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spatstat (version 1.18-3)

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. 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

16,590

Version

1.18-3

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

April 19th, 2010

Functions in spatstat (1.18-3)

Diggle-Gratton model

Nearest Neighbour Distance Function G

The Strauss / Hard Core Point Process Model

Foxall's Distance Functions

The Soft Core Point Process Model

K-function using FFT

Hybrid Geyer Point Process Model

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

Inhomogeneous Multitype K Dot Function

Difference of Disc Areas

Extract Subset of Line Segment Pattern

Extract.splitppp

Extract or Replace Sub-Patterns

K-function of a Three-Dimensional Point Pattern

Subset of Quadrature Scheme

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Marked Nearest Neighbour Distance Function

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Apply Function to Every Neighbourhood in a Point Pattern

Multitype L-function (i-to-any)

Convert Pixel Image from Numeric to Factor

The Area Interaction Point Process Model

Chorley-Ribble Cancer Data

Morphological Closing

Generic Ord Interaction model

Saturated Pairwise Interaction model

Artificial Data Point Pattern

Diameter of a Window

Convert Data to Three-Dimensional Box

The Multitype Strauss Point Process Model

The Lennard-Jones Potential

Estimate the J-function

Extract or Replace Subset of Tessellation

Berman's Tests for Point Process Model

Classify Points in a Point Pattern

The Piecewise Constant Pairwise Interaction Point Process Model

Multitype J Function (i-to-any)

Beta Ganglion Cells in Cat Retina

Convert to Pixel Image

Test Whether Two Function Objects Are Compatible

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Apply Affine Transformation To Window

Generic Pairwise Interaction model

Convert Data To Class owin

Convert a Window to a Polygonal Window

Distance Map of Point Pattern

Combine Two Line Segment Patterns

Test Whether A Point Process Model is Marked

Border Region of a Window

Corners of a rectangle

Interactively Add Points

Hughes' Amacrine Cell Data

Colour Lookup Tables

Apply Affine Transformation To Line Segment Pattern

Coefficients of Fitted Point Process Model

Beadlet Anemones Data

Areas of Morphological Dilations

Extract Original Data from a Fitted Point Process Model

Distance to Boundary of Window

Dirichlet Tessellation of Point Pattern

ANOVA for Fitted Point Process Models

Calculate four standard summary functions of a point pattern.

Area of a Window

Convex Hull of Points

Centroid of a window

as.data.frame.im

Convert Pixel Image to Data Frame

Simulation Envelopes of Summary Function

Distance to Boundary of Window

Hyper Data Frame

Pairwise distances between two different line segment patterns

Determine Duplicated Points in a Spatial Point Pattern

Convert Pixel Image to Matrix

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Intersection of Two Tessellations

Crossing Points of Two Line Segment Patterns

Marked J Function

Bounding Box of a Window or Point Pattern

Estimate the empty space function F

Combine Function Value Tables

Expand Window By Factor

Reset Values in Subset of Image

Evaluate Expression Involving Pixel Images

Kernel Smoothing of Line Segment Pattern

Extract Subset of Function Array

Estimate the I-function

Areas of Morphological Erosions

Convert Data To Class ppp

Area of Part of Disc

Extract Subset of Function Values

Morphological Dilation

Pairwise distances between two different point patterns

Evaluate Expression Involving Function Arrays

Multitype L-function (cross-type)

Clark and Evans Aggregation Index

Extract or Replace Subset of Point Pattern

Inhomogeneous Multitype L Dot Function

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

Calculate Summary Statistic for All Types in a Multitype Point Pattern

The Hard Core Point Process Model

Inhomogeneous K-function

Multitype K Function (Cross-type)

Inhomogeneous Cross Type L Function

The Strauss Point Process Model

Geyer's Saturation Point Process Model

Biological Cells Point Pattern

Inhomogeneous Cross K Function

Apply a Function to a Point Pattern Broken Down by Factor

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

Extract Subset of Image

Circular Window

Marked K-Function

Nearest neighbour

Kernel Smoothed Intensity of Point Pattern

Lengths of Line Segments

Connected components of an image or window

Generate a Default Pattern of Dummy Points

Convert Data To Tessellation

Morphological Erosion

Extract or Replace Subset of a List of Things

Diagnostics for random marking

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Multitype J Function (i-to-j)

