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spatstat (version 1.19-2)

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

18,534

Version

1.19-2

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

June 9th, 2010

Functions in spatstat (1.19-2)

The Fiksel Interaction

Marked Nearest Neighbour Distance Function

Diggle-Gratton model

Foxall's Distance Functions

Estimate the I-function

The Strauss / Hard Core Point Process Model

Spherical Contact Distribution Function

Difference of Disc Areas

Apply Function to Every Neighbourhood in a Point Pattern

Saturated Pairwise Interaction model

The Piecewise Constant Pairwise Interaction Point Process Model

Convert Data To Tessellation

Multitype J Function (i-to-j)

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Reset Values in Subset of Image

Inhomogeneous K-function

Distance to Boundary of Window

Convert Pixel Image from Numeric to Factor

Tropical rain forest trees

The Strauss Point Process Model

Multi-Dimensional Box

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Artificial Data Point Pattern

Inhomogeneous Cross Type L Function

Extract Subset of Function Array

Beadlet Anemones Data

Extract Original Data from a Fitted Point Process Model

Apply Affine Transformation To Line Segment Pattern

Extract.splitppp

Extract or Replace Sub-Patterns

Extract Subset of Image

K-function using FFT

Convert Data To Class owin

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

crossdist.default

Pairwise distances between two different sets of points

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

Reduced Second Moment Measure

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Distance to Boundary of Window

Interactively Add Points

Aherne's hamster tumour data

K-function of a Three-Dimensional Point Pattern

Distance Map of Window

Border Region of a Window

Areas of Morphological Dilations

Calculate four standard summary functions of a point pattern.

Pairwise distances between two different line segment patterns

Harkness-Isham ants' nests data

compatible.fasp

Test Whether Two Function Arrays Are Compatible

The Soft Core Point Process Model

Morphological Closing

Combine Two Line Segment Patterns

Convert Pixel Image to Matrix

Multitype K Function (Cross-type)

Pairwise distances between two different point patterns

Area of a Window

Diameter of an Object

Test Whether A Point Process Model is Marked

Diagnostics for random marking

Estimate the empty space function F

Diagnostic Plots for Fitted Point Process Model

Compute Quadrature Weights Based on Grid Counts

Inhomogeneous Multitype K Dot Function

Extract the Interaction from a Fitted Point Process Model

Difference of Disc Areas

Extract or Replace Subset of a List of Things

The Area Interaction Point Process Model

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

Bronze gradient filter data

Convert a Window to a Polygonal Window

Japanese Pines Point Pattern

Apply Affine Transformation To Point Pattern

Multitype L-function (i-to-any)

Colour Lookup Tables

Convert Data To Class psp

Empty Space Function of a Three-Dimensional Point Pattern

spatstat-internal

Internal spatstat functions

Apply a Function to a Point Pattern Broken Down by Factor

Bounding Box of a Window or Point Pattern

Endpoints of Line Segment Pattern

The Hard Core Point Process Model

Kaplan-Meier Estimator using Histogram Data

Subdivide a Window or Tessellation using a Set of Lines

Fit cluster point process model

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Distance Map as a Function

The Multitype Strauss Point Process Model

Multitype K Function (i-to-any)

Nearest Neighbour Distance Function G

Extract Dummy Points Used to Fit a Point Process Model

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Exponential Energy Marks

Rectangular grid of points

Convert Data To Class ppp

Extract or Replace Subset of Tessellation

Extract Subset of Function Values

Beta Ganglion Cells in Cat Retina

Generic Pairwise Interaction model

Point and Click Interface for Exploratory Analysis of Point Pattern

Ord's Interaction model

Hybrid Geyer Point Process Model

Marked J Function

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Mark Connection Function

Find Largest Circle Inside Window

Inhomogeneous Multitype L Dot Function

Morphological Dilation

Multitype J Function (i-to-any)

Pairwise distances between two different three-dimensional point patterns

Berman's Tests for Point Process Model

Extract or Replace Subset of Point Pattern

Infinite Straight Lines

Test Whether An Object Is A Window

Hughes' Amacrine Cell Data

Determine Duplicated Points in a Spatial Point Pattern

Three-Dimensional Box

Marked K-Function

Extract Subset of Line Segment Pattern

ANOVA for Fitted Point Process Models

Subset of Quadrature Scheme

Lansing Woods Point Pattern

Connected components of an image or window

Pair Correlation Function of Point Pattern

Combine Function Value Tables

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Fitted Conditional Intensity for Point Process Model

as.data.frame.im

Convert Pixel Image to Data Frame

Inhomogeneous Cross K Function

Clark and Evans Aggregation Index

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Kolmogorov-Smirnov Test for Point Process Model

