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spatstat (version 1.22-0)

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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Version

Install

install.packages('spatstat')

Monthly Downloads

17,668

Version

1.22-0

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

April 28th, 2011

Functions in spatstat (1.22-0)

Smooth a Signed or Vector-Valued Measure

Sufficient Statistic of Point Process Model

Hybrid Geyer Point Process Model

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

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

K-function using FFT

Generic Pairwise Interaction model

Collapse Several Function Tables into One

Pairwise distances

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Diameter of an Object

Spatial smoothing of observations at irregular points

Compute Quadrature Weights Based on Grid Counts

Create a Pixel Image Object

Divide Point Pattern into Sub-patterns

Evaluate an Expression in a Function Table

Loglikelihood of Spatial Logistic Regression

Diagnostics for random marking

Diggle-Gratton model

Empty Space Function of a Three-Dimensional Point Pattern

Morphological Closing

Longleaf Pines Point Pattern

Coefficients of Fitted Point Process Model

Pairwise Distances in Any Dimensions

Pairwise distances between two different point patterns

The Fiksel Interaction

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

Data Sharpening of Point Pattern

Print a Quadrature Scheme

The Piecewise Constant Pairwise Interaction Point Process Model

bounding.box.xy

Convex Hull of Points

Nonparametric Estimate of Spatially-Varying Relative Risk

Mosaic Random Set

Set Covariance of a Window

Exponential Energy Marks

Subdivide a Window or Tessellation using a Set of Lines

Distance Map of Line Segment Pattern

Apply Vector Translation To Point Pattern

Extract the Interaction from a Fitted Point Process Model

Define Point Process Model for Metropolis-Hastings Simulation.

Interpret Fitted Model for Metropolis-Hastings Simulation.

Marked Nearest Neighbour Distance Function

Test Whether An Object Is A Pixel Image

Determine Whether One Window is Contained In Another

Hughes' Amacrine Cell Data

Approximate a Polygon by a Simpler Polygon

Estimate the I-function

Japanese Pines Point Pattern

Apply Function to Every Neighbourhood in a Point Pattern

Divide Image Into Sub-images

nearest.raster.point

Find Pixel Nearest to a Given Point

Generate N Random Points

Apply Vector Translation To Window

Summarizing a Fitted Point Process Model

Plot a linear network

Plot Function Values

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

Locally Scaled K-function

Uniform Random Points on a Linear Network

Create a Tessellation

Fit the Thomas Point Process by Minimum Contrast

spatstat-package

The Spatstat Package

Summarizing a Pixel Image

Print Progress Reports

Cross Validated Bandwidth Selection for Relative Risk Estimation

Foxall's Distance Functions

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Apply Vector Translation To Line Segment Pattern

project2segment

Move Point To Nearest Line

Methods for Linear Networks

Cut margins from rectangle

Calculate four standard summary functions of a point pattern.

Difference of Disc Areas

Identify Pixelwise Maximum of Several Pixel Images

Methods for Multidimensional Space-Time Point Patterns

Extract or Replace Subset of a List of Things

Extract or Replace Subset of Tessellation

Fit Point Process Model to Data

Connected components of an image or window

Geometrical Calculations for Multi-Dimensional Box

inforder.family

Infinite Order Interaction Family

Marked K-Function

Extract Original Data from a Fitted Point Process Model

Classify Points in a Point Pattern

Simulate Thomas Process

Extract Subset of Function Array

Distance to Boundary of Window

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

California Redwoods Point Pattern (Entire Dataset)

