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spatstat (version 1.18-1)

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. 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

1.18-1

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

March 19th, 2010

Functions in spatstat (1.18-1)

Inhomogeneous Multitype K Dot Function

Chorley-Ribble Cancer Data

Bounding Box of a Window or Point Pattern

Difference of Disc Areas

Difference of Disc Areas

Coefficients of Fitted Point Process Model

The Soft Core Point Process Model

Harkness-Isham ants' nests data

Reduced Second Moment Measure

Nearest Neighbour Distance Function G

Extract or Replace Subset of Point Pattern

Colour Lookup Tables

Pixel Image Approximation of a Window

Apply Gaussian Blur to a Pixel Image

Estimate the I-function

Multitype L-function (i-to-any)

The Area Interaction Point Process Model

Collapse Several Function Tables into One

Beta Ganglion Cells in Cat Retina

Inhomogeneous Multitype L Dot Function

Convex Hull of Points

Distance to Boundary of Window

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

Evaluate Expression Involving Pixel Images

Dirichlet Tessellation of Point Pattern

Apply Affine Transformation To Point Pattern

Geyer's Saturation Point Process Model

Subset of Quadrature Scheme

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Combine Two Line Segment Patterns

Apply Affine Transformation To Line Segment Pattern

Distance to Boundary of Window

Inhomogeneous Cross K Function

Hutchings' Bramble Canes data

Berman-Huntington points and lines data

Extract or Replace Subset of a List of Things

Pairwise distances

Diggle-Gratton model

Convert Data To Class ppp

The Strauss Point Process Model

Pairwise distances between two different three-dimensional point patterns

Delaunay Triangulation of Point Pattern

Test Whether Points Are Inside A Window

Estimate the empty space function F

Test Whether A Point Process Model is Marked

Biological Cells Point Pattern

Hughes' Amacrine Cell Data

Integral of a Pixel Image

Marked K-Function

Extract Subset of Function Array

Orientation Angles of Line Segments

Test whether Object is Multitype

Generic Pairwise Interaction model

Interpolate a Pixel Image

Multitype L-function (cross-type)

Calculate four standard summary functions of a point pattern.

Kaplan-Meier Estimator using Histogram Data

Lansing Woods Point Pattern

Level Set of a Pixel Image

Convert a Window to a Polygonal Window

Convert Window to Pixel Image

Extract Subset of Line Segment Pattern

Interactively Define a Polygon

Centroid of a window

Convert Pixel Image to Matrix

Extract Subset of Function Values

K-function of a Three-Dimensional Point Pattern

Class of Point Patterns

quadratresample

Resample a Point Pattern by Resampling Quadrats

Convert Data To Class psp

Concatenate x,y Coordinate Vectors

Diameter of a Window

Fit cluster point process model

Safely Convert Point Pattern Window to Binary Mask

crossdist.default

Pairwise distances between two different sets of points

Lengths of Line Segments

Evaluate Expression Involving Functions

Multitype K Function (Cross-type)

Summarise Marks in Every Neighbourhood in a Point Pattern

Geometrical Calculations for Three-Dimensional Box

Print News About Latest Version of Package

The Lennard-Jones Potential

Extract or Replace Subset of Tessellation

Generate a Quadrature Scheme from a Point Pattern

Marked Nearest Neighbour Distance Function

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

complement.owin

Take Complement of a Window

Aherne's hamster tumour data

Sample Quantiles of Pixel Image

Convert to Pixel Image

The Multitype Strauss Point Process Model

Summarizing a Pixel Image

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

Test Whether Two Pixel Images Are Compatible

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

Multitype J Function (i-to-any)

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Test Whether An Object Is A Window

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Distance for a Point Pattern Matching

Log Likelihood for Poisson Point Process Model

Extract.splitppp

Extract or Replace Sub-Patterns

Expand Window By Factor

The Hard Core Point Process Model

Fry Plot of Point Pattern

Convert Polygonal Region into Different Format

Test Whether Two Function Objects Are Compatible

Marked J Function

Area of Part of Disc

Find Largest Circle Inside Window

Create a Point Pattern

Corners of a rectangle

Point and Click Interface for Exploratory Analysis of Point Pattern

Pair Correlation Function of Point Pattern

Nearest neighbour distances between line segments

Extract Dummy Points Used to Fit a Point Process Model

Neighbourhood density function

Longleaf Pines Point Pattern

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Convert Data to Three-Dimensional Box