Convert Data to Hyperframe

Crossing Points of Two Line Segment Patterns

Geyer's Saturation Point Process Model

Evaluate Expression Involving Function Arrays

Collapse Several Function Tables into One

Geometrical Calculations for Three-Dimensional Box

Estimate the J-function

Safely Convert Point Pattern Window to Binary Mask

Point and Click Interface for Displaying a Point Pattern

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Function Arrays for Spatial Patterns

Pairwise Distances in Any Dimensions

Beta Ganglion Cells in Cat Retina, Old Version

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Diggle's Heather Data

Determine Whether One Window is Contained In Another

The Lennard-Jones Potential

Circular Window

Expand Window By Factor

Saturated Pairwise Interaction Point Process Family

Generic Ord Interaction model

Apply Affine Transformation To Window

Lengths of Line Segments

Test Whether An Object Is A Fitted Point Process Model

Multitype L-function (cross-type)

Orientation Angles of Line Segments

Methods for Multi-Dimensional Box

Multidimensional Space-Time Point Pattern

Apply Gaussian Blur to a Pixel Image

Create a Line Segment Pattern

Pairwise distances

Concatenate x,y Coordinate Vectors

Weighted Empirical Cumulative Distribution Function

Nearest neighbours in three dimensions

Data Frames of Function Values

Convert Polygonal Region into Different Format

Test Whether Two Function Objects Are Compatible

Simulation Envelopes of Summary Function for 3D Point Pattern

Dirichlet Tessellation of Point Pattern

Point Patterns of New Brunswick Forest Fires

Intersect Infinite Straight Lines with a Window

Berman-Huntington points and lines data

Pixel Image Approximation of a Window

Apply Function to Image Broken Down by Factor

pairdist.default

Pairwise distances

Humberside Data on Childhood Leukaemia and Lymphoma

Basis for Harmonic Functions

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Interpolate a Pixel Image

Convert Data to Three-Dimensional Box

Poisson Point Process Model

Morphological Erosion

Chorley-Ribble Cancer Data

Apply Affine Transformation

Diameter of a Window

Test whether Object is Multitype

Nearest Neighbour Clutter Removal

Mosaic Random Set

Plot a three-dimensional point pattern

Integral of a Pixel Image

bounding.box.xy

Convex Hull of Points

model.frame.ppm

Extract the Environment of a Point Process Model

Marks of a Point Pattern

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Plot a Pixel Image

Pine saplings in Finland.

Distance Map of Line Segment Pattern

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Simulate Baddeley-Silverman Cell Process

Coefficients of Fitted Point Process Model

Convex Hull of Points

Simulate from a Fitted Point Process Model

Distance to Boundary of Window

Print News About Latest Version of Package

Identify Points in a Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

Kaplan-Meier and Reduced Sample Estimator using Histograms

Test Whether An Object Is A Point Pattern

Print Progress Reports

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Delaunay Triangulation of Point Pattern

Generate a Default Pattern of Dummy Points

Test Whether Marks Are Present

Kernel Smoothing of Line Segment Pattern

Plot a Colour Map

Neighbourhood density function

Convert Line Segment Pattern to Binary Pixel Mask

Convert to Pixel Image

Centroid of a window

Kernel Smoothed Intensity of Point Pattern

Test Whether A Point Pattern is Marked

Evaluate Expression Involving Functions

Methods for Three-Dimensional Box

spatstat-deprecated

Deprecated spatstat functions

Methods for Multidimensional Space-Time Point Patterns

Geometrical Calculations for Multi-Dimensional Box

nearest.raster.point

Find Pixel Nearest to a Given Point

Residuals for Fitted Point Process Model

Distance Map of Point Pattern

Murchison gold deposits

Theoretical Distribution of Nearest Neighbour Distance

Place Points Evenly Along Specified Lines

Pair Correlation Function obtained from array of K functions

plot a Fitted Point Process Model

Mark Correlation Integral

Rotate a Window

Pairwise distances

Plot a List of Point Patterns

Mark Correlation Function

model.matrix.ppm

Extract Design Matrix from Point Process Model

Morishita Index Plot

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Nearest neighbour distances between line segments

