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spatstat (version 1.20-5)

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

16,590

Version

1.20-5

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

October 25th, 2010

Functions in spatstat (1.20-5)

Convert Data To Class owin

Convert Data to Hyperframe

Bounding Box of a Window or Point Pattern

Distance to Boundary of Window

complement.owin

Take Complement of a Window

Apply Function to Image Broken Down by Factor

Test Whether Two Pixel Images Are Compatible

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Safely Convert Point Pattern Window to Binary Mask

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

Apply a Function to a Point Pattern Broken Down by Factor

Exponential Energy Marks

Pairwise distances between two different line segment patterns

Diameter of a Window

Subdivide a Window or Tessellation using a Set of Lines

Histogram of Pixel Values in an Image

Distance Map of Point Pattern

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Expand Window By Factor

Class of Images

Multi-Dimensional Box

Diggle's Heather Data

Test Whether Marks Are Present

Pixel Image Approximation of a Window

Method of Minimum Contrast

Kaplan-Meier and Reduced Sample Estimator using Histograms

Tropical rain forest trees

Convert Line Segment Pattern to Binary Pixel Mask

Collapse Several Function Tables into One

Delaunay Triangulation of Point Pattern

Distance to Boundary of Window

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Point Patterns of New Brunswick Forest Fires

Morishita Index Plot

Data Frames of Function Values

Intersection, Union or Set Subtraction of Two Windows

Summarise Marks in Every Neighbourhood in a Point Pattern

Berman's Tests for Point Process Model

spatstat-internal

Internal spatstat functions

Pairwise distances between line segments

plot a Fitted Point Process Model

Saturated Pairwise Interaction Point Process Family

Dirichlet Tessellation of Point Pattern

Distance Map of Line Segment Pattern

Distance Map of Window

Biological Cells Point Pattern

Interactively Add Points

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Plot a fitted cluster point process

Profile Maximum Pseudolikelihood

Intersect Infinite Straight Lines with a Window

Test Whether An Object Is Empty

Morphological Erosion

Lurking variable plot

Areas of Morphological Dilations

Evaluate Expression Involving Pixel Images

New Zealand Trees Point Pattern

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Centroid of a window

Pair Correlation Function obtained from K Function

Plot a Spatial Window

Morphological Closing

Identify Segments in a Line Segment Pattern

Quadrat counting for a point pattern

Perspective Plot of Pixel Image

Mark Correlation Integral

Aherne's hamster tumour data

Class of Line Segment Patterns

Create a Function Value Table

Create a Point Matching

Multitype pair correlation function (i-to-any)

Convert Data To Class ppp

Identify Points in a Point Pattern

Convert a Window to a Polygonal Window

Find Largest Circle Inside Window

Beta Ganglion Cells in Cat Retina

Function Arrays for Spatial Patterns

Print Brief Details of an Image

Morphological Dilation

Hutchings' Bramble Canes data

The Lennard-Jones Potential

Convert Line Segment Pattern to Another Unit of Length

bounding.box.xy

Convex Hull of Points

Lengths of Line Segments

Apply Gaussian Blur to a Pixel Image

Longleaf Pines Point Pattern

Apply Affine Transformation

Clark and Evans Aggregation Index

Integral of a Pixel Image

Create a Point Pattern

Hyper Data Frame

Simulate Simple Sequential Inhibition

Test Whether An Object Is A Window

Marks of a Point Pattern

Convert Data To Tessellation

Methods for three-dimensional point patterns

Simulate from a Fitted Point Process Model

Coefficients of Fitted Point Process Model

Test Whether An Object Is A Pixel Image

Fit cluster point process model

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Colour Lookup Tables

Simulate point patterns using the Metropolis-Hastings algorithm.

plot.bermantest

Plot Result of Berman Test

Test Whether A Point Pattern is Marked

Test whether Object is Multitype

Generate grid of parallel lines with random displacement

Plot a three-dimensional point pattern

Generate N Uniform Random Points

Generate N Random Points

Extract Original Data from a Fitted Point Process Model

Nearest Neighbour Distances in Any Dimensions

Nearest Neighbours in Any Dimensions

Crossing Points of Two Line Segment Patterns

Estimate window from points alone

Diameter of an Object

Interactively Define a Polygon

Find Line Segment Nearest to Each Point

Kernel Smoothed Intensity of Point Pattern

Kaplan-Meier Estimator using Histogram Data

Compute Integral of Function Against Cumulative Distribution

Three-Dimensional Box

Print News About Latest Version of Package

Generate Poisson Point Pattern in Three Dimensions

Contour plot of pixel image

Apply Smoothing to Function Values

Convex Hull of Points

Test Whether An Object Is A Point Pattern

Convert Pixel Image to Matrix

Distance for a Point Pattern Matching

Summary of a Point Pattern Dataset

Diagnostic Plots for Fitted Point Process Model

Geometrical Calculations for Multi-Dimensional Box

Local pair correlation function

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Multitype pair correlation function (cross-type)