Centroid of a window

Neighbourhood density function

Weighted Histogram

Combine Function Value Tables

Extract Subset of Signed or Vector Measure

Print a Fitted Point Process Model

as.data.frame.im

Convert Pixel Image to Data Frame

Subset of Quadrature Scheme

Estimate the J-function

Extract Subset of Line Segment Pattern

Simulate a Fitted Gibbs Point Process Model

Saturated Pairwise Interaction Point Process Family

Distance Map as a Function

Berman-Huntington points and lines data

Function Arrays for Spatial Patterns

Point and Click Interface for Displaying a Point Pattern

Marked J Function

Extract or Replace Subset of Point Pattern

Convert Pixel Image from Numeric to Factor

Convert Data To Class owin

Apply Gaussian Blur to a Pixel Image

Area of Part of Disc

Plot a Colour Map

Class of Line Segment Patterns

Fitted Conditional Intensity for Point Process Model

Summary of a Line Segment Pattern Dataset

Generic Ord Interaction model

Test Whether An Object Is A Point Pattern

Test Whether Marks Are Present

Fit cluster point process model

Inhomogeneous Cross Type L Function

Harkness-Isham ants' nests data

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Swedish Pines Point Pattern

Stoyan's Rule of Thumb for Bandwidth Selection

Apply Vector Translation

Extract Dummy Points Used to Fit a Point Process Model

Superimpose Several Geometric Patterns

Test Whether An Object Is A Window

Poisson Point Process Model

Rectangular grid of points

Summary of a Spatial Window

Simulate a Fitted Cluster Point Process Model

Summarizing a Quadrature Scheme

Summary of a Point Pattern Dataset

Nearest Neighbours in Any Dimensions

Bronze gradient filter data

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Beadlet Anemones Data

summary.splitppp

Summary of a Split Point Pattern

Evaluate Expression Involving Functions

Apply Affine Transformation To Line Segment Pattern

Convert Polygonal Region into Different Format

Convert Data To Class ppp

Simulation Envelopes of Summary Function for 3D Point Pattern

Nearest neighbours in three dimensions

Interpolate a Pixel Image

Mark Correlation Integral

Basis for Harmonic Functions

Convert Data To Tessellation

Convert Spatial Object to Pixel Image

Class of Images

Union of Data and Dummy Points

Inhomogeneous K-function

Convex Hull of Points

Interactively Add Points

Geyer's Saturation Point Process Model

Intersect Infinite Straight Lines with a Window

spatstat-deprecated

Deprecated spatstat functions

Reset Values in Subset of Image

The Multitype Hard Core Point Process Model

Weighted Empirical Cumulative Distribution Function

The Lennard-Jones Potential

Plot a Function Array

Print News About Latest Version of Package

Simulate Baddeley-Silverman Cell Process

Pair Correlation Function obtained from array of K functions

compatible.fasp

Test Whether Two Function Arrays Are Compatible

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Apply Smoothing to Function Values

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Multitype L-function (cross-type)

Identify Points in a Point Pattern

Contour plot of pixel image

Convert Line Segment Pattern to Binary Pixel Mask

Test Whether An Object Is A Fitted Point Process Model

Print Brief Details of a Spatial Window

Border Region of a Window

Print Brief Details of a Point Pattern Dataset

Distance to Boundary of Window

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Concatenate x,y Coordinate Vectors

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Corners of a rectangle

Summarise Marks in Every Neighbourhood in a Point Pattern

Interactively Define a Polygon

spatstat.options

Internal Options in Spatstat Package

Kaplan-Meier and Reduced Sample Estimator using Histograms

Q-Q Plot of Residuals from Fitted Point Process Model

Nearest neighbour

Kernel Smoothing of Line Segment Pattern

New Zealand Trees Point Pattern

Methods for Point Patterns on a Linear Network

Fit the Matern Cluster Point Process by Minimum Contrast

Simulate Simple Sequential Inhibition

Compute Expansion Window for Simulation

Estimate Variance of Summary Statistic by Subdivision

Create a Window

Find Largest Circle Inside Window

Safely Convert Point Pattern Window to Binary Mask

crossdist.default

Pairwise distances between two different sets of points

Infinite Straight Lines

model.matrix.ppm

Extract Design Matrix from Point Process Model

Methods for Multi-Dimensional Box

Kaplan-Meier Estimator using Histogram Data

Artificial Data Point Pattern

Test Whether Two Function Objects Are Compatible

Kernel Smoothed Intensity of Point Pattern

Integral of a Pixel Image

plot a Spatial Point Pattern

is.multitype.ppm

Test Whether A Point Process Model is Multitype

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

Vertices of a Window

Diameter of a Window

Number of Points in a Point Pattern

The Hard Core Point Process Model

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Morphological Erosion

Distance Map of Point Pattern

Compute Areas of Tiles in a Tessellation

Convert dataset to another unit of length

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Pine saplings in Finland.

Rotate a Point Pattern

Plot a Simulation Envelope

Lurking variable plot

Simulate Matern Model II

Inhomogeneous Cross K Function

Read Point Pattern From Data File

Create Point Pattern on Linear Network

Create a Function Value Table

Point Patterns of New Brunswick Forest Fires

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

Pairwise distances between two different line segment patterns

Fry Plot of Point Pattern

Test Whether A Point Process Model is Marked

Apply Vector Translation To Pixel Image

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Volume of an Object

plot.hyperframe

Plot Entries in a Hyperframe

spatstat-internal

Internal spatstat functions

Beta Ganglion Cells in Cat Retina, Old Version

Spruces Point Pattern

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

pppmatching.object

Class of Point Matchings

Humberside Data on Childhood Leukaemia and Lymphoma

plot a Fitted Point Process Model

Level Set of a Pixel Image

Plot a Pixel Image

Signed or Vector-Valued Measure

Ord's Interaction model

Simulate Matern Cluster Process

Interaction Distance of a Point Process

Nearest Neighbour Distance Function G

Morphological Opening

Create a Linear Network

Nearest Neighbour Distances in Any Dimensions

Compute Integral of Function Against Cumulative Distribution

Multitype J Function (i-to-any)

