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spatstat (version 1.19-0)

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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Install

install.packages('spatstat')

Monthly Downloads

16,590

Version

1.19-0

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

May 16th, 2010

Functions in spatstat (1.19-0)

Methods for Three-Dimensional Box

Create a Window

Ord Interaction Process Family

Pairwise distances

Nearest Neighbour Distances in Any Dimensions

Interpret Fitted Model for Metropolis-Hastings Simulation.

Plot a Spatial Window

Pair Correlation Function obtained from K Function

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Generate N Random Points

Plot Function Values

Make Periodic Copies of a Spatial Pattern

model.matrix.ppm

Extract Design Matrix from Point Process Model

Nearest neighbour distances between line segments

Method of Minimum Contrast

Perspective Plot of Pixel Image

Murchison gold deposits

Saturated Pairwise Interaction Point Process Family

Extract Quadrature Scheme Used to Fit a Point Process Model

Plot a Colour Map

Divide Region into Quadrats

Mosaic Random Set

Generate a Quadrature Scheme from a Point Pattern

Simulate Simple Sequential Inhibition

Create a Point Pattern

Data and Code From JRSS Discussion Paper on Residuals

nearest.raster.point

Find Pixel Nearest to a Given Point

Morishita Index Plot

Compute Images of Constructed Covariates

Convert Point Pattern to Another Unit of Length

Pair Correlation Function

New Zealand Trees Point Pattern

Ponderosa Pine Tree Point Pattern

Nearest neighbour distances in three dimensions

Multitype pair correlation function (cross-type)

plot a Spatial Point Pattern

Nearest Neighbours in Any Dimensions

Convert Spatial Object to Pixel Image

Plot a tessellation

Theoretical Distribution of Nearest Neighbour Distance

Pair Correlation Function of Point Pattern

Morphological Opening

Pairwise Distances in Any Dimensions

Plot a three-dimensional point pattern

Pair Correlation Function obtained from array of K functions

Quadrature Scheme Based on Pixel Grid

Perfect Simulation of the Strauss Process

rescue.rectangle

Convert Window Back To Rectangle

Simulate Thomas Process

Plot a Pixel Image

Print Brief Details of an Image

Rotate a Point Pattern

Fit Point Process Model to Data

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Random Perturbation of a Point Pattern

Cut margins from rectangle

Rotate a Window

Vertices of a Window

Apply Vector Translation To Point Pattern

Update a Fitted Point Process Model

Class of Fitted Point Process Models

Simulate systematic random point pattern

Class of Line Segment Patterns

Generate Poisson Random Line Process

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Distance Between Two Point Patterns

Plot a List of Things

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

Prediction from a Fitted Point Process Model

Simulate Neyman-Scott Process

Simulate Baddeley-Silverman Cell Process

Convert Line Segment Pattern to Pixel Image

Convert Window to Another Unit of Length

Mosaic Random Field

Print a Fitted Point Process Model

pppmatching.object

Class of Point Matchings

Generate Poisson Point Pattern in Three Dimensions

Plot a plotppm Object Created by plot.ppm

California Redwoods Point Pattern (Ripley's Subset)

Sample Quantiles of Pixel Image

Convert Pixel Image to Another Unit of Length

Apply Vector Translation To Pixel Image

project2segment

Move Point To Nearest Line

Apply Vector Translation To Line Segment Pattern

Nearest Neighbour Clutter Removal

Read Point Pattern From Data File

pairdist.default

Pairwise distances

Pairwise distances in Three Dimensions

Random Thinning

Apply Vector Translation

Pairwise distances between line segments

Spruces Point Pattern

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Define Point Process Model for Metropolis-Hastings Simulation.

Cartesian Coordinates for a Pixel Raster

Galaxies in the Shapley Supercluster

Generate N Uniform Random Points in a Disc

multiplicity.ppp

Count Multiplicity of Duplicate Points

Methods for Multidimensional Space-Time Point Patterns

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Nearest Neighbours Between Two Patterns

plot.bermantest

Plot Result of Berman Test

Three Dimensional Point Pattern

Point Patterns of New Brunswick Forest Fires

Midpoints of Line Segment Pattern

Place Points Evenly Along Specified Lines

Multitype pair correlation function (i-to-any)

Create a Line Segment Pattern

plot a Spatial Quadrature Scheme

Plot a List of Point Patterns

Print a Quadrature Scheme

Generate Poisson Point Pattern on Line Segments

Interaction Distance of a Point Process

Nearest neighbour distances

Nearest neighbour

Generate Poisson Point Pattern in Any Dimensions

Pairwise distances

Generate N Uniform Random Points in Three Dimensions

Summary of a List of Things

Plot a fitted cluster point process

Q-Q Plot of Residuals from Fitted Point Process Model

Simulate from a Fitted Point Process Model

Set Control Parameters for Metropolis-Hastings Algorithm.

