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spatstat (version 1.18-0)

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. 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

1.18-0

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

March 10th, 2010

Functions in spatstat (1.18-0)

Multitype J Function (i-to-any)

Hybrid Geyer Point Process Model

Estimate the I-function

Marked K-Function

Extract Subset of Image

Extract or Replace Subset of a List of Things

The Lennard-Jones Potential

Subset of Quadrature Scheme

Geyer's Saturation Point Process Model

Inhomogeneous Multitype L Dot Function

Extract Subset of Function Values

Estimate the empty space function F

Multitype K Function (Cross-type)

Extract or Replace Subset of Point Pattern

Extract Subset of Function Array

Multitype J Function (i-to-j)

Convert a Window to a Polygonal Window

Reset Values in Subset of Image

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

Extract.splitppp

Extract or Replace Sub-Patterns

ANOVA for Fitted Point Process Models

Convert Data To Class owin

Marked J Function

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

Extract or Replace Subset of Tessellation

Inhomogeneous Multitype K Dot Function

Difference of Disc Areas

Function Arrays for Spatial Patterns

Inhomogeneous Cross K Function

Apply Affine Transformation To Line Segment Pattern

Ord's Interaction model

Inhomogeneous Cross Type L Function

Saturated Pairwise Interaction model

Apply Affine Transformation To Window

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

The Soft Core Point Process Model

Tropical rain forest trees

Apply a Function to a Point Pattern Broken Down by Factor

Difference of Disc Areas

Inhomogeneous K-function

The Piecewise Constant Pairwise Interaction Point Process Model

Diggle-Gratton model

Determine Duplicated Points in a Spatial Point Pattern

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Test Whether A Point Process Model is Marked

as.data.frame.im

Convert Pixel Image to Data Frame

Test Whether Points Are Inside A Window

Apply Function to Image Broken Down by Factor

Generic Ord Interaction model

Beta Ganglion Cells in Cat Retina, Old Version

Calculate four standard summary functions of a point pattern.

Extract the Interaction from a Fitted Point Process Model

Convert Data To Class psp

Morphological Erosion

Nearest neighbour

Convert Data to Hyperframe

Area of Part of Disc

Convert Line Segment Pattern to Binary Pixel Mask

Pairwise distances between two different line segment patterns

Harkness-Isham ants' nests data

Convert to Pixel Image

Japanese Pines Point Pattern

The Strauss Point Process Model

Pairwise distances

Beta Ganglion Cells in Cat Retina

Area of a Window

Create a Pixel Image Object

Apply Affine Transformation To Point Pattern

Coefficients of Fitted Point Process Model

Intersect Infinite Straight Lines with a Window

Intersection of Two Tessellations

The Area Interaction Point Process Model

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Distance Map as a Function

Combine Two Line Segment Patterns

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Bounding Box of a Window or Point Pattern

Beadlet Anemones Data

Multitype L-function (cross-type)

Estimate the J-function

Poisson Point Process Model

Generic Pairwise Interaction model

Spherical Contact Distribution Function

Concatenate x,y Coordinate Vectors

Distance Map of Line Segment Pattern

Circular Window

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

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

Point and Click Interface for Exploratory Analysis of Point Pattern

The Strauss / Hard Core Point Process Model

Border Region of a Window

Rectangular grid of points

Distance to Boundary of Window

Pine saplings in Finland.

Pair Correlation Function obtained from array of K functions

bounding.box.xy

Convex Hull of Points

Three-Dimensional Box

Class of Point Patterns

Interactively Add Points

Log Likelihood for Poisson Point Process Model

Pairwise distances between two different three-dimensional point patterns

Fit Point Process Model to Data

Longleaf Pines Point Pattern

Areas of Morphological Erosions

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Evaluate Expression Involving Functions

Interaction Distance of a Point Process

Clark and Evans Aggregation Index

Place Points Evenly Along Specified Lines

Identify Points in a Point Pattern

Convert Polygonal Region into Different Format

Mark Correlation Function

Evaluate Expression Involving Pixel Images

Evaluate Expression Involving Function Arrays

Plot a Function Array

Diagnostic Plots for Fitted Point Process Model

Kernel Smoothing of Line Segment Pattern

Simulation envelopes of summary function

Exponential Energy Marks

Convert Pixel Image to Matrix

Crossing Points of Two Line Segment Patterns

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Geometrical Calculations for Three-Dimensional Box

