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spatstat (version 1.20-2)

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 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

19,373

Version

1.20-2

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

August 10th, 2010

Functions in spatstat (1.20-2)

Multitype K Function (Cross-type)

Inhomogeneous Cross K Function

Artificial Data Point Pattern

Evaluate Expression Involving Function Arrays

Tropical rain forest trees

Extract Subset of Line Segment Pattern

Fit cluster point process model

Difference of Disc Areas

Estimate the empty space function F

Apply Function to Image Broken Down by Factor

Interactively Add Points

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Diagnostics for random marking

Pairwise distances between two different three-dimensional point patterns

Calculate four standard summary functions of a point pattern.

Convert Pixel Image to Matrix

Connected components of an image or window

The Fiksel Interaction

K-function of a Three-Dimensional Point Pattern

Apply Affine Transformation To Line Segment Pattern

Geometrical Calculations for Multi-Dimensional Box

Morphological Dilation

spatstat-deprecated

Deprecated spatstat functions

Intersection, Union or Set Subtraction of Two Windows

Apply Function to Every Neighbourhood in a Point Pattern

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Simulation Envelopes of Summary Function for 3D Point Pattern

Expand Window By Factor

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Summarise Marks in Every Neighbourhood in a Point Pattern

Nearest neighbour distances between line segments

Extract or Replace Subset of Point Pattern

Multitype K Function (i-to-any)

Combine Two Line Segment Patterns

Number of Points in a Point Pattern

Create a Function Value Table

Window in Shape of Letter R

Orientation Angles of Line Segments

Estimate the I-function

multiplicity.ppp

Count Multiplicity of Duplicate Points

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Empty Space Function of a Three-Dimensional Point Pattern

Extract Subset of Function Values

Pairwise distances between two different line segment patterns

Convert Data to Three-Dimensional Box

ANOVA for Fitted Point Process Models

Prediction from a Fitted Cluster Point Process Model

Kolmogorov-Smirnov Test for Point Process Model

Biological Cells Point Pattern

Marked J Function

Estimate the J-function

Multitype pair correlation function (cross-type)

Lengths of Line Segments

Neighbourhood density function

Kernel Smoothed Intensity of Point Pattern

Apply a Function to a Point Pattern Broken Down by Factor

Print News About Latest Version of Package

Contour plot of pixel image

Test Whether Two Pixel Images Are Compatible

Cartesian Coordinates for a Pixel Raster

Simulate Thomas Process

Diggle-Gratton model

The Soft Core Point Process Model

Centroid of a window

Convert Line Segment Pattern to Another Unit of Length

Geometrical Calculations for Three-Dimensional Box

Plot a fitted cluster point process

Convert a Window to a Polygonal Window

Generic Pairwise Interaction model

Crossing Points of Two Line Segment Patterns

Corners of a rectangle

Test Whether Marks Are Present

Classify Points in a Point Pattern

Interaction Distance of a Point Process

Beta Ganglion Cells in Cat Retina

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Apply Affine Transformation To Point Pattern

Plot a three-dimensional point pattern

Diggle's Heather Data

Class of Images

Hybrid Geyer Point Process Model

Class of Quadrature Schemes

Circular Window

Extract.splitppp

Extract or Replace Sub-Patterns

Poisson Line Tessellation

Apply Gaussian Blur to a Pixel Image

Distance Map of Point Pattern

Test whether Object is Multitype

Reset Values in Subset of Image

Convert Spatial Object to Pixel Image

Endpoints of Line Segment Pattern

Set Control Parameters for Metropolis-Hastings Algorithm.

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Areas of Morphological Erosions

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Nearest Neighbour Distance Function G

Distance to Boundary of Window

Convert Window to Pixel Image

Saturated Pairwise Interaction model

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Diameter of an Object

Nearest Neighbour Clutter Removal

The Strauss / Hard Core Point Process Model

Distance to Boundary of Window

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Extract Unique Points from a Spatial Point Pattern

Generate Poisson Point Pattern on Line Segments

Set Covariance of a Window

Pixel Image Approximation of a Window

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Simulate Neyman-Scott Process

Inhomogeneous Cross Type L Function

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

Generate a Quadrature Scheme from a Point Pattern

Morphological Opening

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

California Redwoods Point Pattern (Entire Dataset)

