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spatstat (version 1.17-6)

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

1.17-6

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

February 9th, 2010

Functions in spatstat (1.17-6)

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

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

Marked K-Function

Ord's Interaction model

Saturated Pairwise Interaction model

Area of a Window

Bronze gradient filter data

Extract.splitppp

Extract or Replace Sub-Patterns

Biological Cells Point Pattern

Concatenate x,y Coordinate Vectors

Estimate the I-function

ANOVA for Fitted Point Process Models

Class of Images

K-function of a Three-Dimensional Point Pattern

Generic Pairwise Interaction model

Estimate the J-function

Convert a Window to a Polygonal Window

Diggle-Gratton model

Tropical rain forest trees

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Apply Gaussian Blur to a Pixel Image

Convert Data to Hyperframe

Empty Space Function of a Three-Dimensional Point Pattern

Clark and Evans Aggregation Index

Extract Subset of Function Values

Print Progress Reports

Calculate Summary Statistic for All Types in a Multitype Point Pattern

K-function using FFT

Q-Q Plot of Residuals from Fitted Point Process Model

quadratresample

Resample a Point Pattern by Resampling Quadrats

Chorley-Ribble Cancer Data

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Apply Affine Transformation To Window

Apply a Function to a Point Pattern Broken Down by Factor

Convert Pixel Image to Matrix

Simulate Neyman-Scott Process

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Simulate Stratified Random Point Pattern

Pairwise distances between two different point patterns

Berman's Tests for Point Process Model

Multitype L-function (cross-type)

Coefficients of Fitted Point Process Model

Areas of Morphological Erosions

Combine Two Line Segment Patterns

Morphological Closing

Distance to Boundary of Window

Extract Subset of Function Array

Nearest Neighbour Distance Function G

Extract Subset of Line Segment Pattern

Distance to Boundary of Window

Combine Function Value Tables

Pairwise distances between two different line segment patterns

Diameter of a Window

Diagnostic Plots for Fitted Point Process Model

Inhomogeneous K-function

complement.owin

Take Complement of a Window

Diggle's Heather Data

Create a Function Value Table

The Soft Core Point Process Model

Harkness-Isham ants' nests data

Test Whether a Window is Convex

Inhomogeneous Cross K Function

Beta Ganglion Cells in Cat Retina

Colour Lookup Tables

Extract Dummy Points Used to Fit a Point Process Model

The Piecewise Constant Pairwise Interaction Point Process Model

Apply Affine Transformation To Point Pattern

Apply Affine Transformation

inforder.family

Infinite Order Interaction Family

Geometrical Calculations for Three-Dimensional Box

Bounding Box of a Window or Point Pattern

Connected components of an image or window

Extract Original Data from a Fitted Point Process Model

Artificial Data Point Pattern

Level Set of a Pixel Image

Interactively Add Points

Apply Vector Translation To Pixel Image

Determine Duplicated Points in a Spatial Point Pattern

bounding.box.xy

Convex Hull of Points

Set Covariance of a Window

Fitted Conditional Intensity for Point Process Model

Circular Window

Point Patterns of New Brunswick Forest Fires

Extract or Replace Subset of Point Pattern

Apply Vector Translation To Line Segment Pattern

Multitype L-function (i-to-any)

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Nearest neighbour distances in three dimensions

Spherical Contact Distribution Function

Longleaf Pines Point Pattern

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Estimate the empty space function F

Spokes pattern of dummy points

Weighted Empirical Cumulative Distribution Function

Extract the Interaction from a Fitted Point Process Model

Pine saplings in Finland.

Calculate four standard summary functions of a point pattern.

