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spatstat (version 1.21-5.1)

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 over 1000 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. Exploratory methods include K-functions, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics etc. Point process models can be fitted to point pattern data using functions ppm, kppm, slrm similar to glm. Models may include dependence on covariates, interpoint interaction, cluster formation 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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Install

install.packages('spatstat')

Monthly Downloads

16,590

Version

1.21-5.1

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

March 21st, 2011

Functions in spatstat (1.21-5.1)

Extract Subset of Function Values

The Hard Core Point Process Model

The Fiksel Interaction

Estimate the empty space function F

Apply Affine Transformation To Line Segment Pattern

Multitype K Function (Cross-type)

Chorley-Ribble Cancer Data

The Piecewise Constant Pairwise Interaction Point Process Model

Estimate the I-function

Apply Affine Transformation

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Harkness-Isham ants' nests data

Diggle-Gratton model

Generic Ord Interaction model

Apply Affine Transformation To Window

Intersect Infinite Straight Lines with a Window

Coefficients of Fitted Point Process Model

Foxall's Distance Functions

Convert Data to Hyperframe

Extract Subset of Image

Inhomogeneous K-function

Poisson Point Process Model

The Lennard-Jones Potential

Saturated Pairwise Interaction model

Exponential Energy Marks

Combine Function Value Tables

Biological Cells Point Pattern

Distance to Boundary of Window

Convert and Compare Colours in Different Formats

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

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

The Strauss Point Process Model

Intersection, Union or Set Subtraction of Two Windows

Beadlet Anemones Data

Convert Data To Class ppp

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Convex Hull of Points

Apply Affine Transformation To Point Pattern

as.data.frame.im

Convert Pixel Image to Data Frame

Tropical rain forest trees

Bounding Box of a Window or Point Pattern

Coefficients of Fitted Spatial Logistic Regression Model

Lansing Woods Point Pattern

ANOVA for Fitted Point Process Models

Interactively Add Points

Pairwise distances between two different line segment patterns

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

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Geometrical Calculations for Three-Dimensional Box

Multitype K Function (i-to-any)

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Classify Points in a Point Pattern

Convert Data to Three-Dimensional Box

Extract Subset of Function Array

Hybrid Geyer Point Process Model

Diagnostic Plots for Fitted Point Process Model

K-function using FFT

Convert to Pixel Image

K-function of a Three-Dimensional Point Pattern

Distance Map of Window

Subset of Quadrature Scheme

Extract Subset of Signed or Vector Measure

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Estimate the J-function

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

Ord's Interaction model

Marked J Function

Inhomogeneous Cross Type L Function

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Apply a Function to a Point Pattern Broken Down by Factor

Spherical Contact Distribution Function

Calculate four standard summary functions of a point pattern.

Colour Lookup Tables

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Marked Nearest Neighbour Distance Function

Mark Correlation Integral

Apply Gaussian Blur to a Pixel Image

Safely Convert Point Pattern Window to Binary Mask

Extract or Replace Subset of Point Pattern

crossdist.default

Pairwise distances between two different sets of points

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Diameter of an Object

Scatterplot Matrix for Pixel Images

Difference of Disc Areas

Circular Window

Distance Map of Point Pattern

Simulation Envelopes of Summary Function for 3D Point Pattern

Distance to Boundary of Window

Multitype pair correlation function (cross-type)

Border Region of a Window

Convert Data To Class psp

Multitype L-function (i-to-any)

Create a Function Value Table

Extract Dummy Points Used to Fit a Point Process Model

Pairwise distances between two different point patterns

Aherne's hamster tumour data

Evaluate Expression Involving Pixel Images

Artificial Data Point Pattern

Determine Duplicated Points in a Spatial Point Pattern

Identify Points in a Point Pattern

Morphological Closing

Test Whether An Object Is A Pixel Image

Data Frames of Function Values

Concatenate x,y Coordinate Vectors

Morphological Dilation

Bronze gradient filter data

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

Locally Scaled K-function

Diameter of a Window

plot a Spatial Line Segment Pattern

Analysis of Deviance for Spatial Logistic Regression Models

Class of Images

Three Dimensional Point Pattern

Test Whether Points Are Inside A Window

Evaluate Expression Involving Functions

Morphological Erosion

Identify Segments in a Line Segment Pattern

Japanese Pines Point Pattern

Areas of Morphological Dilations

Collapse Several Function Tables into One

Interpolate a Pixel Image

Fitted Probabilities for Spatial Logistic Regression

spatstat-internal

Internal spatstat functions

The Multitype Strauss Point Process Model

Integral of a Pixel Image

Connected components of an image or window

Inhomogeneous Cross K Function

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Test Whether An Object Is A Point Pattern

