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spatstat (version 1.19-3)

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

16,015

Version

1.19-3

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

June 17th, 2010

Functions in spatstat (1.19-3)

Spherical Contact Distribution Function

Subset of Quadrature Scheme

The Strauss Point Process Model

Diggle-Gratton model

Estimate the I-function

Estimate the empty space function F

Convert to Pixel Image

Border Region of a Window

ANOVA for Fitted Point Process Models

Distance to Boundary of Window

Foxall's Distance Functions

Hughes' Amacrine Cell Data

Convert Pixel Image to Matrix

Diagnostics for random marking

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Inhomogeneous Multitype L Dot Function

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Dirichlet Tessellation of Point Pattern

Apply Affine Transformation To Point Pattern

Apply Gaussian Blur to a Pixel Image

Estimate the J-function

Convert Data To Tessellation

Extract or Replace Subset of Tessellation

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Multitype L-function (i-to-any)

Saturated Pairwise Interaction model

Inhomogeneous Cross Type L Function

Apply Affine Transformation To Line Segment Pattern

Extract or Replace Subset of Point Pattern

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Pixel Image Approximation of a Window

Apply Function to Image Broken Down by Factor

Poisson Point Process Model

Chorley-Ribble Cancer Data

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Extract.splitppp

Extract or Replace Sub-Patterns

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

Generic Ord Interaction model

Inhomogeneous Multitype K Dot Function

Apply Function to Every Neighbourhood in a Point Pattern

Centroid of a window

complement.owin

Take Complement of a Window

Areas of Morphological Dilations

Extract Original Data from a Fitted Point Process Model

Connected components of an image or window

crossdist.default

Pairwise distances between two different sets of points

Marked Nearest Neighbour Distance Function

Integral of a Pixel Image

Area of Part of Disc

Convert Data To Class ppp

Level Set of a Pixel Image

Bounding Box of a Window or Point Pattern

Class of Images

spatstat-deprecated

Deprecated spatstat functions

Extract Dummy Points Used to Fit a Point Process Model

Tropical rain forest trees

Create a Pixel Image Object

Test Whether Points Are Inside A Window

Evaluate Expression Involving Function Arrays

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Morphological Closing

Test Whether An Object Is A Pixel Image

Extract Subset of Image

Geyer's Saturation Point Process Model

Intersection of Two Tessellations

Determine Duplicated Points in a Spatial Point Pattern

Area of a Window

Apply a Function to a Point Pattern Broken Down by Factor

Berman-Huntington points and lines data

Delaunay Triangulation of Point Pattern

Aherne's hamster tumour data

Convert a Window to a Polygonal Window

Log Likelihood for Poisson Point Process Model

Diameter of an Object

Morphological Erosion

Extract the Interaction from a Fitted Point Process Model

Fitted Conditional Intensity for Point Process Model

Nearest Neighbour Distance Function G

Inhomogeneous K-function

Multi-Dimensional Box

Ord's Interaction model

bounding.box.xy

Convex Hull of Points

Three-Dimensional Box

Artificial Data Point Pattern

Exponential Energy Marks

Berman's Tests for Point Process Model

Identify Points in a Point Pattern

Intersect Infinite Straight Lines with a Window

Multitype J Function (i-to-j)

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Print News About Latest Version of Package

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Marks of a Point Pattern

Pairwise distances between two different three-dimensional point patterns

Inhomogeneous Cross K Function

Interpolate a Pixel Image

Determine Whether One Window is Contained In Another

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Distance to Boundary of Window

Collapse Several Function Tables into One

Circular Window

Kolmogorov-Smirnov Test for Point Process Model

Extract Subset of Function Array

Distance Map of Point Pattern

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

Hybrid Geyer Point Process Model

Histogram of Pixel Values in an Image

Point and Click Interface for Displaying a Point Pattern

Rectangular grid of points

Summarise Marks in Every Neighbourhood in a Point Pattern

Combine Function Value Tables

Lengths of Line Segments

The Soft Core Point Process Model

Multitype L-function (cross-type)

Difference of Disc Areas

Mark Correlation Function

Point and Click Interface for Exploratory Analysis of Point Pattern

Reduced Second Moment Measure

Kaplan-Meier and Reduced Sample Estimator using Histograms

Empty Space Function of a Three-Dimensional Point Pattern

Multitype K Function (i-to-any)

