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spatstat (version 1.20-3)

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 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. Point process models can be fitted to point pattern data. Cluster type models are fitted by the method of minimum contrast. Very general Gibbs point process models can be fitted to point pattern data using a function ppm similar to lm or glm. Models may include dependence on covariates, interpoint interaction 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

1.20-3

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

August 24th, 2010

Functions in spatstat (1.20-3)

Diggle-Gratton model

Multitype L-function (cross-type)

Tropical rain forest trees

Geyer's Saturation Point Process Model

The Multitype Strauss Point Process Model

Extract Subset of Image

The Lennard-Jones Potential

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

Apply Affine Transformation To Line Segment Pattern

Marked K-Function

Extract Subset of Line Segment Pattern

Marked J Function

Spherical Contact Distribution Function

Beta Ganglion Cells in Cat Retina

Difference of Disc Areas

The Strauss Point Process Model

Marked Nearest Neighbour Distance Function

The Strauss / Hard Core Point Process Model

Convert a Window to a Polygonal Window

Subset of Quadrature Scheme

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Convert Data to Hyperframe

Pixel Image Approximation of a Window

bounding.box.xy

Convex Hull of Points

Hybrid Geyer Point Process Model

as.data.frame.im

Convert Pixel Image to Data Frame

Berman's Tests for Point Process Model

Ord's Interaction model

Multitype L-function (i-to-any)

Pairwise distances between two different line segment patterns

Inhomogeneous K-function

Apply Affine Transformation

Convert and Compare Colours in Different Formats

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Harkness-Isham ants' nests data

Distance Map as a Function

Saturated Pairwise Interaction model

Difference of Disc Areas

Convert Data To Class ppp

Extract Subset of Function Array

Extract or Replace Subset of a List of Things

Circular Window

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Distance to Boundary of Window

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Hutchings' Bramble Canes data

Histogram of Pixel Values in an Image

Inhomogeneous Cross Type L Function

Inhomogeneous Cross K Function

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Infinite Straight Lines

Centroid of a window

Interpolate a Pixel Image

Bounding Box of a Window or Point Pattern

Foxall's Distance Functions

Multi-Dimensional Box

Geometrical Calculations for Multi-Dimensional Box

Interactively Define a Polygon

Function Arrays for Spatial Patterns

Bronze gradient filter data

Apply Affine Transformation To Window

Print News About Latest Version of Package

The Piecewise Constant Pairwise Interaction Point Process Model

The Area Interaction Point Process Model

Generic Pairwise Interaction model

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Kernel Smoothed Intensity of Point Pattern

Convert to Pixel Image

Pine saplings in Finland.

Crossing Points of Two Line Segment Patterns

Diggle's Heather Data

Corners of a rectangle

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Compute Expansion Window for Simulation

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Convert Data to Three-Dimensional Box

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

Convert Data To Class psp

Morphological Dilation

Exponential Energy Marks

Data Frames of Function Values

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Convert Polygonal Region into Different Format

Diameter of an Object

Multitype J Function (i-to-any)

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

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

Convex Hull of Points

Test Whether An Object Is A Pixel Image

Test Whether a Window is Convex

The Soft Core Point Process Model

ANOVA for Fitted Point Process Models

Fry Plot of Point Pattern

Apply Function to Every Neighbourhood in a Point Pattern

Lansing Woods Point Pattern

Orientation Angles of Line Segments

matclust.estpcf

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

complement.owin

Take Complement of a Window

Classify Points in a Point Pattern

Japanese Pines Point Pattern

Pair Correlation Function obtained from K Function

Nearest Neighbours Between Two Patterns

Contour plot of pixel image

Estimate the empty space function F

Evaluate Expression Involving Function Arrays

Extract or Replace Subset of Tessellation

Three-Dimensional Box

Inhomogeneous Pair Correlation Function

Extract Subset of Function Values

Multitype K Function (i-to-any)

Test Whether An Object Is A Window

spatstat-deprecated

Deprecated spatstat functions

Estimate the J-function

Pairwise distances

Area of Part of Disc

Extract or Replace Subset of Point Pattern

Reduced Sample Estimator using Histogram Data

Create a Point Matching

Create a Pixel Image Object

Class of Quadrature Schemes

Beadlet Anemones Data

Distance to Boundary of Window

Morishita Index Plot

Calculate four standard summary functions of a point pattern.