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

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

Estimate the empty space function F

Evaluate an Expression in a Function Table

Simulate Matern Model II

Find Line Segment Nearest to Each Point

California Redwoods Point Pattern (Entire Dataset)

rshift.splitppp

Randomly Shift a List of Point Patterns

Convert Line Segment Pattern to Another Unit of Length

Inhomogeneous Pair Correlation Function

pairwise.family

Pairwise Interaction Process Family

Weighted Histogram

Generic Pairwise Interaction model

Perimeter Length of Window

Bronze gradient filter data

Biological Cells Point Pattern

Marked Nearest Neighbour Distance Function

Randomly Shift a Point Pattern

plot.hyperframe

Plot Entries in a Hyperframe

Print Brief Details of a Point Pattern Dataset

Convert Data to Hyperframe

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Centroid of a window

Estimate window from points alone

Marked J Function

Distance to Boundary of Window

Rotate a Line Segment Pattern

Foxall's Distance Functions

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Multitype K Function (i-to-any)

Diggle-Gratton model

Inhomogeneous Cross Type L Function

Distance to Boundary of Window

Extract Subset of Function Values

Multitype J Function (i-to-j)

Beadlet Anemones Data

Apply Affine Transformation To Window

Convert to Pixel Image

ANOVA for Fitted Point Process Models

Combine Function Value Tables

Kernel Smoothing of Line Segment Pattern

Inhomogeneous Cross K Function

Extract Subset of Function Array

Extract or Replace Subset of a List of Things

Distance Map of Window

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

The Soft Core Point Process Model

Geometrical Calculations for Three-Dimensional Box

Reduced Second Moment Measure

Estimate the J-function

Convert Data to Three-Dimensional Box

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

Difference of Disc Areas

spatstat-deprecated

Deprecated spatstat functions

Apply Affine Transformation To Point Pattern

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Spherical Contact Distribution Function

Marked K-Function

Compute Quadrature Weights Based on Grid Counts

Convert Data To Class psp

Test Whether An Object Is Empty

Pairwise distances between two different line segment patterns

Reset Values in Subset of Image

Corners of a rectangle

Inhomogeneous K-function

Diagnostic Plots for Fitted Point Process Model

Kolmogorov-Smirnov Test for Point Process Model

Diameter of an Object

Multitype K Function (Cross-type)

The Hard Core Point Process Model

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Infinite Straight Lines

Safely Convert Point Pattern Window to Binary Mask

Rectangular grid of points

Convert Pixel Image from Numeric to Factor

Interactively Define a Polygon

Combine Two Line Segment Patterns

Extract or Replace Subset of Tessellation

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Subset of Quadrature Scheme

Three-Dimensional Box

Area of Part of Disc

Integral of a Pixel Image

Berman's Tests for Point Process Model

Level Set of a Pixel Image

Convert Pixel Image to Matrix

Artificial Data Point Pattern

Point and Click Interface for Exploratory Analysis of Point Pattern

Mark Connection Function

Test Whether An Object Is A Fitted Point Process Model

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Area of a Window

Apply Gaussian Blur to a Pixel Image

Convex Hull of Points

Extract Subset of Line Segment Pattern

Multitype L-function (i-to-any)