Plot a Spatial Kolmogorov-Smirnov Test

Quadrat counting for a point pattern

Local pair correlation function

Area of a Window

Methods for three-dimensional point patterns

pairdist.default

Pairwise distances

Difference of Disc Areas

Extract Subset of Image

Summary of a List of Things

Multitype K Function (i-to-any)

Multitype L-function (i-to-any)

Cartesian Coordinates for a Pixel Raster

matclust.estpcf

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

Plot a List of Things

Methods for Three-Dimensional Box

Generate a Quadrature Scheme from a Point Pattern

Extract Quadrature Scheme Used to Fit a Point Process Model

Reduced Sample Estimator using Histogram Data

Reduced Second Moment Measure

Nearest neighbour distances

Pair Correlation Function of Point Pattern

Residuals for Fitted Point Process Model

Apply a Function to a Point Pattern Broken Down by Factor

Nearest Neighbours Between Two Patterns

Midpoints of Line Segment Pattern

Smoothing Estimate of Covariate Transformation

Apply Affine Transformation

Diggle's Heather Data

The Multitype Strauss Point Process Model

Simulate systematic random point pattern

Extract Unique Points from a Spatial Point Pattern

Extract.splitppp

Extract or Replace Sub-Patterns

Murchison gold deposits

Prediction from a Fitted Cluster Point Process Model

Number of Line Segments in a Line Segment Pattern

Nearest Neighbour Clutter Removal

Update a Fitted Point Process Model

Multi-Dimensional Box

Multidimensional Space-Time Point Pattern

The Strauss / Hard Core Point Process Model

Distance Between Two Point Patterns

Histogram of Pixel Values in an Image

Poisson Point Process on a Linear Network

Generate Poisson Point Pattern in Three Dimensions

Convert Window to Pixel Image

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

quadratresample

Resample a Point Pattern by Resampling Quadrats

Identify Segments in a Line Segment Pattern

rshift.splitppp

Randomly Shift a List of Point Patterns

Window in Shape of Letter R

Clark and Evans Aggregation Index

Biological Cells Point Pattern

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Update a Fitted Cluster Point Process Model

Prediction from a Fitted Point Process Model

ANOVA for Fitted Point Process Models

Combine Two Line Segment Patterns

Apply Affine Transformation To Window

Simulate Gauss-Poisson Process

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Theoretical Distribution of Nearest Neighbour Distance

Urkiola Woods Point Pattern

Plot a Fitted Spatial Logistic Regression

Print Brief Details of an Image

Spherical Contact Distribution Function

Mark Connection Function

Test Whether A Point Pattern is Marked

Hutchings' Bramble Canes data

Create a Point Pattern

Convert and Compare Colours in Different Formats

Profile Maximum Pseudolikelihood

Interactively join vertices on a plot

Evaluate Expression Involving Pixel Images

Saturated Pairwise Interaction model

Delaunay Triangulation of Point Pattern

Poisson Line Tessellation

Generate grid of parallel lines with random displacement

Plot a tessellation

Coefficients of Fitted Spatial Logistic Regression Model

Marks of a Point Pattern

Sample Quantiles of Pixel Image

Define Point Process Model for Metropolis-Hastings Simulation.

Morphological Dilation

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Convert Point Pattern to Another Unit of Length

Simulate Matern Model I

Morishita Index Plot

plot a Spatial Line Segment Pattern

Evaluate Expression Involving Function Arrays

Analysis of Deviance for Spatial Logistic Regression Models

Expand Window By Factor

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Find Line Segment Nearest to Each Point

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Pair Correlation Function obtained from K Function

Generate N Uniform Random Points in Three Dimensions

Convert Line Segment Pattern to Pixel Image

Randomly Shift a Line Segment Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Tropical rain forest trees

Estimate window from points alone

Generate Multitype Poisson Point Pattern

Print Brief Details of a Line Segment Pattern Dataset

Data Frames of Function Values

Plot a plotppm Object Created by plot.ppm

Convert Data to Hyperframe

Plot a Spatial Window

Hyper Data Frame

Test whether Object is Multitype

Bounding Box of a Window or Point Pattern

Nearest neighbour distances between line segments

Randomly Shift a Point Pattern

Convert Line Segment Pattern to Another Unit of Length

Test Whether a Window is Convex

Pairwise distances

Mark Correlation Function

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

plot a Spatial Quadrature Scheme

Apply Function to Image Broken Down by Factor

Perfect Simulation of the Strauss Process

Pairwise distances in Three Dimensions

Set Control Parameters for Metropolis-Hastings Algorithm.