rshift.splitppp

Randomly Shift a List of Point Patterns

Fit the Thomas Point Process by Minimum Contrast

Quadrature Scheme Based on Pixel Grid

Area of Part of Disc

Simulation Envelopes of Summary Function for 3D Point Pattern

Mosaic Random Set

Apply Vector Translation To Pixel Image

Test Whether An Object Is A Fitted Point Process Model

Plot Function Values

Create a Window

crossdist.default

Pairwise distances between two different sets of points

Marked J Function

Spatial smoothing of observations at irregular points

Pairwise distances

Classify Points in a Point Pattern

Mark Correlation Function

Compute Expansion Window for Simulation

Volume of an Object

Nearest Neighbours Between Two Patterns

Plot a plotppm Object Created by plot.ppm

Distance Map as a Function

Kolmogorov-Smirnov Test for Point Process Model

Apply Vector Translation To Line Segment Pattern

Pair Correlation Function obtained from array of K functions

Print a Fitted Point Process Model

Pairwise distances

Randomly Shift a Point Pattern

Multidimensional Space-Time Point Pattern

Extract the Interaction from a Fitted Point Process Model

Border Region of a Window

Create a Pixel Image Object

Plot a tessellation

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Determine Duplicated Points in a Spatial Point Pattern

Superimpose Several Line Segment Patterns

Basis for Harmonic Functions

Multitype K Function (i-to-any)

Level Set of a Pixel Image

Compute Quadrature Weights Based on Grid Counts

pairdist.default

Pairwise distances

Ponderosa Pine Tree Point Pattern

The Fiksel Interaction

Poisson Point Process Model

Fry Plot of Point Pattern

plot.hyperframe

Plot Entries in a Hyperframe

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Nearest neighbour

Place Points Evenly Along Specified Lines

Make Periodic Copies of a Spatial Pattern

Three Dimensional Point Pattern

Humberside Data on Childhood Leukaemia and Lymphoma

Pine saplings in Finland.

Beta Ganglion Cells in Cat Retina, Old Version

Data and Code From JRSS Discussion Paper on Residuals

Multitype K Function (Cross-type)

The Strauss / Hard Core Point Process Model

Distance Between Two Point Patterns

Plot a Spatial Kolmogorov-Smirnov Test

Simulate Stratified Random Point Pattern

Weighted Empirical Cumulative Distribution Function

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Plot a Simulation Envelope

Number of Points in a Point Pattern

Approximate a Polygon by a Simpler Polygon

Infinite Straight Lines

Print Progress Reports

Simulation Envelopes of Summary Function

Point and Click Interface for Exploratory Analysis of Point Pattern

Hughes' Amacrine Cell Data

Simulate Matern Cluster Process

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Divide Region into Quadrats

Inhomogeneous Cross Type L Function

Test Whether a Window is Convex

Japanese Pines Point Pattern

Difference of Disc Areas

Residuals for Fitted Point Process Model

Berman-Huntington points and lines data

Ord Interaction Process Family

Rectangular grid of points

Intersection of Two Tessellations

Print Brief Details of a Line Segment Pattern Dataset

Simulate Baddeley-Silverman Cell Process

Window in Shape of Letter R

Midpoints of Line Segment Pattern

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

Convert Pixel Image to Another Unit of Length

Rotate a Line Segment Pattern

Test Whether A Point Process Model is Marked

Update a Fitted Point Process Model

Lansing Woods Point Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

plot a Spatial Point Pattern

Pairwise distances in Three Dimensions

Convert and Compare Colours in Different Formats

Random Perturbation of a Point Pattern

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Plot a List of Things

Randomly Shift a Line Segment Pattern

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

Log Likelihood for Poisson Point Process Model

Simulate a Fitted Cluster Point Process Model

Distance to Boundary of Window

Corners of a rectangle

Interaction Distance of a Point Process

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Methods for Three-Dimensional Box