Test Whether Two Pixel Images Are Compatible

Test Whether An Object Is Empty

Multitype L-function (cross-type)

Beta Ganglion Cells in Cat Retina

Determine Whether One Window is Contained In Another

Kaplan-Meier and Reduced Sample Estimator using Histograms

Inhomogeneous Multitype K Dot Function

Area of a Window

Inhomogeneous Multitype L Dot Function

Subdivide a Window or Tessellation using a Set of Lines

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Methods for three-dimensional point patterns

Kaplan-Meier Estimator using Histogram Data

Pixel Image Approximation of a Window

Generic Pairwise Interaction model

bounding.box.xy

Convex Hull of Points

Extract Subset of Line Segment Pattern

Test Whether Marks Are Present

Berman-Huntington points and lines data

Kolmogorov-Smirnov Test for Point Process Model

Expand Window By Factor

Window in Shape of Letter R

Number of Points in a Point Pattern

Nearest neighbour distances in three dimensions

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

Create a Point Pattern

Pairwise distances between two different three-dimensional point patterns

Compute Quadrature Weights Based on Grid Counts

Loglikelihood of Spatial Logistic Regression

Hughes' Amacrine Cell Data

Summarise Marks in Every Neighbourhood in a Point Pattern

model.frame.ppm

Extract the Environment of a Point Process Model

Log Likelihood for Poisson Point Process Model

Create a Window

Midpoints of Line Segment Pattern

Nearest neighbours in three dimensions

Mark Connection Function

Method of Minimum Contrast

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Set Control Parameters for Metropolis-Hastings Algorithm.

New Zealand Trees Point Pattern

Humberside Data on Childhood Leukaemia and Lymphoma

Convert a Window to a Polygonal Window

Test Whether A Point Process Model is Marked

Kernel Smoothed Intensity of Point Pattern

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Prediction from a Fitted Point Process Model

Berman's Tests for Point Process Model

Basis for Harmonic Functions

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

Class of Point Patterns

Make Periodic Copies of a Spatial Pattern

Create a Pixel Image Object

Clark and Evans Aggregation Index

Pairwise distances

methods.distfun

Methods for Distance Functions

Morphological Opening

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Hyper Data Frame

Generate Poisson Point Pattern

inforder.family

Infinite Order Interaction Family

Level Set of a Pixel Image

Pair Correlation Function of a Three-Dimensional Point Pattern

The Soft Core Point Process Model

Nonparametric Estimate of Spatially-Varying Relative Risk

Plot a Spatial Window

Simulate from a Fitted Point Process Model

Place Points Evenly Along Specified Lines

Distance for a Point Pattern Matching

Infinite Straight Lines

Nearest Neighbours Between Two Patterns

Cross Validated Bandwidth Selection for Relative Risk Estimation

Ord Interaction Process Family

Convert Window to Pixel Image

Pairwise distances in Three Dimensions

Interactively Define a Polygon

spatstat-deprecated

Deprecated spatstat functions

Point Patterns of New Brunswick Forest Fires

Estimate window from points alone

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Dirichlet Tessellation of Point Pattern

Create a Line Segment Pattern

Convert Spatial Object to Pixel Image

Areas of Morphological Erosions

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Randomly Shift a Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Fitted Conditional Intensity for Point Process Model

Area of Part of Disc

Distance Map as a Function

pairwise.family

Pairwise Interaction Process Family

Pairwise distances

Point and Click Interface for Exploratory Analysis of Point Pattern

Convert Point Pattern to Pixel Image

Test Whether Two Function Objects Are Compatible

pppmatching.object

Class of Point Matchings

Plot a List of Point Patterns

pairdist.default

Pairwise distances

Prediction from a Fitted Cluster Point Process Model

Beta Ganglion Cells in Cat Retina, Old Version

Set Covariance of a Window

Lurking variable plot

Evaluate Expression Involving Function Arrays

Longleaf Pines Point Pattern

Plot a tessellation

Test whether Object is Multitype

Class of Quadrature Schemes

plot.hyperframe

Plot Entries in a Hyperframe

Mosaic Random Set

Perspective Plot of Pixel Image

Class of Fitted Point Process Models

Determine Initial State for Metropolis-Hastings Simulation.