Biological Cells Point Pattern

Hutchings' Bramble Canes data

Print Brief Details of an Image

Nearest Neighbours Between Two Patterns

Level Set of a Pixel Image

Generate Multitype Poisson Point Pattern

Summarizing a Fitted Point Process Model

Generate N Uniform Random Points in Any Dimensions

Test Whether An Object Is Empty

Evaluate Expression Involving Pixel Images

Distance for a Point Pattern Matching

Interactively Define a Polygon

Simulate Matern Model I

Extract Quadrature Scheme Used to Fit a Point Process Model

Nearest neighbour

Randomly Shift a Line Segment Pattern

Create a Function Value Table

New Zealand Trees Point Pattern

Convert Window to Another Unit of Length

Hyper Data Frame

Class of Line Segment Patterns

Rotate a Line Segment Pattern

Convert Window to Pixel Image

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Longleaf Pines Point Pattern

Interpret Fitted Model for Metropolis-Hastings Simulation.

Test Whether An Object Is A Pixel Image

plot.hyperframe

Plot Entries in a Hyperframe

Classify Points in a Point Pattern

Simulate Gauss-Poisson Process

Log Likelihood for Poisson Point Process Model

Midpoints of Line Segment Pattern

Test Whether Two Pixel Images Are Compatible

Nearest neighbour distances

Lurking variable plot

Plot a Function Array

Prediction from a Fitted Cluster Point Process Model

Define Point Process Model for Metropolis-Hastings Simulation.

Apply Smoothing to Function Values

Intersection of Two Tessellations

Number of Points in a Point Pattern

Compute Images of Constructed Covariates

Spruces Point Pattern

Set Control Parameters for Metropolis-Hastings Algorithm.

Area of Part of Disc

Perimeter Length of Window

Simulate systematic random point pattern

Summarise Marks in Every Neighbourhood in a Point Pattern

Estimate window from points alone

complement.owin

Take Complement of a Window

Areas of Morphological Erosions

Multitype pair correlation function (cross-type)

Determine Initial State for Metropolis-Hastings Simulation.

Fry Plot of Point Pattern

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Update a Fitted Point Process Model

Convert Spatial Object to Pixel Image

Contour plot of pixel image

plot a Spatial Line Segment Pattern

Nearest Neighbours in Any Dimensions

Ponderosa Pine Tree Point Pattern

Simulated Point Pattern

Pairwise distances between line segments

Generate Poisson Point Pattern on Line Segments

inforder.family

Infinite Order Interaction Family

Histogram of Pixel Values in an Image

plot a Spatial Point Pattern

Window in Shape of Letter R

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Convert Line Segment Pattern to Pixel Image

Pair Correlation Function obtained from K Function

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Perspective Plot of Pixel Image

Pairwise distances in Three Dimensions

Inhomogeneous Pair Correlation Function

Plot a Spatial Window

Summary of a Spatial Window

Summarizing a Pixel Image

Simulation Envelopes of Summary Function

Rotate a Point Pattern

Nearest neighbour distances in three dimensions

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Divide Region into Quadrats

Plot a tessellation

Simulate Thomas Process

plot a Spatial Quadrature Scheme

Plot Function Values

Random Thinning

Nearest Neighbour Distances in Any Dimensions

multiplicity.ppp

Count Multiplicity of Duplicate Points

Randomly Shift a Point Pattern

rshift.splitppp

Randomly Shift a List of Point Patterns

Generate N Uniform Random Points in a Disc

Plot a Spatial Kolmogorov-Smirnov Test

Corners of a rectangle

spatstat.options

Internal Options in Spatstat Package

Apply Vector Translation To Window

pairwise.family

Pairwise Interaction Process Family

Test Whether Points Are Inside A Window

Swedish Pines Point Pattern

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

Distance Between Two Point Patterns

Pairwise distances

Print Brief Details of a Line Segment Pattern Dataset

Morphological Opening

Evaluate an Expression in a Function Table

Poisson Line Tessellation

Simulate a Fitted Cluster Point Process Model

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Cartesian Coordinates for a Pixel Raster