Inhomogeneous Multitype L Dot Function

Create a Window

Ord Interaction Process Family

Evaluate Expression Involving Function Arrays

Fry Plot of Point Pattern

Create a Pixel Image Object

Areas of Morphological Dilations

Subdivide a Window or Tessellation using a Set of Lines

Nearest neighbours in three dimensions

Collapse Several Function Tables into One

Interactively Define a Polygon

Convert Spatial Object to Pixel Image

Evaluate Expression Involving Pixel Images

Marked J Function

The Strauss / Hard Core Point Process Model

Distance Map of Window

Reset Values in Subset of Image

Lansing Woods Point Pattern

Convert Polygonal Region into Different Format

Hughes' Amacrine Cell Data

Window in Shape of Letter R

Prediction from a Fitted Cluster Point Process Model

Class of Point Patterns

Random Re-Labelling of Point Pattern

Distance Map of Point Pattern

Theoretical Distribution of Nearest Neighbour Distance

Simulate Baddeley-Silverman Cell Process

Convert Data To Class ppp

Interpolate a Pixel Image

Intersect Infinite Straight Lines with a Window

Basis for Harmonic Functions

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Log Likelihood for Poisson Point Process Model

Difference of Disc Areas

Multitype pair correlation function (i-to-any)

Convert Data To Class owin

Nearest neighbour

Pairwise distances

Quadrature Scheme Based on Pixel Grid

Lurking variable plot

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Morphological Dilation

Test Whether An Object Is A Window

Generate a Default Pattern of Dummy Points

Multitype pair correlation function (cross-type)

Nearest Neighbour Clutter Removal

Delaunay Triangulation of Point Pattern

Inhomogeneous Cross Type L Function

Three-Dimensional Box

Simulate Matern Model I

Plot a Pixel Image

Pixel Image Approximation of a Window

Read Point Pattern From Data File

Fit the Matern Cluster Point Process by Minimum Contrast

Inhomogeneous Pair Correlation Function

multiplicity.ppp

Count Multiplicity of Duplicate Points

Plot a plotppm Object Created by plot.ppm

Methods for Multidimensional Space-Time Point Patterns

Pair Correlation Function obtained from array of K functions

plot a Spatial Line Segment Pattern

Spruces Point Pattern

Convex Hull of Points

spatstat-internal

Internal spatstat functions

Exponential Energy Marks

Reduced Second Moment Measure

Compute Images of Constructed Covariates

Murchison gold deposits

Plot a Function Array

Three Dimensional Point Pattern

crossdist.default

Pairwise distances between two different sets of points

Crossing Points of Two Line Segment Patterns

Evaluate an Expression in a Function Table

Saturated Pairwise Interaction Point Process Family

pairdist.default

Pairwise distances

Print a Quadrature Scheme

summary.splitppp

Summary of a Split Point Pattern

Plot a List of Point Patterns

Plot a Colour Map

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Class of Fitted Point Process Models

Plot a tessellation

The Area Interaction Point Process Model

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Generate Multitype Poisson Point Pattern

Distance Between Two Point Patterns

Point and Click Interface for Displaying a Point Pattern

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

Randomly Shift a Point Pattern

Pair Correlation Function obtained from K Function

Classify Points in a Point Pattern

Expand Window By Factor

Apply Function to Every Neighbourhood in a Point Pattern

Distance for a Point Pattern Matching

Summarizing a Fitted Point Process Model

Prediction from a Fitted Point Process Model

Geyer's Saturation Point Process Model

Place Points Evenly Along Specified Lines

Test whether Object is Multitype

Summary of a Line Segment Pattern Dataset

Simulate Matern Cluster Process

Perfect Simulation of the Strauss Process

pppmatching.object

Class of Point Matchings

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Convert Point Pattern to Another Unit of Length

Midpoints of Line Segment Pattern

Class of Line Segment Patterns

Multitype K Function (i-to-any)

Poisson Point Process Model

Hybrid Geyer Point Process Model

Nearest Neighbours Between Two Patterns

Determine Whether One Window is Contained In Another

Define Point Process Model for Metropolis-Hastings Simulation.