Pairwise distances

Endpoints of Line Segment Pattern

Pairwise distances between line segments

Create a Point Pattern

Berman-Huntington points and lines data

Fit Point Process Model to Data

Compute Quadrature Weights Based on Grid Counts

Orientation Angles of Line Segments

Spherical Contact Distribution Function

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Ord's Interaction model

Poisson Point Process Model

Class of Images

Apply Affine Transformation To Point Pattern

Pair Correlation Function obtained from array of K functions

Pairwise distances between two different three-dimensional point patterns

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

Simulation Envelopes of Summary Function for 3D Point Pattern

Multitype K Function (i-to-any)

Harkness-Isham ants' nests data

Fitted Conditional Intensity for Point Process Model

Point and Click Interface for Displaying a Point Pattern

Test Whether Two Pixel Images Are Compatible

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Apply Gaussian Blur to a Pixel Image

Data Frames of Function Values

Test Whether An Object Is Empty

Distance to Boundary of Window

Three-Dimensional Box

Intersect Infinite Straight Lines with a Window

Summarise Marks in Every Neighbourhood in a Point Pattern

Apply Affine Transformation

Convert Line Segment Pattern to Binary Pixel Mask

Empty Space Function of a Three-Dimensional Point Pattern

Test Whether Points Are Inside A Window

Collapse Several Function Tables into One

Difference of Disc Areas

crossdist.default

Pairwise distances between two different sets of points

Methods for Three-Dimensional Box

Evaluate Expression Involving Functions

Pixel Image Approximation of a Window

Diagnostic Plots for Fitted Point Process Model

model.matrix.ppm

Extract Design Matrix from Point Process Model

Convert Data To Class psp

Distance Map of Window

Tropical rain forest trees

Basis for Harmonic Functions

Test whether Object is Multitype

Convert Data to Hyperframe

Determine Whether One Window is Contained In Another

Fit the Matern Cluster Point Process by Minimum Contrast

Profile Maximum Pseudolikelihood

Test Whether An Object Is A Fitted Point Process Model

spatstat-deprecated

Deprecated spatstat functions

Concatenate x,y Coordinate Vectors

Japanese Pines Point Pattern

Interactively Define a Polygon

Prediction from a Fitted Point Process Model

Histogram of Pixel Values in an Image

Plot Function Values

Contour plot of pixel image

Test Whether A Point Pattern is Marked

Safely Convert Point Pattern Window to Binary Mask

Level Set of a Pixel Image

Hutchings' Bramble Canes data

Beta Ganglion Cells in Cat Retina, Old Version

Convert dataset to another unit of length

Print Progress Reports

Infinite Straight Lines

Bronze gradient filter data

Interpolate a Pixel Image

Midpoints of Line Segment Pattern

Test Whether Marks Are Present

Subdivide a Window or Tessellation using a Set of Lines

Pine saplings in Finland.

Simulate Gauss-Poisson Process

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Test Whether An Object Is A Pixel Image

inforder.family

Infinite Order Interaction Family

Mark Correlation Function

Method of Minimum Contrast

Set Control Parameters for Metropolis-Hastings Algorithm.

Morishita Index Plot

Diggle's Heather Data

Extract the Interaction from a Fitted Point Process Model

Apply Function to Image Broken Down by Factor

Reduced Second Moment Measure

Intersection, Union or Set Subtraction of Two Windows

Find Line Segment Nearest to Each Point

Plot a List of Point Patterns

Point and Click Interface for Exploratory Analysis of Point Pattern

complement.owin

Take Complement of a Window

Geometrical Calculations for Three-Dimensional Box

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Pair Correlation Function obtained from K Function

Distance Between Two Point Patterns

Integral of a Pixel Image

bounding.box.xy

Convex Hull of Points

Nearest neighbour distances

Delaunay Triangulation of Point Pattern

Extract Dummy Points Used to Fit a Point Process Model

Function Arrays for Spatial Patterns

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Identify Points in a Point Pattern

Generate a Quadrature Scheme from a Point Pattern

Nearest neighbours in three dimensions

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Multidimensional Space-Time Point Pattern