Update a Fitted Cluster Point Process Model

Three Dimensional Point Pattern

Create a Point Matching

Quadrat counting for a point pattern

Create a Pixel Image Object

Method of Minimum Contrast

Scatterplot Matrix for Pixel Images

Quadrature Scheme Based on Pixel Grid

Q-Q Plot of Residuals from Fitted Point Process Model

Find Line Segment Nearest to Each Point

Test Whether a Window is Convex

Generate N Uniform Random Points in Three Dimensions

Class of Images

Create a Window

Ord Interaction Process Family

Generate N Uniform Random Points

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

spatstat-package

The Spatstat Package

Prediction from a Fitted Point Process Model

Apply Vector Translation To Point Pattern

Simulate Matern Cluster Process

Class of Point Patterns

project2segment

Move Point To Nearest Line

Summary of a Point Pattern Dataset

summary.splitppp

Summary of a Split Point Pattern

Summarizing a Quadrature Scheme

Generate Poisson Point Pattern

Summary of a List of Things

Sufficient Statistic of Point Process Model

Perfect Simulation of the Strauss Process

Simulate Matern Model II

Print a Quadrature Scheme

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Class of Quadrature Schemes

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

Random Perturbation of a Point Pattern

Convert Point Pattern to Another Unit of Length

Print a Fitted Point Process Model

Generate Poisson Point Pattern in Any Dimensions

Generate a Quadrature Scheme from a Point Pattern

Simulate Neyman-Scott Process

Fit Point Process Model to Data

Generate grid of parallel lines with random displacement

Read Point Pattern From Data File

Data and Code From JRSS Discussion Paper on Residuals

Compute Integral of Function Against Cumulative Distribution

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

Reduced Sample Estimator using Histogram Data

Apply Vector Translation

rescue.rectangle

Convert Window Back To Rectangle

Convert dataset to another unit of length

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Union of Data and Dummy Points

California Redwoods Point Pattern (Entire Dataset)

Urkiola Woods Point Pattern

Convert Line Segment Pattern to Another Unit of Length

Plot a fitted cluster point process

Intersection, Union or Set Subtraction of Two Windows

Plot a List of Things

Spatial smoothing of observations at irregular points

Create a Point Pattern

Print Brief Details of a Spatial Window

Fit the Thomas Point Process by Minimum Contrast

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

Pair Correlation Function

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

California Redwoods Point Pattern (Ripley's Subset)

Divide Point Pattern into Sub-patterns

Plot a plotppm Object Created by plot.ppm

Interaction Distance of a Point Process

Print Brief Details of a Point Pattern Dataset

Methods for three-dimensional point patterns

Convert Point Pattern to Pixel Image

Divide Image Into Sub-images

Define Point Process Model for Metropolis-Hastings Simulation.

Make Periodic Copies of a Spatial Pattern

Superimpose Several Line Segment Patterns

Cut margins from rectangle

quadratresample

Resample a Point Pattern by Resampling Quadrats

Vertices of a Window

Variance-Covariance Matrix for a Fitted Point Process Model

Spokes pattern of dummy points

Generate N Random Points

Superimpose Several Point Patterns

Profile Maximum Pseudolikelihood

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Generate Poisson Random Line Process

Weighted Histogram

Generate Poisson Point Pattern in Three Dimensions

Apply Vector Translation To Pixel Image

Set Covariance of a Window

Sample Quantiles of Pixel Image

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Apply Vector Translation To Line Segment Pattern

Summary of a Line Segment Pattern Dataset

Simulate Simple Sequential Inhibition

Multitype pair correlation function (i-to-any)

Simulate a Fitted Gibbs Point Process Model

Convert Pixel Image to Another Unit of Length

plot.bermantest

Plot Result of Berman Test

pppmatching.object

Class of Point Matchings

Mosaic Random Field

Class of Fitted Point Process Models

Simulate Stratified Random Point Pattern

Random Re-Labelling of Point Pattern

Extract List of Tiles in a Tessellation

Create a Tessellation

Name for Unit of Length

Galaxies in the Shapley Supercluster

Generate N Random Multitype Points

Simulate point patterns using the Metropolis-Hastings algorithm.

Extract Unique Points from a Spatial Point Pattern

Volume of an Object

Approximate a Polygon by a Simpler Polygon