Test Whether A Point Process Model is Marked

The Strauss / Hard Core Point Process Model

Test Whether An Object Is A Pixel Image

Distance Map of Line Segment Pattern

Border Region of a Window

Diameter of a Window

The Fiksel Interaction

Neighbourhood density function

Extract Dummy Points Used to Fit a Point Process Model

Aherne's hamster tumour data

Fit the Matern Cluster Point Process by Minimum Contrast

Test Whether An Object Is A Point Pattern

Simulation Envelopes of Summary Function

Hybrid Geyer Point Process Model

Apply Affine Transformation To Line Segment Pattern

Update a Fitted Cluster Point Process Model

Generate N Uniform Random Points in Any Dimensions

Simulate Matern Model I

Fitted Conditional Intensity for Point Process Model

Test whether Object is Multitype

Humberside Data on Childhood Leukaemia and Lymphoma

Name for Unit of Length

Residuals for Fitted Point Process Model

Convert Data To Class owin

Estimate the I-function

Data Frames of Function Values

Contour plot of pixel image

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

The Multitype Strauss Point Process Model

Test Whether A Point Pattern is Marked

Generic Ord Interaction model

Ord's Interaction model

Quadrat counting for a point pattern

Intersection of Two Tessellations

Point and Click Interface for Displaying a Point Pattern

Class of Point Patterns

Lansing Woods Point Pattern

Determine Whether One Window is Contained In Another

Fit the Thomas Point Process by Minimum Contrast

Nearest Neighbour Distance Function G

Interpolate a Pixel Image

Apply Function to Image Broken Down by Factor

Inhomogeneous Multitype L Dot Function

Intersect Infinite Straight Lines with a Window

Tropical rain forest trees

Methods for three-dimensional point patterns

summary.splitppp

Summary of a Split Point Pattern

Distance Map of Point Pattern

Saturated Pairwise Interaction model

Pairwise distances between two different point patterns

Distance Map as a Function

Coefficients of Fitted Point Process Model

Geometrical Calculations for Multi-Dimensional Box

Determine Duplicated Points in a Spatial Point Pattern

Weighted Empirical Cumulative Distribution Function

Distance to Boundary of Window

Kaplan-Meier Estimator using Histogram Data

Summary of a Spatial Window

Simulate Stratified Random Point Pattern

Interactively Add Points

Approximate a Polygon by a Simpler Polygon

Union of Data and Dummy Points

inforder.family

Infinite Order Interaction Family

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

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

The Area Interaction Point Process Model

Set Covariance of a Window

Convert a Window to a Polygonal Window

Apply Vector Translation To Window

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Class of Quadrature Schemes

Extract Original Data from a Fitted Point Process Model

Pairwise distances between two different three-dimensional point patterns

Hutchings' Bramble Canes data

Apply Affine Transformation

Superimpose Several Point Patterns

Expand Window By Factor

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Circular Window

Create a Point Matching

Summary of a Point Pattern Dataset

Divide Point Pattern into Sub-patterns

Geyer's Saturation Point Process Model

Morphological Dilation

Volume of an Object

Spatial smoothing of observations at irregular points

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Identify Points in a Point Pattern

Urkiola Woods Point Pattern

Kernel Smoothed Intensity of Point Pattern

K-function of a Three-Dimensional Point Pattern

Find Largest Circle Inside Window

Orientation Angles of Line Segments

plot a Fitted Point Process Model

Hughes' Amacrine Cell Data

Delaunay Triangulation of Point Pattern

The Strauss Point Process Model

Extract or Replace Subset of Point Pattern

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

Mark Correlation Function

Lengths of Line Segments

Compute Integral of Function Against Cumulative Distribution

Test Whether An Object Is A Window

Divide Image Into Sub-images

Areas of Morphological Dilations

Calculate four standard summary functions of a point pattern.

Longleaf Pines Point Pattern

Print Brief Details of a Spatial Window

Reduced Sample Estimator using Histogram Data

Generate N Uniform Random Points

Apply a Function to a Point Pattern Broken Down by Factor

Generate grid of parallel lines with random displacement

Berman-Huntington points and lines data

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

Simulate a Fitted Gibbs Point Process Model

Subdivide a Window or Tessellation using a Set of Lines

Generate N Random Multitype Points

Simulation Envelopes of Summary Function for 3D Point Pattern

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Beta Ganglion Cells in Cat Retina, Old Version

quadratresample

Resample a Point Pattern by Resampling Quadrats

Areas of Morphological Erosions

Convert Data To Tessellation

Poisson Line Tessellation

Multitype L-function (cross-type)

Create a Pixel Image Object

Classify Points in a Point Pattern

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Multi-Dimensional Box

Connected components of an image or window

Empty Space Function of a Three-Dimensional Point Pattern

Test Whether a Window is Convex

plot a Spatial Line Segment Pattern

Class of Images

Exponential Energy Marks

Pine saplings in Finland.

