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spatstat (version 1.18-4)

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

16,015

Version

1.18-4

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

May 2nd, 2010

Functions in spatstat (1.18-4)

Hybrid Geyer Point Process Model

Apply Affine Transformation To Point Pattern

Inhomogeneous Multitype L Dot Function

Multitype L-function (i-to-any)

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

The Area Interaction Point Process Model

Convert to Pixel Image

Border Region of a Window

Subdivide a Window or Tessellation using a Set of Lines

Geometrical Calculations for Multi-Dimensional Box

Distance to Boundary of Window

Marked J Function

Diggle-Gratton model

Simulation Envelopes of Summary Function for 3D Point Pattern

Convert a Window to a Polygonal Window

Multi-Dimensional Box

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

K-function using FFT

Poisson Point Process Model

Extract Original Data from a Fitted Point Process Model

Extract the Interaction from a Fitted Point Process Model

Distance Map as a Function

The Strauss Point Process Model

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Morphological Erosion

Orientation Angles of Line Segments

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Lengths of Line Segments

Methods for Multidimensional Space-Time Point Patterns

Apply Function to Every Neighbourhood in a Point Pattern

Fitted Conditional Intensity for Point Process Model

Nearest Neighbours in Any Dimensions

Fry Plot of Point Pattern

Difference of Disc Areas

Geyer's Saturation Point Process Model

as.data.frame.im

Convert Pixel Image to Data Frame

Convert Data To Class owin

Combine Function Value Tables

Hutchings' Bramble Canes data

Test Whether Two Function Objects Are Compatible

Pine saplings in Finland.

Artificial Data Point Pattern

Plot a List of Things

complement.owin

Take Complement of a Window

Pairwise distances between two different point patterns

Convert Polygonal Region into Different Format

ANOVA for Fitted Point Process Models

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Pairwise distances in Three Dimensions

Humberside Data on Childhood Leukaemia and Lymphoma

Foxall's Distance Functions

Extract Subset of Function Values

Plot a Spatial Kolmogorov-Smirnov Test

Endpoints of Line Segment Pattern

The Soft Core Point Process Model

Extract or Replace Subset of a List of Things

Convert Spatial Object to Pixel Image

Find Largest Circle Inside Window

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

Convert Data to Hyperframe

Compute Quadrature Weights Based on Grid Counts

Place Points Evenly Along Specified Lines

Generic Ord Interaction model

Convert Pixel Image to Matrix

Apply Affine Transformation To Line Segment Pattern

Mark Correlation Integral

Apply Function to Image Broken Down by Factor

Areas of Morphological Dilations

Area of Part of Disc

Harkness-Isham ants' nests data

Interaction Distance of a Point Process

Pixel Image Approximation of a Window

Coefficients of Fitted Point Process Model

Simulate point patterns using the Metropolis-Hastings algorithm.

Compute Integral of Function Against Cumulative Distribution

Nearest Neighbour Clutter Removal

Connected components of an image or window

Weighted Histogram

Nearest neighbours in three dimensions

Hyper Data Frame

Pair Correlation Function

Evaluate Expression Involving Functions

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Distance Map of Point Pattern

Intersection, Union or Set Subtraction of Two Windows

Integral of a Pixel Image

Perimeter Length of Window

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

is.multitype.ppm

Test Whether A Point Process Model is Multitype

The Piecewise Constant Pairwise Interaction Point Process Model

Spokes pattern of dummy points

plot a Spatial Point Pattern

Methods for Multi-Dimensional Box

Kolmogorov-Smirnov Test for Point Process Model

Convert Data To Class ppp

Combine Two Line Segment Patterns

Dirichlet Tessellation of Point Pattern

Multitype J Function (i-to-any)

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Longleaf Pines Point Pattern

Extract Subset of Line Segment Pattern

Hughes' Amacrine Cell Data

Inhomogeneous Cross Type L Function

Beadlet Anemones Data

Plot a three-dimensional point pattern

California Redwoods Point Pattern (Entire Dataset)

Chorley-Ribble Cancer Data

Fit the Thomas Point Process by Minimum Contrast

Find Line Segment Nearest to Each Point

Marked Nearest Neighbour Distance Function

Interactively Add Points

Saturated Pairwise Interaction Point Process Family

Multitype J Function (i-to-j)