Kaplan-Meier and Reduced Sample Estimator using Histograms

K-function using FFT

Clark and Evans Aggregation Index

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Point and Click Interface for Exploratory Analysis of Point Pattern

Diagnostics for random marking

Reduced Second Moment Measure

Quadrature Scheme Based on Pixel Grid

project2segment

Move Point To Nearest Line

Combine Two Line Segment Patterns

Plot a Pixel Image

Simulate point patterns using the Metropolis-Hastings algorithm.

Convert Pixel Image to Matrix

Distance Between Two Point Patterns

Method of Minimum Contrast

The Hard Core Point Process Model

Diagnostic Plots for Fitted Point Process Model

Convert Data To Tessellation

Pairwise Distances in Any Dimensions

Estimate the I-function

New Zealand Trees Point Pattern

Test Whether An Object Is Empty

Generate Poisson Point Pattern in Any Dimensions

Berman-Huntington points and lines data

Rotate a Point Pattern

Area of a Window

Test Whether Two Function Objects Are Compatible

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Apply Vector Translation To Window

Dirichlet Tessellation of Point Pattern

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Generate Multitype Poisson Point Pattern

Plot Function Values

Beta Ganglion Cells in Cat Retina, Old Version

Inhomogeneous Multitype K Dot Function

Test Whether A Point Process Model is Marked

Simulate Matern Model I

plot a Spatial Quadrature Scheme

Prediction from a Fitted Cluster Point Process Model

Intersection of Two Tessellations

Distance Map of Point Pattern

Convert Window to Another Unit of Length

Apply Gaussian Blur to a Pixel Image

Distance for a Point Pattern Matching

Define Point Process Model for Metropolis-Hastings Simulation.

Interactively Add Points

Morphological Closing

Apply Affine Transformation To Point Pattern

Combine Function Value Tables

Find Line Segment Nearest to Each Point

Plot a plotppm Object Created by plot.ppm

Border Region of a Window

Test Whether An Object Is A Fitted Point Process Model

Simulate Stratified Random Point Pattern

Basis for Harmonic Functions

Inhomogeneous Multitype L Dot Function

Apply Function to Image Broken Down by Factor

Plot a List of Things

Nearest neighbours in three dimensions

Nearest Neighbour Distance Function G

Delaunay Triangulation of Point Pattern

Hyper Data Frame

Generic Ord Interaction model

Poisson Line Tessellation

nearest.raster.point

Find Pixel Nearest to a Given Point

Mosaic Random Set

Evaluate Expression Involving Pixel Images

Biological Cells Point Pattern

Concatenate x,y Coordinate Vectors

Distance to Boundary of Window

quadratresample

Resample a Point Pattern by Resampling Quadrats

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Extract.splitppp

Extract or Replace Sub-Patterns

Plot a tessellation

Create a Point Pattern

Apply a Function to a Point Pattern Broken Down by Factor

Point Patterns of New Brunswick Forest Fires

Extract the Interaction from a Fitted Point Process Model

rescue.rectangle

Convert Window Back To Rectangle

Fit the Matern Cluster Point Process by Minimum Contrast

Geometrical Calculations for Three-Dimensional Box

Class of Images

Update a Fitted Cluster Point Process Model

Generate a Quadrature Scheme from a Point Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

Kolmogorov-Smirnov Test for Point Process Model

Simulated Point Pattern

Summarizing a Quadrature Scheme

Lengths of Line Segments

summary.splitppp

Summary of a Split Point Pattern

Simulation Envelopes of Summary Function

Aherne's hamster tumour data

Generate grid of parallel lines with random displacement

Summary of a List of Things

Extract Quadrature Scheme Used to Fit a Point Process Model

Convert Spatial Object to Pixel Image

Areas of Morphological Dilations

rshift.splitppp

Randomly Shift a List of Point Patterns

Neighbourhood density function

inforder.family

Infinite Order Interaction Family

Plot a Simulation Envelope

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Generate Poisson Random Line Process

Find Largest Circle Inside Window

Pairwise distances between two different point patterns

Test whether Object is Multitype

Create a Function Value Table

Convert Data To Class owin

methods.distfun

Methods for Distance Functions

Methods for Multidimensional Space-Time Point Patterns

Pairwise distances between two different three-dimensional point patterns

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Divide Region into Quadrats

Print a Fitted Point Process Model

Midpoints of Line Segment Pattern

Residuals for Fitted Point Process Model

Level Set of a Pixel Image

Expand Window By Factor

Define Point Process Model for Metropolis-Hastings Simulation.