Pair Correlation Function obtained from K Function

Create a Pixel Image Object

Infinite Straight Lines

Convert Line Segment Pattern to Binary Pixel Mask

Simulation Envelopes of Summary Function

Convert to Pixel Image

Test Whether An Object Is A Window

Convert Data To Class ppp

Geyer's Saturation Point Process Model

Test Whether A Point Pattern is Marked

Extract Subset of Image

Data Frames of Function Values

Spokes pattern of dummy points

Distance to Boundary of Window

K-function using FFT

Extract List of Tiles in a Tessellation

Convert Data to Hyperframe

Print Brief Details of a Line Segment Pattern Dataset

Midpoints of Line Segment Pattern

Apply Affine Transformation

Evaluate Expression Involving Functions

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

Test Whether An Object Is A Pixel Image

Compute Quadrature Weights Based on Grid Counts

Nearest neighbour distances

spatstat-internal

Internal spatstat functions

methods.distfun

Methods for Distance Functions

Colour Lookup Tables

Inhomogeneous Multitype K Dot Function

Murchison gold deposits

Galaxies in the Shapley Supercluster

Create a Window

Reduced Second Moment Measure

Mark Correlation Integral

The Lennard-Jones Potential

Evaluate an Expression in a Function Table

Nearest neighbour

Poisson Point Process Model

Summarizing a Fitted Point Process Model

The Multitype Strauss Point Process Model

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Identify Points in a Point Pattern

Divide Region into Quadrats

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

runifpointOnLines

Generate N Uniform Random Points On Line Segments

nearest.raster.point

Find Pixel Nearest to a Given Point

Hutchings' Bramble Canes data

Inhomogeneous K-function

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Combine Function Value Tables

Concatenate x,y Coordinate Vectors

Summarizing a Quadrature Scheme

Exponential Energy Marks

Delaunay Triangulation of Point Pattern

Spruces Point Pattern

Rectangular grid of points

Simulated Point Pattern

Extract Original Data from a Fitted Point Process Model

Apply Affine Transformation To Window

inforder.family

Infinite Order Interaction Family

Pairwise distances between two different point patterns

Methods for three-dimensional point patterns

Distance Map as a Function

Area of Part of Disc

Generate N Uniform Random Points

pairwise.family

Pairwise Interaction Process Family

Urkiola Woods Point Pattern

Mark Connection Function

Morphological Erosion

Bounding Box of a Window or Point Pattern

Plot a plotppm Object Created by plot.ppm

Aherne's hamster tumour data

Methods for Three-Dimensional Box

The Piecewise Constant Pairwise Interaction Point Process Model

plot.bermantest

Plot Result of Berman Test

Plot a List of Things

Point Patterns of New Brunswick Forest Fires

Areas of Morphological Dilations

Function Arrays for Spatial Patterns

Kernel Smoothing of Line Segment Pattern

Plot a tessellation

Basis for Harmonic Functions

Extract the Interaction from a Fitted Point Process Model

Perspective Plot of Pixel Image

Multitype J Function (i-to-j)

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Extract or Replace Subset of Tessellation

Bronze gradient filter data

Hyper Data Frame

Weighted Histogram

Extract Subset of Function Array

Marked Nearest Neighbour Distance Function

Marked K-Function

Fit Point Process Model to Data

Area of a Window

Three-Dimensional Box

Plot a List of Point Patterns

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Inhomogeneous Multitype L Dot Function

Point and Click Interface for Displaying a Point Pattern

Generate a Default Pattern of Dummy Points

Dirichlet Tessellation of Point Pattern

plot a Fitted Point Process Model

Berman's Tests for Point Process Model

Q-Q Plot of Residuals from Fitted Point Process Model

Determine Whether One Window is Contained In Another

Generate N Uniform Random Points in Three Dimensions

Test Whether An Object Is A Point Pattern

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Spatial smoothing of observations at irregular points

Name for Unit of Length

Pairwise distances in Three Dimensions

bounding.box.xy

Convex Hull of Points

Pine saplings in Finland.

project2segment

Move Point To Nearest Line

Interactively Define a Polygon

Chorley-Ribble Cancer Data

Ponderosa Pine Tree Point Pattern

Berman-Huntington points and lines data

Nearest Neighbour Distances in Any Dimensions

Safely Convert Point Pattern Window to Binary Mask

Pairwise Distances in Any Dimensions

Summary of a Point Pattern Dataset

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

Method of Minimum Contrast

The Hard Core Point Process Model

Subdivide a Window or Tessellation using a Set of Lines

Morphological Closing

Collapse Several Function Tables into One

Test Whether a Window is Convex

Multidimensional Space-Time Point Pattern

Multitype L-function (cross-type)