Ord Interaction Process Family

Distance Map of Line Segment Pattern

K-function of a Three-Dimensional Point Pattern

Distance Between Two Point Patterns

Determine Duplicated Points in a Spatial Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

Basis for Harmonic Functions

Function Arrays for Spatial Patterns

Method of Minimum Contrast

Create a Pixel Image Object

Reset Values in Subset of Image

Simulate Baddeley-Silverman Cell Process

Print a Fitted Point Process Model

Distance to Boundary of Window

Apply Affine Transformation To Window

Convert Data To Tessellation

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Profile Maximum Pseudolikelihood

Generic Pairwise Interaction model

Convex Hull of Points

Plot a Colour Map

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Biological Cells Point Pattern

Print a Quadrature Scheme

Pairwise distances between line segments

Empty Space Function of a Three-Dimensional Point Pattern

Class of Line Segment Patterns

Convert Line Segment Pattern to Binary Pixel Mask

Simulate Simple Sequential Inhibition

Estimate the empty space function F

Centroid of a window

Morphological Closing

plot a Fitted Point Process Model

Extract or Replace Subset of Tessellation

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Generate Poisson Point Pattern

Random Thinning

Fit Point Process Model to Data

crossdist.default

Pairwise distances between two different sets of points

Perspective Plot of Pixel Image

Estimate the I-function

Summarise Marks in Every Neighbourhood in a Point Pattern

Corners of a rectangle

Nearest neighbour distances in three dimensions

Diameter of a Window

Diagnostic Plots for Fitted Point Process Model

Kernel Smoothing of Line Segment Pattern

Simulate Thomas Process

Delaunay Triangulation of Point Pattern

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Extract Subset of Image

Plot a Spatial Window

pairwise.family

Pairwise Interaction Process Family

Beta Ganglion Cells in Cat Retina

model.matrix.ppm

Extract Design Matrix from Point Process Model

Convert Window to Another Unit of Length

Interpret Fitted Model for Metropolis-Hastings Simulation.

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

Generate a Default Pattern of Dummy Points

Randomly Shift a Line Segment Pattern

Residuals for Fitted Point Process Model

Classify Points in a Point Pattern

Make Periodic Copies of a Spatial Pattern

Random Perturbation of a Point Pattern

Aherne's hamster tumour data

Set Covariance of a Window

Extract Subset of Function Array

Berman's Tests for Point Process Model

Pair Correlation Function obtained from K Function

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

spatstat-package

The Spatstat Package

Summarizing a Fitted Point Process Model

Mark Connection Function

Print Brief Details of an Image

Extract.splitppp

Extract or Replace Sub-Patterns

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Crossing Points of Two Line Segment Patterns

Divide Image Into Sub-images

The Multitype Strauss Point Process Model

Circular Window

Plot a tessellation

Convert Pixel Image from Numeric to Factor

Nearest neighbour

Mosaic Random Field

Evaluate Expression Involving Pixel Images

Geometrical Calculations for Three-Dimensional Box

Bounding Box of a Window or Point Pattern

Distance Map of Window

Distance to Boundary of Window

Name for Unit of Length

Ord's Interaction model

Evaluate Expression Involving Function Arrays

Test Whether A Point Pattern is Marked

Create a Tessellation

Prediction from a Fitted Cluster Point Process Model

Inhomogeneous Cross K Function

project2segment

Move Point To Nearest Line

Convert Data To Class psp

Inhomogeneous K-function

Nearest Neighbour Distance Function G

Plot a fitted cluster point process

Plot a plotppm Object Created by plot.ppm

Interactively Define a Polygon

Ponderosa Pine Tree Point Pattern

Kaplan-Meier and Reduced Sample Estimator using Histograms

Update a Fitted Cluster Point Process Model

Print News About Latest Version of Package

Collapse Several Function Tables into One

Urkiola Woods Point Pattern

Concatenate x,y Coordinate Vectors

Class of Images

plot a Spatial Line Segment Pattern

Update a Fitted Point Process Model

Test Whether An Object Is A Window

Class of Fitted Point Process Models

Simulation Envelopes of Summary Function

Quadrat counting for a point pattern

Set Control Parameters for Metropolis-Hastings Algorithm.