Plot a List of Things

Extract Quadrature Scheme Used to Fit a Point Process Model

Generate N Uniform Random Points in Any Dimensions

Perfect Simulation of the Strauss Process

Simulate Neyman-Scott Process

Print Progress Reports

Generate a Quadrature Scheme from a Point Pattern

Test Whether An Object Is A Window

Quadrat counting for a point pattern

Generate Poisson Random Line Process

Sample Quantiles of Pixel Image

Generate N Random Multitype Points

Plot a Simulation Envelope

Multitype pair correlation function (i-to-any)

Signed or Vector-Valued Measure

Rotate a Window

Contour plot of pixel image

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Local pair correlation function

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

Simulate Matern Cluster Process

Plot Function Values

Random Perturbation of a Point Pattern

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Summary of a List of Things

Superimpose Several Line Segment Patterns

Apply Vector Translation To Line Segment Pattern

Nearest Neighbour Clutter Removal

Pairwise Distances in Any Dimensions

Sufficient Statistic of Point Process Model

Reduced Sample Estimator using Histogram Data

Convert Pixel Image to Another Unit of Length

spatstat.options

Internal Options in Spatstat Package

Swedish Pines Point Pattern

Summarizing a Quadrature Scheme

Convert dataset to another unit of length

Crossing Points of Two Line Segment Patterns

Data and Code From JRSS Discussion Paper on Residuals

Simulate point patterns using the Metropolis-Hastings algorithm.

California Redwoods Point Pattern (Entire Dataset)

Print Brief Details of a Spatial Window

Morishita Index Plot

Plot a Spatial Kolmogorov-Smirnov Test

Find Line Segment Nearest to Each Point

Quadrature Scheme Based on Pixel Grid

Endpoints of Line Segment Pattern

Multidimensional Space-Time Point Pattern

Nearest neighbour distances between line segments

Neighbourhood density function

Compute Areas of Tiles in a Tessellation

Plot a plotppm Object Created by plot.ppm

Simulate a Fitted Gibbs Point Process Model

Extract the Interaction from a Fitted Point Process Model

Simulate Thomas Process

Theoretical Distribution of Nearest Neighbour Distance

Pair Correlation Function obtained from K Function

plot a Spatial Quadrature Scheme

Print a Fitted Point Process Model

Simulate Matern Model II

Diggle's Heather Data

Volume of an Object

Rotate a Point Pattern

Intersection of Two Tessellations

Pairwise distances between line segments

Generate grid of parallel lines with random displacement

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

spatstat-package

The Spatstat Package

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Predicted or Fitted Values from Spatial Logistic Regression

Fit Point Process Model to Data

Generate N Uniform Random Points in Three Dimensions

quadratresample

Resample a Point Pattern by Resampling Quadrats

Extract List of Tiles in a Tessellation

Apply Vector Translation To Window

California Redwoods Point Pattern (Ripley's Subset)

Apply Smoothing to Function Values

Spruces Point Pattern

Create a Tessellation

summary.splitppp

Summary of a Split Point Pattern

Convert Line Segment Pattern to Another Unit of Length

Generate N Random Points

Vertices of a Window

Plot a Fitted Spatial Logistic Regression

Urkiola Woods Point Pattern

Rotate a Line Segment Pattern

Superimpose Several Point Patterns

Update a Fitted Cluster Point Process Model

Generate Multitype Poisson Point Pattern

Simulate Baddeley-Silverman Cell Process

Test Whether a Window is Convex

Cut margins from rectangle

Print Brief Details of a Line Segment Pattern Dataset

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Define Point Process Model for Metropolis-Hastings Simulation.

Union of Data and Dummy Points

Generate Poisson Point Pattern on Line Segments

rshift.splitppp

Randomly Shift a List of Point Patterns

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Print Brief Details of a Point Pattern Dataset

Test Whether An Object Is A Fitted Point Process Model

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Convert Data To Class owin

Extract or Replace Subset of a List of Things

Read Point Pattern From Data File

The Multitype Hard Core Point Process Model

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Empty Space Function of a Three-Dimensional Point Pattern

Mosaic Random Field

Apply Function to Image Broken Down by Factor

Nearest Neighbour Distance Function G

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Methods for Multidimensional Space-Time Point Patterns

Marked K-Function

Murchison gold deposits

Generate Poisson Point Pattern in Any Dimensions

Compute Integral of Function Against Cumulative Distribution

Simulate systematic random point pattern

Smooth a Signed or Vector-Valued Measure

Difference of Disc Areas

Extract Unique Points from a Spatial Point Pattern

Summarizing a Fitted Point Process Model

Centroid of a window

Divide Image Into Sub-images

Identify Pixelwise Maximum of Several Pixel Images

Mark Correlation Function

Summary of a Spatial Window

Simulate Stratified Random Point Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