Scatterplot Matrix for Pixel Images

Convert Data to Three-Dimensional Box

Pairwise distances between two different three-dimensional point patterns

Test Whether An Object Is Empty

The Strauss Point Process Model

Spatial Logistic Regression

Convert Data To Class psp

Pair Correlation Function of a Three-Dimensional Point Pattern

Dirichlet Tessellation of Point Pattern

plot.bermantest

Plot Result of Berman Test

Endpoints of Line Segment Pattern

Pairwise distances between line segments

Pair Correlation Function

Create a Point Matching

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Plot a three-dimensional point pattern

Circumradius and Diameter of a Linear Network

Convert Point Pattern to Pixel Image

Convert Window to Another Unit of Length

Distance to Boundary of Window

Intersection, Union or Set Subtraction of Two Windows

Intersection of Two Tessellations

Plot a List of Point Patterns

Fitted Probabilities for Spatial Logistic Regression

Diagnostic Plots for Fitted Point Process Model

Aherne's hamster tumour data

Random Perturbation of a Point Pattern

Class of Fitted Point Process Models

model.frame.ppm

Extract the Environment of a Point Process Model

Log Likelihood for Poisson Point Process Model

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

Divide Region into Quadrats

Generate Poisson Point Pattern

Simulate point patterns using the Metropolis-Hastings algorithm.

Generate Poisson Random Line Process

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Distance for a Point Pattern Matching

Generate Poisson Point Pattern in Any Dimensions

Generate N Uniform Random Points in a Disc

Multitype pair correlation function (cross-type)

methods.distfun

Methods for Distance Functions

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Perspective Plot of Pixel Image

Nearest neighbour distances in three dimensions

Random Re-Labelling of Point Pattern

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

Multitype pair correlation function (i-to-any)

Plot a Signed or Vector-Valued Measure

Plot a fitted cluster point process

Three Dimensional Point Pattern

Name for Unit of Length

Predicted or Fitted Values from Spatial Logistic Regression

Estimate the empty space function F

Generate N Uniform Random Points in Any Dimensions

Multitype J Function (i-to-j)

Inhomogeneous Multitype L Dot Function

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Chorley-Ribble Cancer Data

Berman's Tests for Point Process Model

Inhomogeneous Multitype K Dot Function

Colour Lookup Tables

Beta Ganglion Cells in Cat Retina

Areas of Morphological Dilations

Circular Window

Distance Map of Window

Test Whether Points Are Inside A Window

Kolmogorov-Smirnov Test for Point Process Model

Lengths of Line Segments

Simulated Point Pattern

Simple Example of Linear Network

Point and Click Interface for Exploratory Analysis of Point Pattern

Fit the Thomas Point Process by Minimum Contrast

multiplicity.ppp

Count Multiplicity of Duplicate Points

Variance-Covariance Matrix for a Fitted Point Process Model

Nearest-Neighbour Correlation Indices of Marked Point Pattern

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

The Soft Core Point Process Model

Three-Dimensional Box

Orientation Angles of Line Segments

pairwise.family

Pairwise Interaction Process Family

Make Periodic Copies of a Spatial Pattern

Test Whether Two Pixel Images Are Compatible

Quadrature Scheme Based on Pixel Grid

Inhomogeneous Pair Correlation Function

complement.owin

Take Complement of a Window

Simulation Envelopes of Summary Function

Determine Duplicated Points in a Spatial Point Pattern

Areas of Morphological Erosions

Place Points Evenly Along Specified Lines

Simulate Neyman-Scott Process

rescue.rectangle

Convert Window Back To Rectangle

Marks of a Line Segment Pattern

Method of Minimum Contrast

Compute Images of Constructed Covariates

Ord Interaction Process Family

Galaxies in the Shapley Supercluster

Pairwise distances

Spokes pattern of dummy points

Extract List of Tiles in a Tessellation

Extract Subset of Function Values

The Area Interaction Point Process Model

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

Multitype K Function (Cross-type)

Apply Affine Transformation To Point Pattern

K-function of a Three-Dimensional Point Pattern

Convert to Pixel Image

Pixel Image Approximation of a Window

Convert Pixel Image to Matrix or Array

Convert a Window to a Polygonal Window

clarkevans.test

Clark and Evans Test

Generate a Default Pattern of Dummy Points

Crossing Points of Two Line Segment Patterns

Ponderosa Pine Tree Point Pattern

California Redwoods Point Pattern (Ripley's Subset)

Data and Code From JRSS Discussion Paper on Residuals

Geometrical Calculations for Three-Dimensional Box

Lansing Woods Point Pattern

Rotate a Line Segment Pattern

Perimeter Length of Window

Class of Point Patterns

Create a Line Segment Pattern

Random Thinning

Class of Quadrature Schemes

Mosaic Random Field

Simulate from a Fitted Point Process Model

Generate N Random Multitype Points

Simulate Stratified Random Point Pattern

Rotate a Window

Generate Poisson Point Pattern on Line Segments

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Generate N Uniform Random Points

Convert Pixel Image to Another Unit of Length