Ponderosa Pine Tree Point Pattern

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

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

Convert Line Segment Pattern to Another Unit of Length

Reduced Sample Estimator using Histogram Data

Pair Correlation Function of Point Pattern

Galaxies in the Shapley Supercluster

Poisson Line Tessellation

The Strauss Point Process Model

Neighbourhood density function

Contour plot of pixel image

Methods for Three-Dimensional Box

Residuals for Fitted Point Process Model

compatible.fasp

Test Whether Two Function Arrays Are Compatible

plot a Fitted Point Process Model

Convert Point Pattern to Pixel Image

Simulate from a Fitted Point Process Model

Convert Window to Pixel Image

Perimeter Length of Window

Generate a Quadrature Scheme from a Point Pattern

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Marked Nearest Neighbour Distance Function

Test Whether Two Pixel Images Are Compatible

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Convert Data To Tessellation

Divide Region into Quadrats

Interpret Fitted Model for Metropolis-Hastings Simulation.

Rotate a Point Pattern

Generate Poisson Point Pattern in Three Dimensions

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Print a Fitted Point Process Model

Hyper Data Frame

Set Control Parameters for Metropolis-Hastings Algorithm.

Distance Map of Line Segment Pattern

Simulation envelopes of summary function

Nearest neighbour distances

Simulate Simple Sequential Inhibition

Nearest neighbour distances between line segments

rshift.splitppp

Randomly Shift a List of Point Patterns

model.matrix.ppm

Extract Design Matrix from Point Process Model

Approximate a Polygon by a Simpler Polygon

Sufficient Statistic of Point Process Model

Simulate Thomas Process

Area of Part of Disc

rescue.rectangle

Convert Window Back To Rectangle

Convert Pixel Image from Numeric to Factor

Multitype J Function (i-to-j)

Random Thinning

Apply Vector Translation To Window

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Multitype J Function (i-to-any)

Plot a List of Things

Convert dataset to another unit of length

Define Point Process Model for Metropolis-Hastings Simulation.

Determine Initial State for Metropolis-Hastings Simulation.

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

Convert Data to Three-Dimensional Box

Compute Quadrature Weights Based on Grid Counts

spatstat-package

The Spatstat Package

Beadlet Anemones Data

Extract List of Tiles in a Tessellation

Find Line Segment Nearest to Each Point

Berman-Huntington points and lines data

Generate Poisson Point Pattern

Apply Affine Transformation To Line Segment Pattern

Test Whether Marks Are Present

Union of Data and Dummy Points

Summarizing a Quadrature Scheme

Set or Reset the Marks in a Point Pattern

Generate N Random Multitype Points

Pairwise distances in Three Dimensions

Test Whether Points Are Inside A Window

Rectangular grid of points

Pairwise distances between two different three-dimensional point patterns

Infinite Straight Lines

Extract Unique Points from a Spatial Point Pattern

Safely Convert Point Pattern Window to Binary Mask

Extract or Replace Subset of Tessellation

Apply Vector Translation

Plot a Spatial Kolmogorov-Smirnov Test

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

Intersection, Union or Set Subtraction of Two Windows

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Humberside Data on Childhood Leukaemia and Lymphoma

Divide Point Pattern into Sub-patterns

Generic Ord Interaction model

Test Whether An Object Is A Point Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

Weighted Histogram

Print Brief Details of an Image

Superimpose Several Line Segment Patterns

Spatial smoothing of observations at irregular points

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Create a Tessellation

Find Largest Circle Inside Window

Orientation Angles of Line Segments

Test Whether An Object Is A Pixel Image

Vertices of a Window

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Extract or Replace Subset of a List of Things