Pair Correlation Function

Apply Vector Translation To Pixel Image

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Simulated Point Pattern

Stoyan's Rule of Thumb for Bandwidth Selection

Profile Maximum Pseudolikelihood

clarkevans.test

Clark and Evans Test

Fry Plot of Point Pattern

Compute Expansion Window for Simulation

Generate a Default Pattern of Dummy Points

Approximate a Polygon by a Simpler Polygon

Pairwise distances

Rectangular grid of points

rescue.rectangle

Convert Window Back To Rectangle

Find Largest Circle Inside Window

Random Re-Labelling of Point Pattern

Kernel Smoothing of Line Segment Pattern

Point and Click Interface for Displaying a Point Pattern

Summary of a Line Segment Pattern Dataset

Nearest Neighbours in Any Dimensions

Name for Unit of Length

Weighted Empirical Cumulative Distribution Function

Extract Original Data from a Fitted Point Process Model

Convert Polygonal Region into Different Format

Print News About Latest Version of Package

multiplicity.ppp

Count Multiplicity of Duplicate Points

Lengths of Line Segments

Update a Fitted Point Process Model

Marks of a Point Pattern

Compute Images of Constructed Covariates

Fit the Matern Cluster Point Process by Minimum Contrast

Nearest neighbour

Estimate Variance of Summary Statistic by Subdivision

The Area Interaction Point Process Model

Extract or Replace Subset of Tessellation

Reduced Second Moment Measure

Inhomogeneous Pair Correlation Function

Convert Line Segment Pattern to Pixel Image

Print Brief Details of an Image

plot.bermantest

Plot Result of Berman Test

Ponderosa Pine Tree Point Pattern

Convert Line Segment Pattern to Binary Pixel Mask

Simulate Gauss-Poisson Process

Q-Q Plot of Residuals from Fitted Point Process Model

Three-Dimensional Box

Hutchings' Bramble Canes data

Multi-Dimensional Box

Generate N Uniform Random Points in a Disc

Convert Point Pattern to Another Unit of Length

Delaunay Triangulation of Point Pattern

Galaxies in the Shapley Supercluster

Spatial Logistic Regression

Generate Poisson Point Pattern in Three Dimensions

Spatial smoothing of observations at irregular points

Simulation Envelopes of Summary Function

Summary of a Point Pattern Dataset

Evaluate an Expression in a Function Table

Pine saplings in Finland.

Function Arrays for Spatial Patterns

Apply Vector Translation To Point Pattern

Fit cluster point process model

Data Sharpening of Point Pattern

Fit the Thomas Point Process by Minimum Contrast

Methods for Multi-Dimensional Box

Nearest Neighbour Distances in Any Dimensions

Saturated Pairwise Interaction Point Process Family

Perimeter Length of Window

Plot a Function Array

Plot a Signed or Vector-Valued Measure

Plot a three-dimensional point pattern

plot a Spatial Point Pattern

Simulate Matern Model I

Interpret Fitted Model for Metropolis-Hastings Simulation.

Spokes pattern of dummy points

Diagnostics for random marking

Multitype J Function (i-to-any)

Multitype J Function (i-to-j)

Reset Values in Subset of Image

The Strauss / Hard Core Point Process Model

Apply Function to Every Neighbourhood in a Point Pattern

Orientation Angles of Line Segments

Distance to Boundary of Window

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Corners of a rectangle

Geometrical Calculations for Multi-Dimensional Box

Distance Map of Line Segment Pattern

Histogram of Pixel Values in an Image

Test Whether A Point Pattern is Marked

Geyer's Saturation Point Process Model

nearest.raster.point

Find Pixel Nearest to a Given Point

Extract.splitppp

Extract or Replace Sub-Patterns

Combine Two Line Segment Patterns

Convert Pixel Image to Matrix or Array

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

complement.owin

Take Complement of a Window

Convert Pixel Image from Numeric to Factor

plot a Fitted Point Process Model

Convert Data To Tessellation

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Interaction Distance of a Point Process

matclust.estpcf

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

Methods for Three-Dimensional Box

Convert Window to Another Unit of Length

Residuals for Fitted Point Process Model

Pair Correlation Function obtained from array of K functions

Pair Correlation Function of Point Pattern

model.matrix.ppm

Extract Design Matrix from Point Process Model

Nearest neighbour distances

Plot a Colour Map

Plot a fitted cluster point process

project2segment

Move Point To Nearest Line

Plot a Pixel Image

Class of Line Segment Patterns

Distance Between Two Point Patterns

Generate N Uniform Random Points

Divide Point Pattern into Sub-patterns

Print a Quadrature Scheme

Divide Region into Quadrats

Fit the Thomas Point Process by Minimum Contrast

Create a Point Matching

Cartesian Coordinates for a Pixel Raster

Smoothing Estimate of Covariate Transformation

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

Simulate Simple Sequential Inhibition

Randomly Shift a Line Segment Pattern

Summarizing a Pixel Image

Poisson Line Tessellation

Random Thinning

Apply Vector Translation

Simulate a Fitted Cluster Point Process Model

Weighted Histogram