

Multi-Dimensional Box

Cross Validated Bandwidth Selection for Relative Risk Estimation

Diggle-Gratton model

Test Whether Two Pixel Images Are Compatible

Diameter of an Object

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

Multitype J Function (i-to-any)

Reduced Second Moment Measure

Convert Pixel Image to Matrix or Array

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

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Endpoints of Line Segment Pattern

Dirichlet Tessellation of Point Pattern

Inhomogeneous Multitype L Dot Function

Test Whether Two Function Objects Are Compatible

Safely Convert Point Pattern Window to Binary Mask

spatstat-deprecated

Deprecated spatstat functions

Berman-Huntington points and lines data

Distance to Boundary of Window

Identify Segments in a Line Segment Pattern

matclust.estpcf

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

Identify Points in a Point Pattern

Intersect Infinite Straight Lines with a Window

Fitted Conditional Intensity for Point Process Model

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Distance Map of Window

Diameter of a Window

Signed or Vector-Valued Measure

Weighted Empirical Cumulative Distribution Function

Hyper Data Frame

ANOVA for Fitted Point Process Models

Intersection of Two Tessellations

Morphological Closing

Pixel Image Approximation of a Window

The Multitype Strauss Point Process Model

Interactively join vertices on a plot

Lengths of Line Segments

Humberside Data on Childhood Leukaemia and Lymphoma

Interactively Add Points

Beta Ganglion Cells in Cat Retina

Methods for Cluster Point Process Models

Convert and Compare Colours in Different Formats

Make Periodic Copies of a Spatial Pattern

Determine Duplicated Points in a Spatial Point Pattern

Circumradius and Diameter of a Linear Network

Bronze gradient filter data

Basis for Harmonic Functions

Plot a plotppm Object Created by plot.ppm

Classify Points in a Point Pattern

Pairwise distances

Plot a linear network

clarkevans.test

Clark and Evans Test

Beadlet Anemones Data

Compute Expansion Window for Simulation

Hutchings' Bramble Canes data

Connected components of an image or window

Beta Ganglion Cells in Cat Retina, Old Version

Ord's Interaction model

Bounding Box of a Window or Point Pattern

Delaunay Triangulation of Point Pattern

Integral of a Pixel Image

Aherne's hamster tumour data

Apply Affine Transformation To Window

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Apply a Function to a Point Pattern Broken Down by Factor

