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spatstat (version 1.20-1)

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

18,534

Version

1.20-1

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

July 26th, 2010

Functions in spatstat (1.20-1)

Extract Subset of Function Array

Multitype J Function (i-to-j)

as.data.frame.im

Convert Pixel Image to Data Frame

Estimate the I-function

Extract or Replace Subset of a List of Things

Multitype J Function (i-to-any)

Multitype L-function (i-to-any)

The Multitype Strauss Point Process Model

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

Apply a Function to a Point Pattern Broken Down by Factor

Extract.splitppp

Extract or Replace Sub-Patterns

Apply Affine Transformation To Window

Distance to Boundary of Window

Marked Nearest Neighbour Distance Function

Combine Two Line Segment Patterns

The Lennard-Jones Potential

Corners of a rectangle

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Geometrical Calculations for Three-Dimensional Box

Bounding Box of a Window or Point Pattern

Difference of Disc Areas

Classify Points in a Point Pattern

Extract Dummy Points Used to Fit a Point Process Model

Colour Lookup Tables

bounding.box.xy

Convex Hull of Points

Pixel Image Approximation of a Window

Extract Subset of Image

Convert and Compare Colours in Different Formats

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Morphological Closing

The Hard Core Point Process Model

Function Arrays for Spatial Patterns

Foxall's Distance Functions

Piecewise Constant Saturated Pairwise Interaction Point Process Model

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

Safely Convert Point Pattern Window to Binary Mask

Inhomogeneous K-function

The Fiksel Interaction

Inhomogeneous Cross K Function

Convert Data To Class psp

Diameter of a Window

Beadlet Anemones Data

Test Whether An Object Is A Window

Intersection of Two Tessellations

Distance Map as a Function

Apply Affine Transformation To Line Segment Pattern

Longleaf Pines Point Pattern

spatstat-internal

Internal spatstat functions

Three-Dimensional Box

Pairwise distances

Apply Function to Image Broken Down by Factor

spatstat-deprecated

Deprecated spatstat functions

Evaluate Expression Involving Functions

Level Set of a Pixel Image

Find Largest Circle Inside Window

Rectangular grid of points

model.matrix.ppm

Extract Design Matrix from Point Process Model

Endpoints of Line Segment Pattern

Compute Quadrature Weights Based on Grid Counts

Marks of a Point Pattern

Apply Affine Transformation To Point Pattern

Collapse Several Function Tables into One

Test Whether An Object Is Empty

Estimate the empty space function F

Centroid of a window

Artificial Data Point Pattern

Test Whether Points Are Inside A Window

Delaunay Triangulation of Point Pattern

multiplicity.ppp

Count Multiplicity of Duplicate Points

Midpoints of Line Segment Pattern

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Calculate four standard summary functions of a point pattern.

Kernel Smoothing of Line Segment Pattern

Point Patterns of New Brunswick Forest Fires

Area of a Window

Distance to Boundary of Window

Distance for a Point Pattern Matching

Crossing Points of Two Line Segment Patterns

Fit the Matern Cluster Point Process by Minimum Contrast

Nearest Neighbour Clutter Removal

Inhomogeneous Multitype K Dot Function

Poisson Point Process Model

Print Brief Details of an Image

Pairwise Distances in Any Dimensions

Subset of Quadrature Scheme

Pair Correlation Function of Point Pattern

Pair Correlation Function obtained from K Function

Convert Pixel Image from Numeric to Factor

Class of Fitted Point Process Models

Morphological Dilation

Convert Data to Three-Dimensional Box

The Strauss Point Process Model

Pine saplings in Finland.

Hybrid Geyer Point Process Model

Data Frames of Function Values

Areas of Morphological Dilations

Distance to Boundary of Window

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

The Soft Core Point Process Model

Estimate the J-function

K-function using FFT

Chorley-Ribble Cancer Data

Area of Part of Disc

Interactively Add Points

Subdivide a Window or Tessellation using a Set of Lines

Ord's Interaction model

Summarise Marks in Every Neighbourhood in a Point Pattern

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Connected components of an image or window

Rotate a Line Segment Pattern

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Convex Hull of Points

Rotate a Window

Diagnostic Plots for Fitted Point Process Model

Generate Poisson Point Pattern

Japanese Pines Point Pattern

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Weighted Empirical Cumulative Distribution Function