Fitted Conditional Intensity for Point Process Model

Class of Images

Extract the Interaction from a Fitted Point Process Model

Apply Affine Transformation To Window

plot a Spatial Quadrature Scheme

Japanese Pines Point Pattern

Test Whether Marks Are Present

Morphological Closing

Reset Values in Subset of Image

The Strauss / Hard Core Point Process Model

Apply Function to Image Broken Down by Factor

Fit the Thomas Point Process by Minimum Contrast

Simulate Matern Cluster Process

Pine saplings in Finland.

Test Whether A Point Pattern is Marked

Distance Map as a Function

Simulate Thomas Process

Berman's Tests for Point Process Model

pairdist.default

Pairwise distances

Test Whether An Object Is A Pixel Image

Create a Point Matching

Ord's Interaction model

Plot a Spatial Window

Mark Connection Function

Window in Shape of Letter R

Mean, Median and Range of Pixel Values in an Image

Vertices of a Window

Murchison gold deposits

Areas of Morphological Erosions

Saturated Pairwise Interaction model

Convert Data To Tessellation

Diagnostics for random marking

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Kolmogorov-Smirnov Test for Point Process Model

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

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

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

Interactively Add Points

Distance Map of Window

Extract Original Data from a Fitted Point Process Model

Three Dimensional Point Pattern

Find Line Segment Nearest to Each Point

Lurking variable plot

Pair Correlation Function

Mark Correlation Function

Inhomogeneous Pair Correlation Function

K-function using FFT

Extract Unique Points from a Spatial Point Pattern

Generic Ord Interaction model

Test Whether An Object Is Empty

Connected components of an image or window

Convert Pixel Image to Another Unit of Length

Convert Point Pattern to Pixel Image

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Pairwise distances

Simulate a Fitted Cluster Point Process Model

Beta Ganglion Cells in Cat Retina, Old Version

Create a Window

Generate Poisson Random Line Process

Extract List of Tiles in a Tessellation

Test Whether a Window is Convex

Inhomogeneous Cross Type L Function

Simulate Baddeley-Silverman Cell Process

Compute Quadrature Weights Based on Grid Counts

Plot a Pixel Image

Point and Click Interface for Displaying a Point Pattern

Intersection, Union or Set Subtraction of Two Windows

Distance to Boundary of Window

Number of Points in a Point Pattern

Quadrat counting for a point pattern

Kaplan-Meier and Reduced Sample Estimator using Histograms

Endpoints of Line Segment Pattern

Basis for Harmonic Functions

Morphological Dilation

Artificial Data Point Pattern

Multitype pair correlation function (i-to-any)

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Diggle's Heather Data

Generate Multitype Poisson Point Pattern

Spruces Point Pattern

Plot a Function Array

nearest.raster.point

Find Pixel Nearest to a Given Point

Define Point Process Model for Metropolis-Hastings Simulation.

Pairwise distances between two different point patterns

Divide Point Pattern into Sub-patterns

Empty Space Function of a Three-Dimensional Point Pattern

Diagnostic Plots for Fitted Point Process Model

Distance Map of Point Pattern

Compute Images of Constructed Covariates

Determine Whether One Window is Contained In Another

Convert Line Segment Pattern to Binary Pixel Mask

Interpret Fitted Model for Metropolis-Hastings Simulation.