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

crossdist.default

Pairwise distances between two different sets of points

Kaplan-Meier Estimator using Histogram Data

Nearest Neighbours in Any Dimensions

plot a Spatial Point Pattern

Nearest neighbours in three dimensions

Hughes' Amacrine Cell Data

Evaluate Expression Involving Function Arrays

Geometrical Calculations for Multi-Dimensional Box

Extract the Interaction from a Fitted Point Process Model

Distance Map of Line Segment Pattern

Evaluate Expression Involving Pixel Images

Nearest neighbour distances in three dimensions

Test Whether Points Are Inside A Window

Areas of Morphological Dilations

Fry Plot of Point Pattern

Coefficients of Fitted Point Process Model

Convert Data To Class owin

Determine Whether One Window is Contained In Another

Clark and Evans Aggregation Index

Pairwise distances between two different line segment patterns

Contour plot of pixel image

Diggle's Heather Data

complement.owin

Take Complement of a Window

Rectangular grid of points

Function Arrays for Spatial Patterns

Convert Data to Three-Dimensional Box

Test Whether A Point Pattern is Marked

The Multitype Hard Core Point Process Model

Plot a Spatial Kolmogorov-Smirnov Test

Distance Between Two Point Patterns

Area of a Window

Test Whether a Window is Convex

Kernel Smoothing of Line Segment Pattern

Stoyan's Rule of Thumb for Bandwidth Selection

Class of Point Patterns

Log Likelihood and AIC for Point Process Model

Interactively Define a Polygon

Kolmogorov-Smirnov Test for Point Process Model

Create a Window

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Morphological Dilation

Distance Map of Point Pattern

Japanese Pines Point Pattern

Methods for Point Patterns on a Linear Network

Mosaic Random Set

Ord Interaction Process Family

Neighbourhood density function

pairdist.default

Pairwise distances

Window in Shape of Letter R

Cartesian Coordinates for a Pixel Raster

pairwise.family

Pairwise Interaction Process Family

Find Line Segment Nearest to Each Point

Saturated Pairwise Interaction Point Process Family

Infinite Straight Lines

Generate Poisson Point Pattern in Three Dimensions

Nearest Neighbours Between Two Patterns

Distance Map as a Function

Reduced Sample Estimator using Histogram Data

Simulate Baddeley-Silverman Cell Process

Convert Point Pattern to Pixel Image

Areas of Morphological Erosions

Nearest Neighbour Clutter Removal

spatstat-internal

Internal spatstat functions

Colour Lookup Tables

Pairwise Distances in Any Dimensions

inforder.family

Infinite Order Interaction Family

Evaluate Expression Involving Functions

Pairwise shortest-path distances between points on a linear network

Class of Images

Methods for Multidimensional Space-Time Point Patterns

Create Colour-Valued Pixel Image

Pairwise distances between line segments

Convert Point Pattern to Another Unit of Length

Simulation Envelopes of Summary Function

Level Set of a Pixel Image

Create Point Pattern on Linear Network

Apply Gaussian Blur to a Pixel Image

Fitted Probabilities for Spatial Logistic Regression

Exponential Energy Marks

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Generate a Quadrature Scheme from a Point Pattern

Interpret Fitted Model for Metropolis-Hastings Simulation.

Rotate a Line Segment Pattern

Methods for Multi-Dimensional Box

Test Whether An Object Is A Pixel Image

Randomly Shift a Point Pattern

Test Whether An Object Is Empty

Border Region of a Window

Morphological Opening

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Generate N Uniform Random Points

Longleaf Pines Point Pattern

Quadrature Scheme Based on Pixel Grid

Network K Function

Profile Maximum Pseudolikelihood

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

Model Formulae for Gibbs Point Process Models

Point Patterns of New Brunswick Forest Fires

multiplicity.ppp

Count Multiplicity of Duplicate Points

rshift.splitppp

Randomly Shift a List of Point Patterns

Generate Poisson Point Pattern in Any Dimensions

Methods for three-dimensional point patterns

Pair Correlation Function of a Three-Dimensional Point Pattern

Lurking variable plot

Scatterplot Matrix for Pixel Images

Test Whether Marks Are Present

Test whether Object is Multitype

Convert dataset to another unit of length

Mark Correlation Integral

plot a Fitted Point Process Model

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Midpoints of Line Segment Pattern

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

Perimeter Length of Window

Multitype pair correlation function (cross-type)

Residuals for Fitted Point Process Model

Create a Pixel Image Object

Collapse Several Function Tables into One

plot.hyperframe

Plot Entries in a Hyperframe

Plot a List of Things

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Smoothing Estimate of Covariate Transformation

Test Whether An Object Is A Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Plot a Fitted Spatial Logistic Regression

Area of Part of Disc

Apply Vector Translation To Window

Create a Function Value Table

Name for Unit of Length

Summary of a Line Segment Pattern Dataset

Fit Cluster or Cox Point Process Model

Plot a Signed or Vector-Valued Measure

Generate Multitype Poisson Point Pattern

Histogram of Pixel Values in an Image

Plot a tessellation

Poisson Point Process on a Linear Network

Spatial smoothing of observations at irregular points

Multidimensional Space-Time Point Pattern

plot a Spatial Line Segment Pattern

methods.distfun

Methods for Distance Functions

Intersection, Union or Set Subtraction of Two Windows

Inhomogeneous Pair Correlation Function

Evaluate an Expression in a Function Table

Test Whether An Object Is A Fitted Point Process Model

Pairwise distances in Three Dimensions

Marks of a Point Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Nearest neighbour

Q-Q Plot of Residuals from Fitted Point Process Model

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Fit Point Process Model to Data

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Create a Tessellation

Summary of a Point Pattern Dataset

Rotate a Point Pattern

pppmatching.object

Class of Point Matchings

Lansing Woods Point Pattern

Generate N Uniform Random Points in Any Dimensions

Print Brief Details of a Point Pattern Dataset

Number of Points in a Point Pattern

Pair Correlation Function obtained from K Function

Loglikelihood of Spatial Logistic Regression

Generate N Random Points

Distance for a Point Pattern Matching

Simulate point patterns using the Metropolis-Hastings algorithm.