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

Scatterplot Matrix for Pixel Images

Nearest Neighbour Distance Function G

Nearest neighbours in three dimensions

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Evaluate an Expression in a Function Table

Pair Correlation Function of a Three-Dimensional Point Pattern

Generate a Quadrature Scheme from a Point Pattern

Extract or Replace Subset of a List of Things

matclust.estpcf

Fit the Matern Cluster Point Process by Minimum Contrast Using Pair Correlation

Plot a Colour Map

Inhomogeneous K-function

Generate a Default Pattern of Dummy Points

Interpret Fitted Model for Metropolis-Hastings Simulation.

multiplicity.ppp

Count Multiplicity of Duplicate Points

Estimate the I-function

nearest.raster.point

Find Pixel Nearest to a Given Point

Fit the Matern Cluster Point Process by Minimum Contrast

Convert Data To Class psp

Poisson Line Tessellation

Convert Line Segment Pattern to Pixel Image

Concatenate x,y Coordinate Vectors

spatstat-package

The Spatstat Package

Theoretical Distribution of Nearest Neighbour Distance

Swedish Pines Point Pattern

Methods for Multidimensional Space-Time Point Patterns

Print Brief Details of a Spatial Window

spatstat.options

Internal Options in Spatstat Package

Union of Data and Dummy Points

Nearest neighbour distances between line segments

Convert Spatial Object to Pixel Image

pairwise.family

Pairwise Interaction Process Family

Weighted Histogram

Pair Correlation Function of Point Pattern

Create a Line Segment Pattern

Rotate a Window

Generate Poisson Point Pattern on Line Segments

Connected components of an image or window

Perimeter Length of Window

The Soft Core Point Process Model

Divide Image Into Sub-images

Nearest neighbour distances

Extract Quadrature Scheme Used to Fit a Point Process Model

Murchison gold deposits

Kernel Smoothing of Line Segment Pattern

plot a Spatial Quadrature Scheme

Nearest neighbour distances in three dimensions

Divide Point Pattern into Sub-patterns

Sample Quantiles of Pixel Image

Sufficient Statistic of Point Process Model

model.matrix.ppm

Extract Design Matrix from Point Process Model

Extract Unique Points from a Spatial Point Pattern

Summarizing a Pixel Image

Pairwise distances

The Area Interaction Point Process Model

Morphological Opening

K-function using FFT

spatstat-deprecated

Deprecated spatstat functions

Extract Dummy Points Used to Fit a Point Process Model

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

Apply Function to Every Neighbourhood in a Point Pattern

Class of Fitted Point Process Models

Pairwise distances between two different point patterns

Generate Poisson Point Pattern in Any Dimensions

Simulate Matern Model I

Reduced Sample Estimator using Histogram Data

Apply Affine Transformation To Point Pattern

Orientation Angles of Line Segments

Plot a Function Array

Generic Pairwise Interaction model

Mosaic Random Field

Simulate a Fitted Gibbs Point Process Model

Convert Data to Three-Dimensional Box

Fit Point Process Model to Data

Foxall's Distance Functions

Evaluate Expression Involving Functions

Simulate Gauss-Poisson Process

Convert Point Pattern to Pixel Image

Convert Window to Another Unit of Length

Read Point Pattern From Data File

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

Generate N Uniform Random Points in a Disc

Empty Space Function of a Three-Dimensional Point Pattern

Class of Quadrature Schemes

Endpoints of Line Segment Pattern

Data Sharpening of Point Pattern

Set Control Parameters for Metropolis-Hastings Algorithm.

Simulate systematic random point pattern

Apply Vector Translation To Window

summary.splitppp

Summary of a Split Point Pattern

quadratresample

Resample a Point Pattern by Resampling Quadrats

Summarizing a Fitted Point Process Model

Convert Polygonal Region into Different Format

Apply Vector Translation To Point Pattern

Apply Vector Translation

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

California Redwoods Point Pattern (Ripley's Subset)

Reset Values in Subset of Image

California Redwoods Point Pattern (Entire Dataset)

Test Whether Points Are Inside A Window

Generic Ord Interaction model

Variance-Covariance Matrix for a Fitted Point Process Model

Random Re-Labelling of Point Pattern

Simulate Neyman-Scott Process

Fit the Thomas Point Process by Minimum Contrast

Area of a Window

Calculate four standard summary functions of a point pattern.