Plot a List of Things

Morphological Erosion

Extract or Replace Subset of Point Pattern

Class of Point Patterns

Mark Connection Function

Empty Space Function of a Three-Dimensional Point Pattern

nearest.raster.point

Find Pixel Nearest to a Given Point

Geyer's Saturation Point Process Model

Cartesian Coordinates for a Pixel Raster

Ord Interaction Process Family

Pairwise distances between line segments

Plot a Pixel Image

Distance Map of Window

Generate a Default Pattern of Dummy Points

Contour plot of pixel image

Test Whether An Object Is A Point Pattern

Compute Images of Constructed Covariates

Multitype pair correlation function (i-to-any)

Evaluate Expression Involving Function Arrays

pppmatching.object

Class of Point Matchings

plot.bermantest

Plot Result of Berman Test

Profile Maximum Pseudolikelihood

Inhomogeneous Pair Correlation Function

Coefficients of Fitted Point Process Model

Make Periodic Copies of a Spatial Pattern

Generate a Quadrature Scheme from a Point Pattern

Diameter of an Object

Find Line Segment Nearest to Each Point

Infinite Straight Lines

Fry Plot of Point Pattern

Methods for Three-Dimensional Box

Expand Window By Factor

Window in Shape of Letter R

Test Whether A Point Process Model is Marked

California Redwoods Point Pattern (Ripley's Subset)

Quadrat counting for a point pattern

Murchison gold deposits

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

Create a Point Pattern

Print Brief Details of a Point Pattern Dataset

Convert Point Pattern to Another Unit of Length

Prediction from a Fitted Point Process Model

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Fit Point Process Model to Data

Pairwise distances between two different line segment patterns

Reduced Sample Estimator using Histogram Data

Simulate Matern Model II

Create a Line Segment Pattern

Marked J Function

Random Perturbation of a Point Pattern

model.frame.ppm

Extract the Environment of a Point Process Model

Simulate Baddeley-Silverman Cell Process

Convert Window to Pixel Image

Convert Line Segment Pattern to Another Unit of Length

Nearest neighbour distances between line segments

Pairwise distances between two different three-dimensional point patterns

Morphological Opening

Diggle's Heather Data

Convert Data To Class ppp

Pairwise distances

Multitype K Function (i-to-any)

Simulate a Fitted Gibbs Point Process Model

Diggle-Gratton model

Determine Duplicated Points in a Spatial Point Pattern

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

Galaxies in the Shapley Supercluster

Extract or Replace Subset of Tessellation

Berman's Tests for Point Process Model

Fitted Conditional Intensity for Point Process Model

Mark Correlation Integral

Integral of a Pixel Image

Apply Gaussian Blur to a Pixel Image

Multitype L-function (cross-type)

Beta Ganglion Cells in Cat Retina

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

Apply Vector Translation To Point Pattern

Generic Pairwise Interaction model

Extract Subset of Function Values

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

K-function of a Three-Dimensional Point Pattern

Generic Ord Interaction model

Nearest neighbour

Simulate Matern Cluster Process

Test Whether Marks Are Present

Approximate a Polygon by a Simpler Polygon

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Intersect Infinite Straight Lines with a Window

Extract Subset of Line Segment Pattern

Spherical Contact Distribution Function

project2segment

Move Point To Nearest Line

Mosaic Random Field

Convert to Pixel Image

Nearest Neighbour Distance Function G

Divide Image Into Sub-images

Divide Region into Quadrats

Convert dataset to another unit of length

rescue.rectangle

Convert Window Back To Rectangle

Reset Values in Subset of Image

The Piecewise Constant Pairwise Interaction Point Process Model

Lansing Woods Point Pattern

Combine Function Value Tables

Mark Correlation Function

Difference of Disc Areas

Generate Multitype Poisson Point Pattern

Lurking variable plot

Define Point Process Model for Metropolis-Hastings Simulation.