Point and Click Interface for Displaying a Point Pattern

K-function of a Three-Dimensional Point Pattern

Fitted Conditional Intensity for Point Process Model

Convert Line Segment Pattern to Pixel Image

Fit the Thomas Point Process by Minimum Contrast

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

Distance Map of Window

Methods for Three-Dimensional Box

Kernel Smoothing of Line Segment Pattern

Window in Shape of Letter R

Determine Duplicated Points in a Spatial Point Pattern

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Nearest Neighbours in Any Dimensions

Create a Tessellation

Log Likelihood for Poisson Point Process Model

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

Ord Interaction Process Family

Simulate Simple Sequential Inhibition

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Diameter of a Window

Humberside Data on Childhood Leukaemia and Lymphoma

Test Whether Two Pixel Images Are Compatible

multiplicity.ppp

Count Multiplicity of Duplicate Points

Generate N Uniform Random Points in Any Dimensions

Class of Line Segment Patterns

Sufficient Statistic of Point Process Model

Apply Vector Translation To Line Segment Pattern

Create a Line Segment Pattern

Convert Pixel Image to Another Unit of Length

Quadrat counting for a point pattern

Divide Point Pattern into Sub-patterns

Marks of a Point Pattern

Nearest Neighbour Clutter Removal

Generate Poisson Point Pattern in Three Dimensions

Print Brief Details of a Spatial Window

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Convert Window to Pixel Image

Murchison gold deposits

Simulate a Fitted Cluster Point Process Model

Print Brief Details of an Image

Artificial Data Point Pattern

Q-Q Plot of Residuals from Fitted Point Process Model

Reset Values in Subset of Image

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

Nearest neighbour distances between line segments

pairdist.default

Pairwise distances

Simulate from a Fitted Point Process Model

Generate N Random Multitype Points

Randomly Shift a Point Pattern

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Perimeter Length of Window

Areas of Morphological Erosions

Safely Convert Point Pattern Window to Binary Mask

Profile Maximum Pseudolikelihood

Multitype pair correlation function (cross-type)

Summarizing a Fitted Point Process Model

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Sample Quantiles of Pixel Image

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Multidimensional Space-Time Point Pattern

Weighted Empirical Cumulative Distribution Function

Methods for three-dimensional point patterns

Plot a fitted cluster point process

Simulate systematic random point pattern

Mark Correlation Integral

Simulate Matern Cluster Process

Simulate Matern Model II

Simulation Envelopes of Summary Function for 3D Point Pattern

Volume of an Object

Read Point Pattern From Data File

plot.bermantest

Plot Result of Berman Test

Saturated Pairwise Interaction Point Process Family

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Scatterplot Matrix for Pixel Images

Class of Point Patterns

Data and Code From JRSS Discussion Paper on Residuals

Nearest neighbour distances

Generate N Uniform Random Points in a Disc

Compute Integral of Function Against Cumulative Distribution

Number of Points in a Point Pattern

Integral of a Pixel Image

Test Whether An Object Is A Point Pattern

Summary of a Spatial Window

spatstat-package

The Spatstat Package

Multitype pair correlation function (i-to-any)

Rotate a Line Segment Pattern

Plot a Function Array

Extract List of Tiles in a Tessellation

Create a Window

Place Points Evenly Along Specified Lines

Morphological Erosion

Interpret Fitted Model for Metropolis-Hastings Simulation.

Fit Point Process Model to Data

Apply Vector Translation

Summarizing a Pixel Image

spatstat.options

Internal Options in Spatstat Package

Identify Points in a Point Pattern

Extract Unique Points from a Spatial Point Pattern

Spatial smoothing of observations at irregular points

Cartesian Coordinates for a Pixel Raster

Theoretical Distribution of Nearest Neighbour Distance

Summarise Marks in Every Neighbourhood in a Point Pattern

Rotate a Window

plot.hyperframe

Plot Entries in a Hyperframe

Apply Vector Translation To Point Pattern

Print Brief Details of a Point Pattern Dataset

Random Perturbation of a Point Pattern

Randomly Shift a Line Segment Pattern

Subdivide a Window or Tessellation using a Set of Lines

Set Control Parameters for Metropolis-Hastings Algorithm.