Crossing Points of Two Line Segment Patterns

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Read Point Pattern From Data File

Pair Correlation Function obtained from array of K functions

The Piecewise Constant Pairwise Interaction Point Process Model

Name for Unit of Length

Fit the Matern Cluster Point Process by Minimum Contrast

Test Whether An Object Is A Fitted Point Process Model

Simulate Matern Model I

Convert Data To Class owin

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Point Patterns of New Brunswick Forest Fires

Update a Fitted Point Process Model

Histogram of Pixel Values in an Image

Kernel Smoothed Intensity of Point Pattern

Ord Interaction Process Family

Bronze gradient filter data

Evaluate an Expression in a Function Table

Test Whether An Object Is A Point Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Print Brief Details of a Spatial Window

Convert Spatial Object to Pixel Image

is.multitype.ppm

Test Whether A Point Process Model is Multitype

as.data.frame.im

Convert Pixel Image to Data Frame

Print Brief Details of an Image

Print a Fitted Point Process Model

Infinite Straight Lines

Pairwise distances between line segments

Nearest neighbour distances

Summarizing a Fitted Point Process Model

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Methods for three-dimensional point patterns

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

multiplicity.ppp

Count Multiplicity of Duplicate Points

Mark Correlation Integral

Apply Vector Translation To Point Pattern

Q-Q Plot of Residuals from Fitted Point Process Model

Union of Data and Dummy Points

Fit Point Process Model to Data

Beadlet Anemones Data

Cartesian Coordinates for a Pixel Raster

Perfect Simulation of the Strauss Process

Multidimensional Space-Time Point Pattern

Simulation Envelopes of Summary Function

Convert Line Segment Pattern to Pixel Image

Perspective Plot of Pixel Image

Humberside Data on Childhood Leukaemia and Lymphoma

Plot a List of Point Patterns

Identify Points in a Point Pattern

plot a Spatial Line Segment Pattern

Determine Duplicated Points in a Spatial Point Pattern

Spatial smoothing of observations at irregular points

plot a Spatial Point Pattern

Extract Subset of Image

Data Frames of Function Values

Urkiola Woods Point Pattern

Circular Window

Poisson Line Tessellation

inforder.family

Infinite Order Interaction Family

Reduced Sample Estimator using Histogram Data

New Zealand Trees Point Pattern

Midpoints of Line Segment Pattern

Divide Region into Quadrats

Rectangular grid of points

Convert Point Pattern to Another Unit of Length

California Redwoods Point Pattern (Entire Dataset)

Summary of a Line Segment Pattern Dataset

bounding.box.xy

Convex Hull of Points

Generate N Uniform Random Points

Area of a Window

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

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

Estimate window from points alone

Generate a Default Pattern of Dummy Points

Pairwise distances between two different line segment patterns

Pair Correlation Function obtained from K Function

Simulate Simple Sequential Inhibition

plot.bermantest

Plot Result of Berman Test

Kernel Smoothing of Line Segment Pattern

Generate Poisson Point Pattern in Three Dimensions

Set Covariance of a Window

Distance Map of Line Segment Pattern

project2segment

Move Point To Nearest Line

spatstat-internal

Internal spatstat functions

plot a Fitted Point Process Model

Convert Window to Another Unit of Length

Data and Code From JRSS Discussion Paper on Residuals

Create a Function Value Table

Spherical Contact Distribution Function

Place Points Evenly Along Specified Lines

Generate N Random Points

Quadrature Scheme Based on Pixel Grid

Generate Poisson Point Pattern on Line Segments

Plot a List of Things

Methods for Multidimensional Space-Time Point Patterns

Poisson Point Process Model

Multitype K Function (i-to-any)