K-function of a Three-Dimensional Point Pattern

Extract Subset of Line Segment Pattern

Clark and Evans Aggregation Index

Convert Pixel Image from Numeric to Factor

The Multitype Strauss Point Process Model

Test whether Object is Multitype

The Area Interaction Point Process Model

Generic Pairwise Interaction model

Harkness-Isham ants' nests data

The Fiksel Interaction

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

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Weighted Empirical Cumulative Distribution Function

Multitype J Function (i-to-any)

The Piecewise Constant Pairwise Interaction Point Process Model

Basis for Harmonic Functions

Convert Data To Class owin

Multitype K Function (Cross-type)

Pine saplings in Finland.

Interactively Define a Polygon

Distance Map as a Function

Pairwise distances between two different point patterns

Apply Affine Transformation To Window

Window in Shape of Letter R

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

The Hard Core Point Process Model

The Strauss / Hard Core Point Process Model

Extract or Replace Subset of a List of Things

Convert Data To Class psp

Colour Lookup Tables

Distance to Boundary of Window

The Lennard-Jones Potential

Endpoints of Line Segment Pattern

Pairwise distances between two different line segment patterns

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Test Whether An Object Is A Fitted Point Process Model

Diggle's Heather Data

Hyper Data Frame

Expand Window By Factor

Interactively Add Points

Find Largest Circle Inside Window

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

Orientation Angles of Line Segments

Hutchings' Bramble Canes data

Reset Values in Subset of Image

Diagnostic Plots for Fitted Point Process Model

Diameter of a Window

Concatenate x,y Coordinate Vectors

Marked J Function

Compute Quadrature Weights Based on Grid Counts

Combine Two Line Segment Patterns

Convert Data to Three-Dimensional Box

inforder.family

Infinite Order Interaction Family

Convex Hull of Points

Bronze gradient filter data

Subdivide a Window or Tessellation using a Set of Lines

Calculate four standard summary functions of a point pattern.

Distance Map of Window

Test Whether Marks Are Present

Beadlet Anemones Data

Distance Map of Line Segment Pattern

Neighbourhood density function

Corners of a rectangle

K-function using FFT

Kernel Smoothed Intensity of Point Pattern

Biological Cells Point Pattern

Generate a Default Pattern of Dummy Points

Geometrical Calculations for Multi-Dimensional Box

Mark Connection Function

Convert Line Segment Pattern to Binary Pixel Mask

Simulation Envelopes of Summary Function

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Areas of Morphological Erosions

Apply Affine Transformation

Simulation Envelopes of Summary Function for 3D Point Pattern

Morphological Dilation

Contour plot of pixel image

Pairwise distances

Geometrical Calculations for Three-Dimensional Box

Crossing Points of Two Line Segment Patterns

Convert Polygonal Region into Different Format

Evaluate Expression Involving Pixel Images

Fry Plot of Point Pattern

Test Whether A Point Pattern is Marked

Create a Function Value Table

Convert and Compare Colours in Different Formats

Fit cluster point process model

Beta Ganglion Cells in Cat Retina, Old Version

Evaluate Expression Involving Functions

Infinite Straight Lines

Test Whether An Object Is Empty

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Test Whether a Window is Convex

Test Whether An Object Is A Point Pattern

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Test Whether A Point Process Model is Marked

Longleaf Pines Point Pattern

spatstat-internal

Internal spatstat functions

Beta Ganglion Cells in Cat Retina

Extract Subset of Function Values

Marked K-Function

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Test Whether Two Function Objects Are Compatible