Test Whether Two Function Objects Are Compatible

Summarise Marks in Every Neighbourhood in a Point Pattern

Intersection, Union or Set Subtraction of Two Windows

Beta Ganglion Cells in Cat Retina

Bounding Box of a Window or Point Pattern

Function Arrays for Spatial Patterns

Simulate Matern Cluster Process

Crossing Points of Two Line Segment Patterns

Generate Multitype Poisson Point Pattern

Convert Line Segment Pattern to Binary Pixel Mask

complement.owin

Take Complement of a Window

Print Brief Details of a Line Segment Pattern Dataset

Convert Data To Class ppp

Morphological Closing

Kaplan-Meier and Reduced Sample Estimator using Histograms

Test Whether Points Are Inside A Window

Multitype J Function (i-to-any)

The Piecewise Constant Pairwise Interaction Point Process Model

Number of Points in a Point Pattern

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Extract Subset of Image

Distance for a Point Pattern Matching

Plot a Function Array

Generate a Default Pattern of Dummy Points

Summarizing a Pixel Image

Marks of a Point Pattern

Methods for Multi-Dimensional Box

Inhomogeneous Multitype K Dot Function

The Lennard-Jones Potential

Create a Function Value Table

Log Likelihood for Poisson Point Process Model

Diggle's Heather Data

Evaluate Expression Involving Pixel Images

Chorley-Ribble Cancer Data

Variance-Covariance Matrix for a Fitted Point Process Model

Evaluate Expression Involving Function Arrays

Diagnostics for random marking

Clark and Evans Aggregation Index

Window in Shape of Letter R

crossdist.default

Pairwise distances between two different sets of points

Evaluate Expression Involving Functions

Basis for Harmonic Functions

Simulate a Fitted Cluster Point Process Model

Extract the Interaction from a Fitted Point Process Model

Random Re-Labelling of Point Pattern

Randomly Shift a Line Segment Pattern

Extract.splitppp

Extract or Replace Sub-Patterns

Fit cluster point process model

Apply Smoothing to Function Values

Fry Plot of Point Pattern

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Summary of a Line Segment Pattern Dataset

Prediction from a Fitted Cluster Point Process Model

Test Whether Marks Are Present

Pixel Image Approximation of a Window

Nearest neighbours in three dimensions

Dirichlet Tessellation of Point Pattern

Collapse Several Function Tables into One

spatstat-internal

Internal spatstat functions

as.data.frame.im

Convert Pixel Image to Data Frame

Multidimensional Space-Time Point Pattern

K-function using FFT

Simulated Point Pattern

bounding.box.xy

Convex Hull of Points

Poisson Point Process Model

Concatenate x,y Coordinate Vectors

Convert Point Pattern to Pixel Image

spatstat-package

The Spatstat Package

spatstat.options

Internal Options in Spatstat Package

Harkness-Isham ants' nests data

Spokes pattern of dummy points

Histogram of Pixel Values in an Image

Test Whether Two Pixel Images Are Compatible

Difference of Disc Areas

Plot a Spatial Kolmogorov-Smirnov Test

Print News About Latest Version of Package

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Colour Lookup Tables

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

Define Point Process Model for Metropolis-Hastings Simulation.

Pairwise distances

Extract Unique Points from a Spatial Point Pattern

Convert Polygonal Region into Different Format

Convert dataset to another unit of length

Simulate point patterns using the Metropolis-Hastings algorithm.

Mark Correlation Integral

Japanese Pines Point Pattern

Simulate Gauss-Poisson Process

Create a Tessellation

Lurking variable plot

Hyper Data Frame

Extract List of Tiles in a Tessellation

Print Progress Reports

Morphological Erosion

Endpoints of Line Segment Pattern

Convert Window to Pixel Image

Apply Function to Every Neighbourhood in a Point Pattern

Swedish Pines Point Pattern

Summarizing a Quadrature Scheme

Superimpose Several Line Segment Patterns

Generate Poisson Point Pattern

Sufficient Statistic of Point Process Model

Summarizing a Fitted Point Process Model

Profile Maximum Pseudolikelihood