Theoretical Distribution of Nearest Neighbour Distance

Method of Minimum Contrast

Print Brief Details of a Line Segment Pattern Dataset

Random Perturbation of a Point Pattern

Prediction from a Fitted Cluster Point Process Model

Plot a fitted cluster point process

Create a Line Segment Pattern

Combine Function Value Tables

Apply Vector Translation

Clark and Evans Aggregation Index

Morishita Index Plot

Generate N Uniform Random Points in a Disc

Cut margins from rectangle

Plot a plotppm Object Created by plot.ppm

Prediction from a Fitted Point Process Model

Class of Quadrature Schemes

pairwise.family

Pairwise Interaction Process Family

Mosaic Random Field

Plot a Colour Map

Nearest neighbour

Simulate Stratified Random Point Pattern

Interaction Distance of a Point Process

Class of Line Segment Patterns

Simulate Matern Model II

Simulate systematic random point pattern

Plot a three-dimensional point pattern

Nearest Neighbours Between Two Patterns

spatstat.options

Internal Options in Spatstat Package

Perimeter Length of Window

Three-Dimensional Box

Contour plot of pixel image

Mosaic Random Set

Random Re-Labelling of Point Pattern

Summary of a Spatial Window

Extract Quadrature Scheme Used to Fit a Point Process Model

Methods for Three-Dimensional Box

Generate N Uniform Random Points in Three Dimensions

Randomly Shift a Line Segment Pattern

plot.hyperframe

Plot Entries in a Hyperframe

Hyper Data Frame

pppmatching.object

Class of Point Matchings

Generate grid of parallel lines with random displacement

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Tropical rain forest trees

Simulate from a Fitted Point Process Model

Marks of a Point Pattern

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Print a Quadrature Scheme

Plot a tessellation

Convert dataset to another unit of length

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Simulate Neyman-Scott Process

Morphological Opening

Apply Affine Transformation

Define Point Process Model for Metropolis-Hastings Simulation.

Simulate point patterns using the Metropolis-Hastings algorithm.

Morphological Erosion

Profile Maximum Pseudolikelihood

Random Thinning

Distance Between Two Point Patterns

Plot a Spatial Kolmogorov-Smirnov Test

Variance-Covariance Matrix for a Fitted Point Process Model

California Redwoods Point Pattern (Ripley's Subset)

Update a Fitted Cluster Point Process Model

Rotate a Point Pattern

Apply Vector Translation To Line Segment Pattern

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Spokes pattern of dummy points

Superimpose Several Line Segment Patterns

Print Brief Details of a Point Pattern Dataset

Galaxies in the Shapley Supercluster

Simulate a Fitted Gibbs Point Process Model

Generate Poisson Point Pattern

Classify Points in a Point Pattern

Rotate a Line Segment Pattern

Areas of Morphological Dilations

Pairwise distances

Plot Function Values

Weighted Histogram

Class of Fitted Point Process Models

Evaluate Expression Involving Function Arrays

Exponential Energy Marks

Ponderosa Pine Tree Point Pattern

Summary of a Point Pattern Dataset

Weighted Empirical Cumulative Distribution Function

rshift.splitppp

Randomly Shift a List of Point Patterns

Print Progress Reports

Apply Vector Translation To Pixel Image

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

Simulate Gauss-Poisson Process

Nearest neighbours in three dimensions

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Convert Pixel Image from Numeric to Factor

Saturated Pairwise Interaction Point Process Family

Simulated Point Pattern

Generate N Random Multitype Points

Function Arrays for Spatial Patterns

Superimpose Several Point Patterns

rescue.rectangle

Convert Window Back To Rectangle

Residuals for Fitted Point Process Model

Divide Image Into Sub-images

Intersection of Two Tessellations

Nearest neighbour distances in three dimensions

Set Control Parameters for Metropolis-Hastings Algorithm.

Summarizing a Quadrature Scheme

Multitype J Function (i-to-j)

model.matrix.ppm

Extract Design Matrix from Point Process Model

Create a Tessellation

Swedish Pines Point Pattern

Apply Vector Translation To Window

summary.splitppp

Summary of a Split Point Pattern

ANOVA for Fitted Point Process Models

Hybrid Geyer Point Process Model

Summary of a List of Things

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Estimate the J-function

Border Region of a Window

Inhomogeneous K-function

Convert Data to Hyperframe

Subdivide a Window or Tessellation using a Set of Lines

Intersect Infinite Straight Lines with a Window

Apply a Function to a Point Pattern Broken Down by Factor

spatstat-deprecated

Deprecated spatstat functions

Simulation Envelopes of Summary Function for 3D Point Pattern

Nearest Neighbour Clutter Removal

Multitype pair correlation function (cross-type)

Make Periodic Copies of a Spatial Pattern

Convert Line Segment Pattern to Another Unit of Length

Sufficient Statistic of Point Process Model

Apply Function to Every Neighbourhood in a Point Pattern

Randomly Shift a Point Pattern

Compute Integral of Function Against Cumulative Distribution

spatstat-package

The Spatstat Package

Approximate a Polygon by a Simpler Polygon

Rotate a Window

Create a Pixel Image Object

Pairwise distances in Three Dimensions