Pair Correlation Function obtained from array of K functions

Mosaic Random Field

Generate a Default Pattern of Dummy Points

Prediction from a Fitted Cluster Point Process Model

Divide Region into Quadrats

Generate grid of parallel lines with random displacement

Apply Smoothing to Function Values

Convert Data To Class psp

plot.bermantest

Plot Result of Berman Test

Summarise Marks in Every Neighbourhood in a Point Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

Extract Quadrature Scheme Used to Fit a Point Process Model

Simulate a Fitted Cluster Point Process Model

Quadrat counting for a point pattern

Simulate Gauss-Poisson Process

Simulate from a Fitted Point Process Model

plot a Spatial Quadrature Scheme

Generate N Random Multitype Points

Convert Line Segment Pattern to Pixel Image

Set Covariance of a Window

Geometrical Calculations for Three-Dimensional Box

Diagnostic Plots for Fitted Point Process Model

nearest.raster.point

Find Pixel Nearest to a Given Point

scaletointerval

Rescale Data to Lie Between Specified Limits

California Redwoods Point Pattern (Ripley's Subset)

Compute Images of Constructed Covariates

Print a Quadrature Scheme

Pairwise distances

Simulate Stratified Random Point Pattern

Murchison gold deposits

Divide Point Pattern into Sub-patterns

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Create a Point Pattern

Number of Line Segments in a Line Segment Pattern

Nearest neighbour distances between line segments

Theoretical Distribution of Nearest Neighbour Distance

Plot a Function Array

Simulated Point Pattern

Generate N Uniform Random Points in Three Dimensions

Print Brief Details of a Line Segment Pattern Dataset

Plot a three-dimensional point pattern

Data and Code From JRSS Discussion Paper on Residuals

Predicted or Fitted Values from Spatial Logistic Regression

Summarizing a Quadrature Scheme

Simulate systematic random point pattern

Prediction from a Fitted Point Process Model

Class of Fitted Point Process Models

Generate Poisson Random Line Process

Spruces Point Pattern

Simulate Log-Gaussian Cox Process

Perspective Plot of Pixel Image

Simulation Envelopes of Summary Function for 3D Point Pattern

Spokes pattern of dummy points

quadratresample

Resample a Point Pattern by Resampling Quadrats

Estimate window from points alone

Sufficient Statistic of Point Process Model

Randomly Shift a Line Segment Pattern

Sample Quantiles of Pixel Image

Galaxies in the Shapley Supercluster

Plot a Colour Map

Print Brief Details of an Image

Poisson Line Tessellation

Circular Window

Simulate Matern Cluster Process

Superimpose Several Geometric Patterns

Simulate Matern Model II

Simulate Matern Model I

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Fit the Thomas Point Process by Minimum Contrast

Simulate Simple Sequential Inhibition

project2segment

Move Point To Nearest Line

Urkiola Woods Point Pattern

Mark Connection Function

Expand Window By Factor

Methods for Three-Dimensional Box

Generate N Uniform Random Points in a Disc

Apply Vector Translation

Pairwise distances

Read Point Pattern From Data File

Simulate Neyman-Scott Process

Apply Vector Translation To Pixel Image

Vertices of a Window

Update a Fitted Cluster Point Process Model

Apply Vector Translation To Point Pattern

Summarizing a Fitted Point Process Model

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Compute Integral of Function Against Cumulative Distribution

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

Apply Vector Translation To Line Segment Pattern

Swedish Pines Point Pattern

Volume of an Object

Class of Quadrature Schemes

Define Point Process Model for Metropolis-Hastings Simulation.