Test Whether A Point Pattern is Marked

Point and Click Interface for Exploratory Analysis of Point Pattern

Japanese Pines Point Pattern

project2segment

Move Point To Nearest Line

Difference of Disc Areas

Swedish Pines Point Pattern

plot a Spatial Point Pattern

Evaluate Expression Involving Functions

Endpoints of Line Segment Pattern

nearest.raster.point

Find Pixel Nearest to a Given Point

Summary of a Point Pattern Dataset

Histogram of Pixel Values in an Image

Apply Function to Image Broken Down by Factor

Centroid of a window

Integral of a Pixel Image

Fit cluster point process model

Test Whether Two Function Objects Are Compatible

Inhomogeneous Multitype K Dot Function

Intersection of Two Tessellations

Rotate a Window

Hutchings' Bramble Canes data

Print News About Latest Version of Package

Generate grid of parallel lines with random displacement

Function Arrays for Spatial Patterns

plot.hyperframe

Plot Entries in a Hyperframe

Morishita Index Plot

Kolmogorov-Smirnov Test for Point Process Model

Make Periodic Copies of a Spatial Pattern

Mark Correlation Integral

Multidimensional Space-Time Point Pattern

Corners of a rectangle

Test Whether A Point Process Model is Marked

Aherne's hamster tumour data

Subset of Quadrature Scheme

Plot Function Values

Create a Point Matching

Distance Map as a Function

Class of Quadrature Schemes

Print Brief Details of a Spatial Window

Simulate point patterns using the Metropolis-Hastings algorithm.

Lengths of Line Segments

Test Whether An Object Is Empty

Kaplan-Meier Estimator using Histogram Data

The Lennard-Jones Potential

Cut margins from rectangle

Mark Connection Function

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Multitype K Function (Cross-type)

Perspective Plot of Pixel Image

Morphological Erosion

Mosaic Random Set

Print Brief Details of a Line Segment Pattern Dataset

Beta Ganglion Cells in Cat Retina, Old Version

Simulate Matern Model II

Interaction Distance of a Point Process

Extract Quadrature Scheme Used to Fit a Point Process Model

Distance to Boundary of Window

Data and Code From JRSS Discussion Paper on Residuals

Mark Correlation Function

Summary of a Spatial Window

California Redwoods Point Pattern (Ripley's Subset)

Generate N Random Points

Generate Poisson Point Pattern on Line Segments

Extract Subset of Image

Kernel Smoothed Intensity of Point Pattern

Data Frames of Function Values

Random Perturbation of a Point Pattern

spatstat-deprecated

Deprecated spatstat functions

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Plot a Spatial Window

plot a Spatial Quadrature Scheme

Simulated Point Pattern

Create a Point Pattern

Convert Pixel Image to Another Unit of Length

Dirichlet Tessellation of Point Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Convert Window to Another Unit of Length

The Multitype Strauss Point Process Model

Simulate a Fitted Gibbs Point Process Model

Convert to Pixel Image

Generate N Uniform Random Points

Convert Data To Class psp

Test Whether An Object Is A Fitted Point Process Model

Randomly Shift a Line Segment Pattern

Update a Fitted Point Process Model

Update a Fitted Cluster Point Process Model

Print Brief Details of a Point Pattern Dataset

Create a Line Segment Pattern

Method of Minimum Contrast

Simulate a Fitted Cluster Point Process Model

Summary of a List of Things

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Fit the Thomas Point Process by Minimum Contrast

Border Region of a Window

Quadrat counting for a point pattern

Generate N Uniform Random Points in a Disc

Pairwise distances

Summarizing a Pixel Image

Kernel Smoothing of Line Segment Pattern

Name for Unit of Length

Sample Quantiles of Pixel Image

Identify Points in a Point Pattern

California Redwoods Point Pattern (Entire Dataset)

Estimate window from points alone

Fit Point Process Model to Data

Diagnostics for random marking

plot.bermantest

Plot Result of Berman Test

Profile Maximum Pseudolikelihood

Generate N Uniform Random Points in Three Dimensions

Cartesian Coordinates for a Pixel Raster

Kaplan-Meier and Reduced Sample Estimator using Histograms

Summarise Marks in Every Neighbourhood in a Point Pattern

spatstat.options

Internal Options in Spatstat Package

Mean, Median and Range of Pixel Values in an Image

Pairwise distances

Rotate a Line Segment Pattern

Simulate Gauss-Poisson Process

Methods for three-dimensional point patterns

Morphological Opening

Generate Poisson Random Line Process

Pairwise distances between line segments

Superimpose Several Point Patterns

pairwise.family

Pairwise Interaction Process Family

Divide Image Into Sub-images

Urkiola Woods Point Pattern

Pair Correlation Function

New Zealand Trees Point Pattern

Plot a fitted cluster point process

Plot a three-dimensional point pattern

Mosaic Random Field

Simulate systematic random point pattern

Apply Vector Translation To Point Pattern

Compute Integral of Function Against Cumulative Distribution