Reduced Second Moment Measure

Marked K-Function

Determine Whether One Window is Contained In Another

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

Apply Smoothing to Function Values

Calculate four standard summary functions of a point pattern.

Sample Quantiles of Pixel Image

Rotate a Window

Clark and Evans Aggregation Index

Methods for three-dimensional point patterns

Window in Shape of Letter R

Generate N Random Multitype Points

Simulate from a Fitted Point Process Model

Diagnostics for random marking

Simulate systematic random point pattern

Point and Click Interface for Exploratory Analysis of Point Pattern

Weighted Empirical Cumulative Distribution Function

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Area of a Window

Multidimensional Space-Time Point Pattern

pppmatching.object

Class of Point Matchings

plot a Spatial Quadrature Scheme

Test Whether A Point Process Model is Marked

nearest.raster.point

Find Pixel Nearest to a Given Point

Nearest Neighbours Between Two Patterns

Apply Affine Transformation

Read Point Pattern From Data File

Estimate the J-function

Union of Data and Dummy Points

Approximate a Polygon by a Simpler Polygon

Difference of Disc Areas

pairdist.default

Pairwise distances

Rotate a Point Pattern

Inhomogeneous Multitype K Dot Function

Data Frames of Function Values

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Print Brief Details of a Point Pattern Dataset

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Distance for a Point Pattern Matching

Bronze gradient filter data

Multitype K Function (Cross-type)

Subset of Quadrature Scheme

Diggle's Heather Data

bounding.box.xy

Convex Hull of Points

Multitype K Function (i-to-any)

Create a Point Matching

Colour Lookup Tables

Expand Window By Factor

Prediction from a Fitted Point Process Model

Generate grid of parallel lines with random displacement

Pairwise distances

Simulate a Fitted Cluster Point Process Model

Random Re-Labelling of Point Pattern

Multitype L-function (cross-type)

Generate Multitype Poisson Point Pattern

Generate Poisson Point Pattern in Any Dimensions

Apply Gaussian Blur to a Pixel Image

Pairwise Distances in Any Dimensions

Generate N Uniform Random Points in Three Dimensions

Determine Initial State for Metropolis-Hastings Simulation.

Generate N Uniform Random Points

Summarizing a Pixel Image

Create a Function Value Table

Class of Quadrature Schemes

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Simulate Matern Model II

The Strauss / Hard Core Point Process Model

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Plot a List of Point Patterns

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Infinite Straight Lines

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Murchison gold deposits

Neighbourhood density function

Nearest neighbour distances between line segments

Extract Unique Points from a Spatial Point Pattern

Apply a Function to a Point Pattern Broken Down by Factor

Intersect Infinite Straight Lines with a Window

The Lennard-Jones Potential

Kaplan-Meier Estimator using Histogram Data

Lansing Woods Point Pattern

Apply Vector Translation

Apply Vector Translation To Window

Lurking variable plot

Pairwise distances

Summary of a Point Pattern Dataset

Test Whether Two Pixel Images Are Compatible

rshift.splitppp

Randomly Shift a List of Point Patterns

Pairwise distances between two different three-dimensional point patterns

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

Convert Data to Three-Dimensional Box

New Zealand Trees Point Pattern

Three-Dimensional Box

Convert Line Segment Pattern to Another Unit of Length

Spruces Point Pattern

plot.bermantest

Plot Result of Berman Test

Pairwise distances between two different line segment patterns

Extract or Replace Subset of Point Pattern

Convert Point Pattern to Pixel Image

Divide Region into Quadrats

Mark Correlation Function

Data and Code From JRSS Discussion Paper on Residuals

Superimpose Several Line Segment Patterns

Kernel Smoothed Intensity of Point Pattern

Extract List of Tiles in a Tessellation

Morishita Index Plot

Berman-Huntington points and lines data

Summary of a Spatial Window

Marks of a Point Pattern

Safely Convert Point Pattern Window to Binary Mask

Tropical rain forest trees

Swedish Pines Point Pattern

Perfect Simulation of the Strauss Process

Q-Q Plot of Residuals from Fitted Point Process Model

California Redwoods Point Pattern (Ripley's Subset)

Superimpose Several Point Patterns

Spatial smoothing of observations at irregular points

Generate N Uniform Random Points in a Disc

Exponential Energy Marks

Extract Dummy Points Used to Fit a Point Process Model

Number of Points in a Point Pattern

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

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Diameter of an Object

Test Whether Points Are Inside A Window

Areas of Morphological Erosions

Beta Ganglion Cells in Cat Retina, Old Version

Spherical Contact Distribution Function

Define Point Process Model for Metropolis-Hastings Simulation.