Test Whether An Object Is A Fitted Point Process Model

Print a Fitted Point Process Model

Kaplan-Meier Estimator using Histogram Data

Coefficients of Fitted Point Process Model

Generate Poisson Point Pattern in Three Dimensions

Find Line Segment Nearest to Each Point

Point and Click Interface for Exploratory Analysis of Point Pattern

Humberside Data on Childhood Leukaemia and Lymphoma

Quadrat counting for a point pattern

Generic Ord Interaction model

model.matrix.ppm

Extract Design Matrix from Point Process Model

Lurking variable plot

Class of Line Segment Patterns

Pairwise distances

Ord Interaction Process Family

Generate Poisson Random Line Process

Simulate from a Fitted Point Process Model

Intersect Infinite Straight Lines with a Window

Perfect Simulation of the Strauss Process

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Generate N Uniform Random Points in Any Dimensions

Extract or Replace Subset of a List of Things

Level Set of a Pixel Image

Convert dataset to another unit of length

Simulate Baddeley-Silverman Cell Process

Subset of Quadrature Scheme

model.frame.ppm

Extract the Environment of a Point Process Model

Pair Correlation Function of Point Pattern

The Strauss Point Process Model

Inhomogeneous Pair Correlation Function

Plot Function Values

Generate Multitype Poisson Point Pattern

Multitype pair correlation function (i-to-any)

Make Periodic Copies of a Spatial Pattern

Convex Hull of Points

Simulate Simple Sequential Inhibition

Convert Data To Tessellation

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Morishita Index Plot

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Generate Poisson Point Pattern

Fry Plot of Point Pattern

complement.owin

Take Complement of a Window

Beadlet Anemones Data

Print Brief Details of a Point Pattern Dataset

Profile Maximum Pseudolikelihood

Test Whether A Point Process Model is Marked

Multitype L-function (i-to-any)

Interpolate a Pixel Image

Border Region of a Window

Print Brief Details of a Spatial Window

plot a Spatial Point Pattern

Distance Map of Line Segment Pattern

Create a Point Pattern

Convert Point Pattern to Another Unit of Length

Convert and Compare Colours in Different Formats

Nearest Neighbours in Any Dimensions

Apply Vector Translation To Window

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Apply Vector Translation

Log Likelihood for Poisson Point Process Model

Update a Fitted Point Process Model

Ord's Interaction model

Distance Between Two Point Patterns

Extract Dummy Points Used to Fit a Point Process Model

Fitted Conditional Intensity for Point Process Model

Simulate point patterns using the Metropolis-Hastings algorithm.

Random Thinning

Cut margins from rectangle

Diagnostic Plots for Fitted Point Process Model

Nearest neighbours in three dimensions

Distance Map of Window

The Area Interaction Point Process Model

Diameter of a Window

Create a Point Matching

Convert Window to Another Unit of Length

Mark Correlation Function

Plot a Function Array

Foxall's Distance Functions

crossdist.default

Pairwise distances between two different sets of points

Spherical Contact Distribution Function

Weighted Empirical Cumulative Distribution Function

Evaluate Expression Involving Pixel Images

Intersection of Two Tessellations

Simulate Gauss-Poisson Process

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Compute Expansion Window for Simulation

Sample Quantiles of Pixel Image

spatstat-package

The Spatstat Package

Saturated Pairwise Interaction Point Process Family

Convert Polygonal Region into Different Format

Sufficient Statistic of Point Process Model

Multi-Dimensional Box

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Hughes' Amacrine Cell Data

Summary of a Spatial Window

Simulate Matern Cluster Process

Summary of a Line Segment Pattern Dataset

Pairwise distances

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Find Largest Circle Inside Window

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Approximate a Polygon by a Simpler Polygon