Simulated Point Pattern

Compute Images of Constructed Covariates

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

Generate Multitype Poisson Point Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Simulate Thomas Process

Extract Subset of Function Array

Pairwise Distances in Any Dimensions

Difference of Disc Areas

Pair Correlation Function

Galaxies in the Shapley Supercluster

Generate N Uniform Random Points in Any Dimensions

Generate Poisson Random Line Process

Extract List of Tiles in a Tessellation

Convert Point Pattern to Another Unit of Length

Rotate a Point Pattern

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Extract or Replace Subset of Point Pattern

Vertices of a Window

Reduced Second Moment Measure

Beadlet Anemones Data

Extract or Replace Subset of Tessellation

plot a Spatial Line Segment Pattern

Estimate the empty space function F

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Update a Fitted Cluster Point Process Model

The Piecewise Constant Pairwise Interaction Point Process Model

Hybrid Geyer Point Process Model

Inhomogeneous Pair Correlation Function

Inhomogeneous Cross K Function

Mark Connection Function

Plot a List of Point Patterns

Superimpose Several Point Patterns

Perfect Simulation of the Strauss Process

Harkness-Isham ants' nests data

Cut margins from rectangle

Circular Window

Multitype L-function (cross-type)

Generate Poisson Point Pattern

Summary of a Line Segment Pattern Dataset

Inhomogeneous Multitype L Dot Function

Diagnostics for random marking

Calculate Summary Statistic for All Types in a Multitype Point Pattern

pppmatching.object

Class of Point Matchings

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Summary of a Spatial Window

Name for Unit of Length

Nearest Neighbour Clutter Removal

Q-Q Plot of Residuals from Fitted Point Process Model

Extract Subset of Function Values

Cartesian Coordinates for a Pixel Raster

as.data.frame.im

Convert Pixel Image to Data Frame

Class of Point Patterns

Extract.splitppp

Extract or Replace Sub-Patterns

Random Thinning

Extract Subset of Image

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Geyer's Saturation Point Process Model

Marked Nearest Neighbour Distance Function

Spherical Contact Distribution Function

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

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

Marked K-Function

The Multitype Strauss Point Process Model

Estimate the J-function

Evaluate Expression Involving Function Arrays

Define Point Process Model for Metropolis-Hastings Simulation.

Define Point Process Model for Metropolis-Hastings Simulation.

Prediction from a Fitted Point Process Model

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Print a Quadrature Scheme

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Geometrical Calculations for Three-Dimensional Box

model.frame.ppm

Extract the Environment of a Point Process Model

methods.distfun

Methods for Distance Functions

K-function of a Three-Dimensional Point Pattern

Spruces Point Pattern

Urkiola Woods Point Pattern

Create a Tessellation

Fitted Conditional Intensity for Point Process Model

Test Whether Two Function Objects Are Compatible

Summarizing a Quadrature Scheme

Combine Two Line Segment Patterns

Multitype L-function (i-to-any)

inforder.family

Infinite Order Interaction Family

Multitype J Function (i-to-any)

Generate N Random Multitype Points

Inhomogeneous Multitype K Dot Function

Saturated Pairwise Interaction model

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Neighbourhood density function

Multitype J Function (i-to-j)

ANOVA for Fitted Point Process Models

Methods for Multi-Dimensional Box

Interpolate a Pixel Image

Spokes pattern of dummy points

The Hard Core Point Process Model

Generate N Uniform Random Points in Three Dimensions

Ord's Interaction model

The Strauss Point Process Model

Convert Pixel Image from Numeric to Factor

Subset of Quadrature Scheme

Convert to Pixel Image

Combine Function Value Tables

Bronze gradient filter data

Chorley-Ribble Cancer Data

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Pairwise distances between two different three-dimensional point patterns

Artificial Data Point Pattern

Areas of Morphological Erosions

Point and Click Interface for Displaying a Point Pattern

Determine Whether One Window is Contained In Another

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Convert Window to Pixel Image

Prediction from a Fitted Cluster Point Process Model

Plot a Pixel Image

Print Brief Details of a Point Pattern Dataset

project2segment

Move Point To Nearest Line

Simulate Matern Model II

Set Covariance of a Window

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Diggle-Gratton model

Extract Subset of Line Segment Pattern

rescue.rectangle

Convert Window Back To Rectangle

Convert dataset to another unit of length

Summary of a List of Things

Apply Affine Transformation To Window

Apply Affine Transformation To Line Segment Pattern

Locally Scaled K-function