Humberside Data on Childhood Leukaemia and Lymphoma

as.data.frame.im

Convert Pixel Image to Data Frame

Test Whether Two Pixel Images Are Compatible

Pair Correlation Function

Intersection, Union or Set Subtraction of Two Windows

Nearest neighbour

Three Dimensional Point Pattern

Safely Convert Point Pattern Window to Binary Mask

Midpoints of Line Segment Pattern

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Mark Correlation Integral

Convert Spatial Object to Pixel Image

Class of Fitted Point Process Models

Ord Interaction Process Family

Class of Quadrature Schemes

Test Whether An Object Is A Window

Plot a tessellation

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

Convert Data to Hyperframe

Print Brief Details of a Line Segment Pattern Dataset

pppmatching.object

Class of Point Matchings

plot.bermantest

Plot Result of Berman Test

Coefficients of Fitted Point Process Model

Simulate Baddeley-Silverman Cell Process

Pairwise Distances in Any Dimensions

Simulate Gauss-Poisson Process

Classify Points in a Point Pattern

Simulate Neyman-Scott Process

Reduced Sample Estimator using Histogram Data

Morishita Index Plot

Generate N Random Points

Print Brief Details of a Spatial Window

Difference of Disc Areas

Plot a List of Point Patterns

Plot a Simulation Envelope

Plot a plotppm Object Created by plot.ppm

Nearest Neighbour Distances in Any Dimensions

Plot a Function Array

Rotate a Line Segment Pattern

Nearest Neighbours in Any Dimensions

Pairwise distances

Multitype pair correlation function (i-to-any)

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Print Brief Details of a Point Pattern Dataset

pairdist.default

Pairwise distances

Compute Images of Constructed Covariates

Nearest Neighbours Between Two Patterns

Convert Line Segment Pattern to Pixel Image

Nearest Neighbour Clutter Removal

Create a Line Segment Pattern

Class of Point Patterns

Kernel Smoothing of Line Segment Pattern

Convert Point Pattern to Pixel Image

Generate a Quadrature Scheme from a Point Pattern

plot a Fitted Point Process Model

Sample Quantiles of Pixel Image

Methods for Multidimensional Space-Time Point Patterns

plot.hyperframe

Plot Entries in a Hyperframe

Simulate Matern Cluster Process

Divide Region into Quadrats

Find Line Segment Nearest to Each Point

Volume of an Object

Nearest neighbour distances between line segments

Create a Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

Print a Quadrature Scheme

Plot a three-dimensional point pattern

Random Perturbation of a Point Pattern

Divide Point Pattern into Sub-patterns

Plot a List of Things

Multitype pair correlation function (cross-type)

Inhomogeneous Pair Correlation Function

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Methods for Three-Dimensional Box

Simulate Matern Model II

summary.splitppp

Summary of a Split Point Pattern

quadratresample

Resample a Point Pattern by Resampling Quadrats

Apply Vector Translation To Window

Randomly Shift a Point Pattern

Simulate Simple Sequential Inhibition

Class of Line Segment Patterns

Print Progress Reports

Print a Fitted Point Process Model

Random Re-Labelling of Point Pattern

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

Murchison gold deposits

Plot a Spatial Kolmogorov-Smirnov Test

Number of Points in a Point Pattern

Multidimensional Space-Time Point Pattern

plot a Spatial Line Segment Pattern

Quadrature Scheme Based on Pixel Grid

model.frame.ppm

Extract the Environment of a Point Process Model

Pair Correlation Function of Point Pattern

Prediction from a Fitted Cluster Point Process Model

pairwise.family

Pairwise Interaction Process Family

Rotate a Window

Extract Quadrature Scheme Used to Fit a Point Process Model

Variance-Covariance Matrix for a Fitted Point Process Model

Define Point Process Model for Metropolis-Hastings Simulation.

Summarizing a Pixel Image

Simulate from a Fitted Point Process Model

Generate N Uniform Random Points in Any Dimensions

Convert Window to Another Unit of Length

Plot a fitted cluster point process

Generate Poisson Point Pattern on Line Segments

Morphological Opening

Simulate Matern Model I

Pairwise distances

Saturated Pairwise Interaction Point Process Family

plot a Spatial Quadrature Scheme

plot a Spatial Point Pattern

Kaplan-Meier Estimator using Histogram Data

Fit the Thomas Point Process by Minimum Contrast

Convert dataset to another unit of length

Rotate a Point Pattern

Function Arrays for Spatial Patterns

Generate Poisson Point Pattern in Any Dimensions

Update a Fitted Point Process Model

Convert Pixel Image to Another Unit of Length

Apply Vector Translation To Pixel Image

Create a Point Matching

Generate grid of parallel lines with random displacement

Convert Window to Pixel Image

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Pair Correlation Function obtained from K Function