Integral of a Pixel Image

Summarizing a Pixel Image

plot.hyperframe

Plot Entries in a Hyperframe

Convert Point Pattern to Pixel Image

Compute Images of Constructed Covariates

Random Re-Labelling of Point Pattern

Longleaf Pines Point Pattern

Reduced Sample Estimator using Histogram Data

Difference of Disc Areas

Generate Poisson Point Pattern in Any Dimensions

Pairwise distances between line segments

New Zealand Trees Point Pattern

Nearest Neighbours Between Two Patterns

Randomly Shift a Line Segment Pattern

Test Whether An Object Is Empty

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

Plot a Spatial Window

Rotate a Window

Convert Line Segment Pattern to Pixel Image

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

rshift.splitppp

Randomly Shift a List of Point Patterns

Simulate Stratified Random Point Pattern

Estimate window from points alone

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Japanese Pines Point Pattern

Distance for a Point Pattern Matching

Fit the Matern Cluster Point Process by Minimum Contrast

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

Nearest neighbour distances in three dimensions

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Convert Data To Class psp

Divide Image Into Sub-images

Print a Quadrature Scheme

Apply Vector Translation To Point Pattern

Scatterplot Matrix for Pixel Images

Pair Correlation Function

Beta Ganglion Cells in Cat Retina, Old Version

Read Point Pattern From Data File

Marks of a Point Pattern

Pairwise distances

Multitype J Function (i-to-any)

Pair Correlation Function obtained from array of K functions

Simulate Matern Model I

as.data.frame.im

Convert Pixel Image to Data Frame

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

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Harkness-Isham ants' nests data

Lansing Woods Point Pattern

Summary of a List of Things

Fit the Thomas Point Process by Minimum Contrast

Update a Fitted Cluster Point Process Model

Convert Data To Class owin

Test Whether Points Are Inside A Window

Plot a Pixel Image

matclust.estpcf

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

Methods for Multidimensional Space-Time Point Patterns

Plot a Colour Map

Perimeter Length of Window

quadratresample

Resample a Point Pattern by Resampling Quadrats

pairdist.default

Pairwise distances

Apply Smoothing to Function Values

Convert Pixel Image to Another Unit of Length

Create a Tessellation

Place Points Evenly Along Specified Lines

Clark and Evans Aggregation Index

plot a Spatial Quadrature Scheme

Divide Point Pattern into Sub-patterns

Generate N Random Points

Define Point Process Model for Metropolis-Hastings Simulation.

Quadrature Scheme Based on Pixel Grid

pppmatching.object

Class of Point Matchings

summary.splitppp

Summary of a Split Point Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

Simulate Matern Model II

Prediction from a Fitted Point Process Model

rescue.rectangle

Convert Window Back To Rectangle

Plot a Simulation Envelope

Extract Quadrature Scheme Used to Fit a Point Process Model

California Redwoods Point Pattern (Ripley's Subset)

Data and Code From JRSS Discussion Paper on Residuals

Vertices of a Window

Union of Data and Dummy Points

Test Whether Two Function Objects Are Compatible

Mosaic Random Field

Plot a Spatial Kolmogorov-Smirnov Test

Define Point Process Model for Metropolis-Hastings Simulation.

Print Progress Reports

Convert Pixel Image from Numeric to Factor

Print Brief Details of an Image

Residuals for Fitted Point Process Model

plot a Spatial Line Segment Pattern

Determine Duplicated Points in a Spatial Point Pattern

Class of Point Patterns

Theoretical Distribution of Nearest Neighbour Distance

Generate grid of parallel lines with random displacement

Interpret Fitted Model for Metropolis-Hastings Simulation.

Three Dimensional Point Pattern

Random Perturbation of a Point Pattern

Rotate a Point Pattern

Histogram of Pixel Values in an Image

Determine Initial State for Metropolis-Hastings Simulation.

Kaplan-Meier and Reduced Sample Estimator using Histograms

Mosaic Random Set

Apply Vector Translation To Pixel Image

Swedish Pines Point Pattern

Apply Vector Translation To Line Segment Pattern

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Compute Integral of Function Against Cumulative Distribution

spatstat.options

Internal Options in Spatstat Package

Volume of an Object

Superimpose Several Line Segment Patterns

Superimpose Several Point Patterns

Generate N Random Multitype Points

Simulate a Fitted Cluster Point Process Model

Methods for Multi-Dimensional Box

Simulate systematic random point pattern

Rotate a Line Segment Pattern

Randomly Shift a Point Pattern

Generate N Uniform Random Points in a Disc

Create a Line Segment Pattern

Fit the Thomas Point Process by Minimum Contrast

Simulate a Fitted Gibbs Point Process Model

Class of Fitted Point Process Models