Humberside Data on Childhood Leukaemia and Lymphoma

Test Whether An Object Is A Window

Distance Map as a Function

Data and Code From JRSS Discussion Paper on Residuals

Ord Interaction Process Family

Marks of a Point Pattern

Exponential Energy Marks

Create a Function Value Table

Methods for three-dimensional point patterns

Create a Pixel Image Object

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Compute Images of Constructed Covariates

Plot a Pixel Image

Perimeter Length of Window

Rotate a Point Pattern

Randomly Shift a Point Pattern

Class of Quadrature Schemes

plot.bermantest

Plot Result of Berman Test

Find Largest Circle Inside Window

Neighbourhood density function

Nearest neighbour distances between line segments

quadratresample

Resample a Point Pattern by Resampling Quadrats

spatstat-internal

Internal spatstat functions

Weighted Empirical Cumulative Distribution Function

Generate N Uniform Random Points

Methods for Multidimensional Space-Time Point Patterns

Convert Line Segment Pattern to Another Unit of Length

Rotate a Window

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Plot a List of Things

Kaplan-Meier and Reduced Sample Estimator using Histograms

Plot a Colour Map

Pairwise distances in Three Dimensions

Distance Map of Line Segment Pattern

pairwise.family

Pairwise Interaction Process Family

Summarizing a Quadrature Scheme

Lansing Woods Point Pattern

Aherne's hamster tumour data

Print a Quadrature Scheme

Plot a fitted cluster point process

Test Whether a Window is Convex

Create a Point Matching

Saturated Pairwise Interaction Point Process Family

Log Likelihood for Poisson Point Process Model

Plot a three-dimensional point pattern

Murchison gold deposits

Longleaf Pines Point Pattern

Pair Correlation Function of Point Pattern

Ponderosa Pine Tree Point Pattern

Apply Vector Translation To Point Pattern

Convert Window to Pixel Image

Class of Point Patterns

Fit cluster point process model

Test Whether An Object Is A Point Pattern

Convert Point Pattern to Another Unit of Length

Divide Point Pattern into Sub-patterns

Nearest neighbour distances in three dimensions

Plot a Function Array

Apply Vector Translation To Line Segment Pattern

Distance for a Point Pattern Matching

Print Brief Details of an Image

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Superimpose Several Line Segment Patterns

Simulate Neyman-Scott Process

Number of Points in a Point Pattern

Simulate Simple Sequential Inhibition

Plot a Spatial Kolmogorov-Smirnov Test

Print a Fitted Point Process Model

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

Fit the Thomas Point Process by Minimum Contrast

Plot a tessellation

Name for Unit of Length

pppmatching.object

Class of Point Matchings

Inhomogeneous Pair Correlation Function

Convert Line Segment Pattern to Pixel Image

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Window in Shape of Letter R

Fry Plot of Point Pattern

Nearest Neighbours Between Two Patterns

Reduced Sample Estimator using Histogram Data

Plot a Spatial Window

California Redwoods Point Pattern (Ripley's Subset)

Print Brief Details of a Point Pattern Dataset

Generate N Random Multitype Points

Convert Pixel Image to Another Unit of Length

Convert Spatial Object to Pixel Image

Mean, Median and Range of Pixel Values in an Image

Convert Polygonal Region into Different Format

Mark Connection Function

Class of Line Segment Patterns

Plot a plotppm Object Created by plot.ppm

Generate Poisson Point Pattern on Line Segments

Print Brief Details of a Line Segment Pattern Dataset

plot a Spatial Point Pattern

Lurking variable plot

Rectangular grid of points

Mark Correlation Integral

Read Point Pattern From Data File

Place Points Evenly Along Specified Lines

Make Periodic Copies of a Spatial Pattern

Theoretical Distribution of Nearest Neighbour Distance

multiplicity.ppp

Count Multiplicity of Duplicate Points

Kolmogorov-Smirnov Test for Point Process Model

nearest.raster.point

Find Pixel Nearest to a Given Point

Random Re-Labelling of Point Pattern

Simulate Matern Model II

Simulate a Fitted Gibbs Point Process Model

Print News About Latest Version of Package

Extract Quadrature Scheme Used to Fit a Point Process Model

Nearest Neighbour Clutter Removal

Update a Fitted Point Process Model

Convert Window to Another Unit of Length

Quadrature Scheme Based on Pixel Grid

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Interpret Fitted Model for Metropolis-Hastings Simulation.