Superimpose Several Line Segment Patterns

Inhomogeneous Cross Type L Function

Neighbourhood density function

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Basis for Harmonic Functions

Inhomogeneous Multitype L Dot Function

Q-Q Plot of Residuals from Fitted Point Process Model

Nearest Neighbours in Any Dimensions

Saturated Pairwise Interaction model

Pair Correlation Function

Convert Point Pattern to Pixel Image

Orientation Angles of Line Segments

Spruces Point Pattern

Simulate Simple Sequential Inhibition

Reduced Second Moment Measure

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Rotate a Point Pattern

Generate Poisson Point Pattern in Three Dimensions

Biological Cells Point Pattern

Simulate Gauss-Poisson Process

Residuals for Fitted Point Process Model

Extract Unique Points from a Spatial Point Pattern

Generate grid of parallel lines with random displacement

Generate N Uniform Random Points in Three Dimensions

Urkiola Woods Point Pattern

Hutchings' Bramble Canes data

Hyper Data Frame

pairwise.family

Pairwise Interaction Process Family

Summary of a List of Things

Beta Ganglion Cells in Cat Retina, Old Version

Theoretical Distribution of Nearest Neighbour Distance

Point and Click Interface for Displaying a Point Pattern

Randomly Shift a Point Pattern

plot a Spatial Quadrature Scheme

ANOVA for Fitted Point Process Models

Test Whether A Point Pattern is Marked

Apply Function to Every Neighbourhood in a Point Pattern

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

Generate N Random Multitype Points

Apply Vector Translation To Line Segment Pattern

Plot a Simulation Envelope

Simulate Matern Model I

Simulate Thomas Process

Three Dimensional Point Pattern

Diagnostics for random marking

California Redwoods Point Pattern (Entire Dataset)

Simulate a Fitted Cluster Point Process Model

The Area Interaction Point Process Model

Methods for Multidimensional Space-Time Point Patterns

Nearest Neighbours Between Two Patterns

plot a Fitted Point Process Model

Convert Pixel Image to Matrix

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Nearest neighbour distances in three dimensions

Methods for three-dimensional point patterns

Pair Correlation Function obtained from array of K functions

Multi-Dimensional Box

Convert Line Segment Pattern to Binary Pixel Mask

Concatenate x,y Coordinate Vectors

Berman-Huntington points and lines data

Extract Original Data from a Fitted Point Process Model

Geometrical Calculations for Multi-Dimensional Box

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Convert a Window to a Polygonal Window

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Test Whether Two Pixel Images Are Compatible

Hughes' Amacrine Cell Data

Marked K-Function

Plot a three-dimensional point pattern

Exponential Energy Marks

Circular Window

Generate N Uniform Random Points

Plot a Spatial Window

Plot a Function Array

Convert Data to Hyperframe

Pairwise distances between two different point patterns

Bronze gradient filter data

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

crossdist.default

Pairwise distances between two different sets of points

Distance Map of Line Segment Pattern

Simulation Envelopes of Summary Function

complement.owin

Take Complement of a Window

Print Progress Reports

Interaction Distance of a Point Process

Border Region of a Window

Clark and Evans Aggregation Index

Method of Minimum Contrast

Set Covariance of a Window

Kernel Smoothed Intensity of Point Pattern

Spatial smoothing of observations at irregular points

Compute Integral of Function Against Cumulative Distribution

Determine Initial State for Metropolis-Hastings Simulation.

Class of Line Segment Patterns

Plot a Spatial Kolmogorov-Smirnov Test

Convert Data To Tessellation

Print Brief Details of a Line Segment Pattern Dataset

Update a Fitted Cluster Point Process Model

Apply Vector Translation To Window

Dirichlet Tessellation of Point Pattern

inforder.family

Infinite Order Interaction Family

Name for Unit of Length

Aherne's hamster tumour data

Divide Point Pattern into Sub-patterns

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

summary.splitppp

Summary of a Split Point Pattern

Interactively Define a Polygon

pairdist.default

Pairwise distances

Random Re-Labelling of Point Pattern

Multitype pair correlation function (cross-type)

Multitype K Function (Cross-type)

Evaluate Expression Involving Pixel Images

Convert Polygonal Region into Different Format

Create a Tessellation

Weighted Histogram

Create a Point Matching

Class of Quadrature Schemes

plot a Spatial Line Segment Pattern

The Strauss / Hard Core Point Process Model

Test Whether Two Function Objects Are Compatible

Test Whether a Window is Convex

Apply Affine Transformation

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

Areas of Morphological Erosions

Harkness-Isham ants' nests data

Convert Line Segment Pattern to Pixel Image

Test Whether An Object Is A Fitted Point Process Model

Sample Quantiles of Pixel Image

Class of Images

Distance Map of Point Pattern

Estimate window from points alone

Humberside Data on Childhood Leukaemia and Lymphoma

Histogram of Pixel Values in an Image

Test Whether An Object Is A Pixel Image

Kaplan-Meier Estimator using Histogram Data

Random Thinning

Point and Click Interface for Exploratory Analysis of Point Pattern

Simulate Stratified Random Point Pattern

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Generate Poisson Point Pattern on Line Segments