Point and Click Interface for Displaying a Point Pattern

Morphological Closing

Divide Region into Quadrats

Distance for a Point Pattern Matching

Multidimensional Space-Time Point Pattern

Test Whether A Point Pattern is Marked

Basis for Harmonic Functions

Fry Plot of Point Pattern

Integral of a Pixel Image

Methods for three-dimensional point patterns

Nearest Neighbours Between Two Patterns

Artificial Data Point Pattern

Mark Connection Function

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Generate Multitype Poisson Point Pattern

Fitted Conditional Intensity for Point Process Model

Test Whether An Object Is A Fitted Point Process Model

Find Largest Circle Inside Window

Window in Shape of Letter R

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Areas of Morphological Dilations

Weighted Empirical Cumulative Distribution Function

Test Whether An Object Is A Point Pattern

Convert Data to Three-Dimensional Box

Fit the Matern Cluster Point Process by Minimum Contrast

Compute Images of Constructed Covariates

Make Periodic Copies of a Spatial Pattern

Generate Poisson Random Line Process

Convert Data To Class ppp

Nearest neighbour distances in three dimensions

Apply Function to Every Neighbourhood in a Point Pattern

Combine Function Value Tables

Level Set of a Pixel Image

Quadrat counting for a point pattern

Simulate Baddeley-Silverman Cell Process

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Apply Vector Translation To Pixel Image

Summary of a Line Segment Pattern Dataset

spatstat-package

The Spatstat Package

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Morishita Index Plot

Randomly Shift a Point Pattern

Berman's Tests for Point Process Model

Convex Hull of Points

Plot a List of Point Patterns

Extract Original Data from a Fitted Point Process Model

Pairwise distances

Aherne's hamster tumour data

Infinite Straight Lines

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Test Whether An Object Is Empty

Data Frames of Function Values

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Midpoints of Line Segment Pattern

Empty Space Function of a Three-Dimensional Point Pattern

Convert Line Segment Pattern to Pixel Image

Plot a Spatial Kolmogorov-Smirnov Test

plot a Spatial Quadrature Scheme

quadratresample

Resample a Point Pattern by Resampling Quadrats

Mark Correlation Integral

plot.hyperframe

Plot Entries in a Hyperframe

pairdist.default

Pairwise distances

Plot a tessellation

nearest.raster.point

Find Pixel Nearest to a Given Point

runifpointOnLines

Generate N Uniform Random Points On Line Segments

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

plot a Fitted Point Process Model

Test Whether a Window is Convex

model.matrix.ppm

Extract Design Matrix from Point Process Model

Multitype pair correlation function (i-to-any)

Nearest neighbour distances

Plot a Colour Map

Point Patterns of New Brunswick Forest Fires

Perspective Plot of Pixel Image

Biological Cells Point Pattern

Compute Quadrature Weights Based on Grid Counts

multiplicity.ppp

Count Multiplicity of Duplicate Points

Murchison gold deposits

Prediction from a Fitted Cluster Point Process Model

Plot a fitted cluster point process

Print Brief Details of a Point Pattern Dataset

Superimpose Several Point Patterns

Pair Correlation Function

Create a Line Segment Pattern

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

Create a Point Pattern

Ord Interaction Process Family

Convert Point Pattern to Another Unit of Length

Prediction from a Fitted Point Process Model

Plot Function Values

Convert Spatial Object to Pixel Image

Summarise Marks in Every Neighbourhood in a Point Pattern

Orientation Angles of Line Segments

Mosaic Random Field

Lansing Woods Point Pattern

Approximate a Polygon by a Simpler Polygon

Colour Lookup Tables

Pair Correlation Function obtained from K Function

Simulate Gauss-Poisson Process

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Class of Line Segment Patterns

Simulate point patterns using the Metropolis-Hastings algorithm.