New Zealand Trees Point Pattern

Convert Pixel Image to Another Unit of Length

Plot a fitted cluster point process

Generate Poisson Point Pattern

Simulate a Fitted Gibbs Point Process Model

Rotate a Window

Create a Point Matching

Create a Line Segment Pattern

Convert Spatial Object to Pixel Image

Smooth a Signed or Vector-Valued Measure

Data Sharpening of Point Pattern

Simple Example of Linear Network

Extract Unique Points from a Spatial Point Pattern

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

Estimate Variance of Summary Statistic by Subdivision

Perfect Simulation of the Strauss Process

Variance-Covariance Matrix for a Fitted Cluster Point Process Model

California Redwoods Point Pattern (Entire Dataset)

Identify Pixelwise Maximum of Several Pixel Images

Divide Image Into Sub-images

summary.splitppp

Summary of a Split Point Pattern

Weighted Histogram

Random Re-Labelling of Point Pattern

Extract List of Tiles in a Tessellation

The Soft Core Point Process Model

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Berman's Tests for Point Process Model

Corners of a rectangle

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Extract Dummy Points Used to Fit a Point Process Model

Function Value Table

Compute Quadrature Weights Based on Grid Counts

Find Largest Circle Inside Window

Interpolate a Pixel Image

Point and Click Interface for Displaying a Point Pattern

Test Whether An Object Is A Window

Kaplan-Meier and Reduced Sample Estimator using Histograms

Plot a Simulation Envelope

Class of Line Segment Patterns

rescue.rectangle

Convert Window Back To Rectangle

Interaction Distance of a Point Process

Random Perturbation of a Point Pattern

Generate Poisson Point Pattern on Line Segments

Random Thinning

Fit the Thomas Point Process by Minimum Contrast

Compute Areas of Tiles in a Tessellation

Extract Subset of Function Array

Generic Pairwise Interaction model

Apply Function to Image Broken Down by Factor

Distance to Boundary of Window

Centroid of a window

Chorley-Ribble Cancer Data

Morphological Erosion

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Test Whether A Point Process Model is Marked

Create a Linear Network

Methods for Linear Networks

Methods for Intensity Functions of Spatial Covariate

Pair Correlation Function of Point Pattern

Plot Function Values

Plot a List of Point Patterns

Place Points Evenly Along Specified Lines

Ponderosa Pine Tree Point Pattern

Print Progress Reports

Simulate Thomas Process

Cut margins from rectangle

spatstat-package

The Spatstat Package

Summary of a Spatial Window

Extract.splitppp

Extract or Replace Sub-Patterns

Calculate four standard summary functions of a point pattern.

Difference of Disc Areas

Convert Function Value Table to Function

Convert Data To Class ppp

Biological Cells Point Pattern

Crossing Points of Two Line Segment Patterns

Morishita Index Plot

Method of Minimum Contrast

Nearest neighbour distances

Pair Correlation Function

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Multitype pair correlation function (i-to-any)

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Convert Window to Pixel Image

Print Brief Details of a Spatial Window

Print a Fitted Point Process Model

Convert Window to Another Unit of Length

Convert Line Segment Pattern to Another Unit of Length

Nonparametric Estimate of Spatially-Varying Relative Risk

Set Control Parameters for Metropolis-Hastings Algorithm.

Determine Initial State for Metropolis-Hastings Simulation.

Summary of a List of Things

Union of Data and Dummy Points

Update a Fitted Point Process Model

K function of a model

Local pair correlation function

Convex Hull of Points

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

Pine saplings in Finland.

Harkness-Isham ants' nests data

Three Dimensional Point Pattern

Uniform Random Points on a Linear Network

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Nearest Neighbour Distance Function G

model.frame.ppm

Extract the Environment of a Point Process Model

spatstat.options

Internal Options in Spatstat Package

Fit the Matern Cluster Point Process by Minimum Contrast

Mark Correlation Function

Approximate a Polygon by a Simpler Polygon

Print News About Latest Version of Package

Convert Pixel Image from Numeric to Factor

Marks of a Line Segment Pattern

model.matrix.ppm

Extract Design Matrix from Point Process Model

Nearest Neighbour Distances in Any Dimensions

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

Plot a Pixel Image

Plot a Spatial Window

Spatial Logistic Regression

Summarizing a Pixel Image