New Zealand Trees Point Pattern

Pairwise distances

plot a Fitted Point Process Model

Summarizing a Fitted Point Process Model

Perfect Simulation of the Strauss Process

Generate grid of parallel lines with random displacement

Define Point Process Model for Metropolis-Hastings Simulation.

Define Point Process Model for Metropolis-Hastings Simulation.

Pair Correlation Function

Create a Window

Residuals for Fitted Point Process Model

Simulate Matern Model I

Point Patterns of New Brunswick Forest Fires

Generate N Uniform Random Points in Three Dimensions

pairdist.default

Pairwise distances

Weighted Histogram

Random Thinning

Simulate a Fitted Cluster Point Process Model

Cartesian Coordinates for a Pixel Raster

Apply Vector Translation To Pixel Image

rescue.rectangle

Convert Window Back To Rectangle

Simulated Point Pattern

Multitype pair correlation function (i-to-any)

Evaluate an Expression in a Function Table

Perspective Plot of Pixel Image

Convert Point Pattern to Pixel Image

Three Dimensional Point Pattern

plot.hyperframe

Plot Entries in a Hyperframe

Multitype pair correlation function (cross-type)

Simulate Baddeley-Silverman Cell Process

Compute Integral of Function Against Cumulative Distribution

Simulate systematic random point pattern

California Redwoods Point Pattern (Entire Dataset)

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

Extract List of Tiles in a Tessellation

Urkiola Woods Point Pattern

Morphological Opening

Pairwise distances

project2segment

Move Point To Nearest Line

Spatial smoothing of observations at irregular points

Summary of a Point Pattern Dataset

Divide Region into Quadrats

plot a Spatial Quadrature Scheme

Summary of a Spatial Window

spatstat-package

The Spatstat Package

Union of Data and Dummy Points

Superimpose Several Point Patterns

Interaction Distance of a Point Process

plot a Spatial Line Segment Pattern

Simulate from a Fitted Point Process Model

Summary of a Line Segment Pattern Dataset

Galaxies in the Shapley Supercluster

Prediction from a Fitted Cluster Point Process Model

Class of Fitted Point Process Models

Q-Q Plot of Residuals from Fitted Point Process Model

Mosaic Random Set

Print Brief Details of a Spatial Window

Sample Quantiles of Pixel Image

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Simulate Thomas Process

Simulate Matern Cluster Process

rshift.splitppp

Randomly Shift a List of Point Patterns

Apply Smoothing to Function Values

Estimate window from points alone

Randomly Shift a Line Segment Pattern

Set Covariance of a Window

Summarizing a Pixel Image

Quadrat counting for a point pattern

Vertices of a Window

Spruces Point Pattern

Apply Vector Translation To Window

Poisson Line Tessellation

Apply Vector Translation

Create a Line Segment Pattern

Sufficient Statistic of Point Process Model

Mosaic Random Field

Random Perturbation of a Point Pattern

Generate Poisson Random Line Process

Create a Tessellation

Approximate a Polygon by a Simpler Polygon

Kaplan-Meier Estimator using Histogram Data

Determine Initial State for Metropolis-Hastings Simulation.

Simulate point patterns using the Metropolis-Hastings algorithm.

Simulate Stratified Random Point Pattern

Generate Multitype Poisson Point Pattern

Summary of a List of Things

Extract Unique Points from a Spatial Point Pattern

summary.splitppp

Summary of a Split Point Pattern

Generate N Random Points

Generate Poisson Point Pattern in Three Dimensions

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

Rotate a Line Segment Pattern

Divide Image Into Sub-images

Generate Poisson Point Pattern

Generate N Uniform Random Points in a Disc

Update a Fitted Cluster Point Process Model

spatstat.options

Internal Options in Spatstat Package

Spokes pattern of dummy points

Swedish Pines Point Pattern

Cut margins from rectangle

Variance-Covariance Matrix for a Fitted Point Process Model