Contour plot of pixel image

Define Point Process Model for Metropolis-Hastings Simulation.

Generate N Uniform Random Points in a Disc

Pair Correlation Function of Point Pattern

summary.splitppp

Summary of a Split Point Pattern

Class of Fitted Point Process Models

Test Whether Two Pixel Images Are Compatible

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Sample Quantiles of Pixel Image

complement.owin

Take Complement of a Window

Convert Window to Pixel Image

Simulate Stratified Random Point Pattern

Q-Q Plot of Residuals from Fitted Point Process Model

Urkiola Woods Point Pattern

Extract Dummy Points Used to Fit a Point Process Model

Hughes' Amacrine Cell Data

Set Control Parameters for Metropolis-Hastings Algorithm.

Generate N Uniform Random Points in Three Dimensions

Perfect Simulation of the Strauss Process

Create a Function Value Table

Extract Unique Points from a Spatial Point Pattern

Fit the Thomas Point Process by Minimum Contrast

Distance to Boundary of Window

Morphological Dilation

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

Endpoints of Line Segment Pattern

Determine Whether One Window is Contained In Another

spatstat-internal

Internal spatstat functions

Saturated Pairwise Interaction Point Process Family

pppmatching.object

Class of Point Matchings

Convert Pixel Image to Another Unit of Length

pairwise.family

Pairwise Interaction Process Family

Three Dimensional Point Pattern

Distance Between Two Point Patterns

Diagnostics for random marking

Vertices of a Window

Set Covariance of a Window

Extract Quadrature Scheme Used to Fit a Point Process Model

Multitype K Function (i-to-any)

Create a Window

Update a Fitted Cluster Point Process Model

Print News About Latest Version of Package

Reduced Second Moment Measure

Rotate a Point Pattern

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Centroid of a window

Rotate a Window

Rotate a Line Segment Pattern

Generate Poisson Point Pattern in Three Dimensions

Nearest Neighbour Clutter Removal

rescue.rectangle

Convert Window Back To Rectangle

Random Re-Labelling of Point Pattern

Multitype pair correlation function (cross-type)

spatstat.options

Internal Options in Spatstat Package

Residuals for Fitted Point Process Model

Simulate a Fitted Gibbs Point Process Model

Spatial smoothing of observations at irregular points

Cartesian Coordinates for a Pixel Raster

Plot a plotppm Object Created by plot.ppm

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Sufficient Statistic of Point Process Model

Find Line Segment Nearest to Each Point

California Redwoods Point Pattern (Ripley's Subset)

Compute Integral of Function Against Cumulative Distribution

Perimeter Length of Window

Print Brief Details of a Line Segment Pattern Dataset

Poisson Line Tessellation

crossdist.default

Pairwise distances between two different sets of points

Print a Fitted Point Process Model

Simulate Matern Cluster Process

Convert dataset to another unit of length

Divide Point Pattern into Sub-patterns

Convert Point Pattern to Pixel Image

Determine Initial State for Metropolis-Hastings Simulation.

Theoretical Distribution of Nearest Neighbour Distance

Generate N Random Multitype Points

Diameter of a Window

Convert Window to Another Unit of Length

Generate grid of parallel lines with random displacement

Mean, Median and Range of Pixel Values in an Image

Simulate Matern Model I

New Zealand Trees Point Pattern

Plot a Pixel Image

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Simulate Simple Sequential Inhibition

Simulate systematic random point pattern

Generate N Random Points

Update a Fitted Point Process Model

Safely Convert Point Pattern Window to Binary Mask

Profile Maximum Pseudolikelihood

Random Thinning

Randomly Shift a Line Segment Pattern

Convert Line Segment Pattern to Another Unit of Length

Simulate from a Fitted Point Process Model

Apply Vector Translation

Summarizing a Fitted Point Process Model

Print Progress Reports

Apply Gaussian Blur to a Pixel Image

California Redwoods Point Pattern (Entire Dataset)

Summary of a List of Things

Test Whether Two Function Objects Are Compatible

Simulate Neyman-Scott Process

Pairwise distances between two different point patterns

Name for Unit of Length

Estimate window from points alone

Spruces Point Pattern

Generate Poisson Point Pattern

Delaunay Triangulation of Point Pattern

Kernel Smoothed Intensity of Point Pattern

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Extract List of Tiles in a Tessellation