Mosaic Random Set

Q-Q Plot of Residuals from Fitted Point Process Model

Plot a Pixel Image

Summary of a Line Segment Pattern Dataset

Fit Point Process Model to Data

Generate Poisson Point Pattern in Three Dimensions

Nearest neighbours in three dimensions

Plot a Spatial Window

Summary of a List of Things

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

Distance Between Two Point Patterns

Simulate a Fitted Cluster Point Process Model

Distance for a Point Pattern Matching

Methods for Multi-Dimensional Box

Plot Function Values

Make Periodic Copies of a Spatial Pattern

Cut margins from rectangle

Spatial smoothing of observations at irregular points

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Scatterplot Matrix for Pixel Images

Nearest neighbour distances in three dimensions

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Set Covariance of a Window

Simulate systematic random point pattern

Simulate Stratified Random Point Pattern

Japanese Pines Point Pattern

Read Point Pattern From Data File

model.matrix.ppm

Extract Design Matrix from Point Process Model

Generate Multitype Poisson Point Pattern

Extract List of Tiles in a Tessellation

nearest.raster.point

Find Pixel Nearest to a Given Point

New Zealand Trees Point Pattern

Data Frames of Function Values

Interaction Distance of a Point Process

Simulate a Fitted Gibbs Point Process Model

Spruces Point Pattern

Apply Smoothing to Function Values

rshift.splitppp

Randomly Shift a List of Point Patterns

Quadrat counting for a point pattern

Simulate point patterns using the Metropolis-Hastings algorithm.

Method of Minimum Contrast

Compute Integral of Function Against Cumulative Distribution

Theoretical Distribution of Nearest Neighbour Distance

Methods for three-dimensional point patterns

Poisson Line Tessellation

California Redwoods Point Pattern (Entire Dataset)

Randomly Shift a Line Segment Pattern

Place Points Evenly Along Specified Lines

Convert Line Segment Pattern to Another Unit of Length

Perfect Simulation of the Strauss Process

Perspective Plot of Pixel Image

Summarizing a Fitted Point Process Model

Profile Maximum Pseudolikelihood

Vertices of a Window

Interpret Fitted Model for Metropolis-Hastings Simulation.

Simulate Thomas Process

Ponderosa Pine Tree Point Pattern

spatstat-package

The Spatstat Package

Prediction from a Fitted Point Process Model

Update a Fitted Cluster Point Process Model

Summary of a Point Pattern Dataset

Name for Unit of Length

Superimpose Several Point Patterns

Determine Initial State for Metropolis-Hastings Simulation.

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Estimate window from points alone

Residuals for Fitted Point Process Model

Create a Window

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

Plot a Colour Map

Sufficient Statistic of Point Process Model

Define Point Process Model for Metropolis-Hastings Simulation.

Generate Poisson Random Line Process

Approximate a Polygon by a Simpler Polygon

Print Brief Details of an Image

selfcrossing.psp

Crossing Points in a Line Segment Pattern

California Redwoods Point Pattern (Ripley's Subset)

Superimpose Several Line Segment Patterns

project2segment

Move Point To Nearest Line

Mosaic Random Field

Simulated Point Pattern

Generate N Random Multitype Points

Extract Unique Points from a Spatial Point Pattern

Spokes pattern of dummy points

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Summarizing a Quadrature Scheme

Urkiola Woods Point Pattern

Point Patterns of New Brunswick Forest Fires

Nearest neighbour distances

Pair Correlation Function obtained from array of K functions

Pairwise distances in Three Dimensions

rescue.rectangle

Convert Window Back To Rectangle

Apply Vector Translation To Point Pattern

Divide Image Into Sub-images

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Generate N Uniform Random Points in Three Dimensions

Lansing Woods Point Pattern

Generate N Uniform Random Points

Set Control Parameters for Metropolis-Hastings Algorithm.

Apply Vector Translation

Perimeter Length of Window

multiplicity.ppp

Count Multiplicity of Duplicate Points

Random Thinning

Generate N Uniform Random Points in a Disc

spatstat.options

Internal Options in Spatstat Package

Generate Poisson Point Pattern

Data and Code From JRSS Discussion Paper on Residuals

Convert Point Pattern to Another Unit of Length

Lurking variable plot

Pairwise distances between line segments

Swedish Pines Point Pattern

Evaluate an Expression in a Function Table

Galaxies in the Shapley Supercluster

Union of Data and Dummy Points

Weighted Histogram

Apply Vector Translation To Line Segment Pattern

Cartesian Coordinates for a Pixel Raster

Create a Tessellation

Summary of a Spatial Window