Inhomogeneous Pair Correlation Function

spatstat-internal

Internal spatstat functions

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Plot a Function Array

Print Progress Reports

Simulate Matern Model I

Variance-Covariance Matrix for a Fitted Point Process Model

Simulate Gauss-Poisson Process

Simulated Point Pattern

Convert Line Segment Pattern to Pixel Image

Test Whether An Object Is Empty

Histogram of Pixel Values in an Image

Test whether Object is Multitype

The Hard Core Point Process Model

Identify Points in a Point Pattern

inforder.family

Infinite Order Interaction Family

Test Whether An Object Is A Fitted Point Process Model

Point and Click Interface for Displaying a Point Pattern

Convert Window to Pixel Image

Apply Vector Translation To Pixel Image

Galaxies in the Shapley Supercluster

Test Whether a Window is Convex

Methods for Three-Dimensional Box

Log Likelihood for Poisson Point Process Model

Convert Pixel Image to Another Unit of Length

Saturated Pairwise Interaction model

Apply Vector Translation To Line Segment Pattern

Class of Point Patterns

Contour plot of pixel image

spatstat.options

Internal Options in Spatstat Package

Summary of a List of Things

Create a Line Segment Pattern

Apply Vector Translation To Point Pattern

Test Whether Marks Are Present

Create a Window

Midpoints of Line Segment Pattern

Japanese Pines Point Pattern

Nearest neighbour distances

Compute Images of Constructed Covariates

Evaluate an Expression in a Function Table

spatstat-deprecated

Deprecated spatstat functions

Define Point Process Model for Metropolis-Hastings Simulation.

Morphological Dilation

Test Whether An Object Is A Pixel Image

plot.hyperframe

Plot Entries in a Hyperframe

Simulate a Fitted Gibbs Point Process Model

Level Set of a Pixel Image

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Simulate Neyman-Scott Process

multiplicity.ppp

Count Multiplicity of Duplicate Points

Pair Correlation Function obtained from array of K functions

Convert Point Pattern to Another Unit of Length

Print Brief Details of a Spatial Window

Rectangular grid of points

Simulate Matern Cluster Process

Pairwise distances

rescue.rectangle

Convert Window Back To Rectangle

Divide Point Pattern into Sub-patterns

Plot Function Values

Cartesian Coordinates for a Pixel Raster

Pair Correlation Function of Point Pattern

Interpolate a Pixel Image

Quadrature Scheme Based on Pixel Grid

Summarizing a Quadrature Scheme

Nearest Neighbour Distances in Any Dimensions

Theoretical Distribution of Nearest Neighbour Distance

Intersection of Two Tessellations

Summary of a Line Segment Pattern Dataset

Test Whether An Object Is A Point Pattern

Multitype pair correlation function (i-to-any)

Multitype pair correlation function (cross-type)

Volume of an Object

quadratresample

Resample a Point Pattern by Resampling Quadrats

Randomly Shift a Point Pattern

Fit cluster point process model

Mosaic Random Set

Three Dimensional Point Pattern

Print Brief Details of a Line Segment Pattern Dataset

Create a Point Pattern

Point Patterns of New Brunswick Forest Fires

Generate N Uniform Random Points in Any Dimensions

Convert dataset to another unit of length

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

Morphological Opening

Estimate window from points alone

Plot a Pixel Image

Generate N Random Points

summary.splitppp

Summary of a Split Point Pattern

Extract Quadrature Scheme Used to Fit a Point Process Model

Rotate a Line Segment Pattern

Generate a Quadrature Scheme from a Point Pattern

Generate Poisson Point Pattern in Three Dimensions

Simulate Stratified Random Point Pattern

Poisson Line Tessellation

Reduced Sample Estimator using Histogram Data

Generate Poisson Random Line Process

Vertices of a Window

Generate Poisson Point Pattern on Line Segments

Sufficient Statistic of Point Process Model

Cut margins from rectangle