Method of Minimum Contrast

Weighted Histogram

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Random Perturbation of a Point Pattern

Lurking variable plot

Simulated Point Pattern

plot a Spatial Point Pattern

Plot a three-dimensional point pattern

Kaplan-Meier Estimator using Histogram Data

Expand Window By Factor

Berman-Huntington points and lines data

Galaxies in the Shapley Supercluster

Dirichlet Tessellation of Point Pattern

Swedish Pines Point Pattern

Diggle's Heather Data

Fit cluster point process model

Class of Images

Intersection, Union or Set Subtraction of Two Windows

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Test Whether An Object Is A Pixel Image

Create a Tessellation

Connected components of an image or window

Humberside Data on Childhood Leukaemia and Lymphoma

Generate Poisson Point Pattern on Line Segments

Evaluate an Expression in a Function Table

Quadrature Scheme Based on Pixel Grid

Simulate Thomas Process

Print Brief Details of a Spatial Window

Spokes pattern of dummy points

Distance Map of Point Pattern

Pixel Image Approximation of a Window

spatstat-deprecated

Deprecated spatstat functions

Pairwise distances in Three Dimensions

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Hyper Data Frame

Distance to Boundary of Window

K-function using FFT

Test whether Object is Multitype

Classify Points in a Point Pattern

Kolmogorov-Smirnov Test for Point Process Model

Morphological Opening

Read Point Pattern From Data File

plot a Spatial Line Segment Pattern

Generate a Default Pattern of Dummy Points

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Simulate a Fitted Cluster Point Process Model

Interpret Fitted Model for Metropolis-Hastings Simulation.

Summary of a Spatial Window

Marks of a Point Pattern

Apply Vector Translation To Line Segment Pattern

Pairwise distances between line segments

Divide Image Into Sub-images

Summarizing a Pixel Image

Plot a List of Things

Plot a Spatial Window

Data and Code From JRSS Discussion Paper on Residuals

Extract Subset of Line Segment Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

Nearest Neighbour Distance Function G

Marked Nearest Neighbour Distance Function

Union of Data and Dummy Points

Interactively Define a Polygon

Generate N Uniform Random Points

Cut margins from rectangle

Ponderosa Pine Tree Point Pattern

Apply Vector Translation To Window

Summarizing a Quadrature Scheme

plot.bermantest

Plot Result of Berman Test

Chorley-Ribble Cancer Data

Print a Quadrature Scheme

Multitype L-function (i-to-any)

Apply Affine Transformation

Bronze gradient filter data

Hutchings' Bramble Canes data

Subdivide a Window or Tessellation using a Set of Lines

K-function of a Three-Dimensional Point Pattern

Convert Data To Tessellation

The Multitype Strauss Point Process Model

Corners of a rectangle

Methods for Three-Dimensional Box

Nearest neighbour distances between line segments

Nearest neighbours in three dimensions

Methods for Multidimensional Space-Time Point Patterns

Pairwise distances

Convert Pixel Image from Numeric to Factor

Distance Map of Window

Collapse Several Function Tables into One

Histogram of Pixel Values in an Image

inforder.family

Infinite Order Interaction Family

Test Whether An Object Is A Window

Class of Quadrature Schemes

Test Whether Marks Are Present

Print Brief Details of an Image

Apply Vector Translation To Point Pattern

Interpolate a Pixel Image

Kaplan-Meier and Reduced Sample Estimator using Histograms

Neighbourhood density function

Inhomogeneous Pair Correlation Function

Define Point Process Model for Metropolis-Hastings Simulation.

project2segment

Move Point To Nearest Line

Simulate Matern Model II

Mosaic Random Set

Reduced Sample Estimator using Histogram Data

Generate a Quadrature Scheme from a Point Pattern

rshift.splitppp

Randomly Shift a List of Point Patterns

Superimpose Several Line Segment Patterns

Lengths of Line Segments

Create a Point Matching

Summary of a Point Pattern Dataset