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Intersection, Union or Set Subtraction of Two Windows

Perspective Plot of Pixel Image

Plot a Colour Map

Apply Vector Translation

Interpolate a Pixel Image

Kaplan-Meier and Reduced Sample Estimator using Histograms

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Create a Function Value Table

Determine Whether One Window is Contained In Another

Create a Window

Generate N Uniform Random Points in a Disc

Prediction from a Fitted Cluster Point Process Model

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

New Zealand Trees Point Pattern

Scatterplot Matrix for Pixel Images

Extract the Interaction from a Fitted Point Process Model

Apply Smoothing to Function Values

Kolmogorov-Smirnov Test for Point Process Model

Lengths of Line Segments

Quadrature Scheme Based on Pixel Grid

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Log Likelihood for Poisson Point Process Model

Identify Points in a Point Pattern

Read Point Pattern From Data File

Convert Data To Class owin

Poisson Line Tessellation

Sufficient Statistic of Point Process Model

Swedish Pines Point Pattern

Methods for Multi-Dimensional Box

Nearest Neighbour Distances in Any Dimensions

Tropical rain forest trees

Perimeter Length of Window

Evaluate an Expression in a Function Table

Nearest neighbour distances

Fit cluster point process model

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Simulation Envelopes of Summary Function for 3D Point Pattern

Convert Spatial Object to Pixel Image

Plot Function Values

Multidimensional Space-Time Point Pattern

Number of Points in a Point Pattern

Print Brief Details of a Spatial Window

Ponderosa Pine Tree Point Pattern

Simulate Neyman-Scott Process

Convert Window to Another Unit of Length

Summarizing a Pixel Image

Simulate point patterns using the Metropolis-Hastings algorithm.

Generate N Uniform Random Points in Any Dimensions

Plot a tessellation

Superimpose Several Point Patterns

Summary of a Line Segment Pattern Dataset

Pairwise distances in Three Dimensions

plot.hyperframe

Plot Entries in a Hyperframe

Print a Fitted Point Process Model

Data and Code From JRSS Discussion Paper on Residuals

Perfect Simulation of the Strauss Process

Pairwise distances

Generate Poisson Point Pattern in Any Dimensions

spatstat.options

Internal Options in Spatstat Package

Interpret Fitted Model for Metropolis-Hastings Simulation.

Create a Pixel Image Object

Union of Data and Dummy Points

Plot a fitted cluster point process

Saturated Pairwise Interaction Point Process Family

Extract Quadrature Scheme Used to Fit a Point Process Model

plot a Spatial Point Pattern

Simulate from a Fitted Point Process Model

Set Control Parameters for Metropolis-Hastings Algorithm.

Define Point Process Model for Metropolis-Hastings Simulation.

Extract List of Tiles in a Tessellation

Generate N Random Points

Plot a plotppm Object Created by plot.ppm

spatstat-package

The Spatstat Package

Test whether Object is Multitype

Print News About Latest Version of Package

Plot a List of Point Patterns

Place Points Evenly Along Specified Lines

Distance Between Two Point Patterns

Generate Poisson Random Line Process

Morishita Index Plot

Fit the Thomas Point Process by Minimum Contrast

Nearest neighbours in three dimensions

Spokes pattern of dummy points

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Mosaic Random Set

Summarizing a Quadrature Scheme

Print a Quadrature Scheme

Variance-Covariance Matrix for a Fitted Point Process Model

Volume of an Object

Summarizing a Fitted Point Process Model

Summary of a Spatial Window

rshift.splitppp

Randomly Shift a List of Point Patterns

Apply Vector Translation To Pixel Image

Simulated Point Pattern

Convert Pixel Image to Another Unit of Length

Vertices of a Window

Simulate systematic random point pattern

Randomly Shift a Line Segment Pattern

quadratresample

Resample a Point Pattern by Resampling Quadrats

Cut margins from rectangle

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

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

Update a Fitted Point Process Model

Summary of a Point Pattern Dataset