Perspective Plot of Pixel Image

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Compute Quadrature Weights Based on Grid Counts

Mark Connection Function

Summary of a Line Segment Pattern Dataset

Urkiola Woods Point Pattern

Evaluate an Expression in a Function Table

Collapse Several Function Tables into One

Nearest neighbour

Plot a List of Point Patterns

plot a Spatial Point Pattern

Generate N Uniform Random Points

Estimate window from points alone

Convert Point Pattern to Another Unit of Length

Convert Point Pattern to Pixel Image

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Mosaic Random Field

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

Intersection, Union or Set Subtraction of Two Windows

Pairwise distances in Three Dimensions

Class of Fitted Point Process Models

Pair Correlation Function of Point Pattern

Plot a Spatial Window

Interaction Distance of a Point Process

Superimpose Several Line Segment Patterns

Endpoints of Line Segment Pattern

spatstat-internal

Internal spatstat functions

Weighted Histogram

Approximate a Polygon by a Simpler Polygon

Summary of a Point Pattern Dataset

Spruces Point Pattern

Name for Unit of Length

Pair Correlation Function obtained from array of K functions

Simulate Gauss-Poisson Process

Poisson Point Process Model

Plot a Spatial Kolmogorov-Smirnov Test

Simulate Thomas Process

Simulate a Fitted Gibbs Point Process Model

Rectangular grid of points

Random Thinning

Convert Line Segment Pattern to Another Unit of Length

model.frame.ppm

Extract the Environment of a Point Process Model

Generate N Uniform Random Points in Three Dimensions

Empty Space Function of a Three-Dimensional Point Pattern

Convert dataset to another unit of length

Print a Quadrature Scheme

Print Progress Reports

Nearest Neighbour Distances in Any Dimensions

Generate Poisson Point Pattern on Line Segments

pppmatching.object

Class of Point Matchings

Perfect Simulation of the Strauss Process

Nearest neighbour distances in three dimensions

Fit the Thomas Point Process by Minimum Contrast

Update a Fitted Point Process Model

Generate N Random Points

Mark Correlation Function

Multitype K Function (Cross-type)

Pairwise distances

Generate a Default Pattern of Dummy Points

Determine Initial State for Metropolis-Hastings Simulation.

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

Generate Poisson Point Pattern

Plot a Colour Map

Three Dimensional Point Pattern

Set Covariance of a Window

Spokes pattern of dummy points

Hughes' Amacrine Cell Data

Simulate Baddeley-Silverman Cell Process

Divide Image Into Sub-images

Apply Vector Translation To Pixel Image

Vertices of a Window

model.matrix.ppm

Extract Design Matrix from Point Process Model

Cut margins from rectangle

Compute Images of Constructed Covariates

Kaplan-Meier Estimator using Histogram Data

Superimpose Several Point Patterns

Determine Whether One Window is Contained In Another

The Fiksel Interaction

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Convert Line Segment Pattern to Binary Pixel Mask

Union of Data and Dummy Points

Pair Correlation Function

Colour Lookup Tables

Multitype J Function (i-to-j)

Coefficients of Fitted Point Process Model

Random Re-Labelling of Point Pattern

Extract Dummy Points Used to Fit a Point Process Model

Simulate Neyman-Scott Process

Distance Map of Line Segment Pattern

Extract Original Data from a Fitted Point Process Model

Intersect Infinite Straight Lines with a Window

Test Whether Points Are Inside A Window

Evaluate Expression Involving Functions

Lurking variable plot

Test Whether Marks Are Present

Test Whether A Point Pattern is Marked

Chorley-Ribble Cancer Data

Plot a three-dimensional point pattern

Methods for Multi-Dimensional Box

Prediction from a Fitted Point Process Model

plot a Spatial Line Segment Pattern

Pairwise distances between line segments

Print Brief Details of a Line Segment Pattern Dataset

pairwise.family

Pairwise Interaction Process Family

Connected components of an image or window

Ponderosa Pine Tree Point Pattern

Pairwise distances

California Redwoods Point Pattern (Entire Dataset)

Convert Pixel Image from Numeric to Factor

Fit cluster point process model

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Morphological Opening

Make Periodic Copies of a Spatial Pattern

Galaxies in the Shapley Supercluster

Apply Smoothing to Function Values

Swedish Pines Point Pattern

California Redwoods Point Pattern (Ripley's Subset)

crossdist.default

Pairwise distances between two different sets of points

plot a Fitted Point Process Model

Longleaf Pines Point Pattern