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spatstat (version 1.21-2)

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

16,015

Version

1.21-2

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

November 29th, 2010

Functions in spatstat (1.21-2)

The Strauss Point Process Model

Neighbourhood density function

Compute Quadrature Weights Based on Grid Counts

Distance Map of Window

Generic Ord Interaction model

Kolmogorov-Smirnov Test for Point Process Model

Lurking variable plot

Method of Minimum Contrast

Determine Whether One Window is Contained In Another

crossdist.default

Pairwise distances between two different sets of points

Apply Affine Transformation To Line Segment Pattern

Convert Data to Three-Dimensional Box

Subdivide a Window or Tessellation using a Set of Lines

Bronze gradient filter data

Nearest Neighbour Distances in Any Dimensions

matclust.estpcf

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

Pairwise distances

Print Progress Reports

Plot a List of Things

Convert Pixel Image to Another Unit of Length

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Orientation Angles of Line Segments

Difference of Disc Areas

Harkness-Isham ants' nests data

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Ord's Interaction model

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Create a Pixel Image Object

Artificial Data Point Pattern

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Extract Quadrature Scheme Used to Fit a Point Process Model

Convert dataset to another unit of length

Combine Function Value Tables

Dirichlet Tessellation of Point Pattern

Poisson Point Process Model

Mosaic Random Set

Quadrat counting for a point pattern

Beadlet Anemones Data

Coefficients of Fitted Spatial Logistic Regression Model

Corners of a rectangle

Test Whether Two Function Objects Are Compatible

Cross Validated Bandwidth Selection for Relative Risk Estimation

The Multitype Strauss Point Process Model

Kernel Smoothed Intensity of Point Pattern

Fry Plot of Point Pattern

The Piecewise Constant Pairwise Interaction Point Process Model

Interpolate a Pixel Image

Border Region of a Window

Distance to Boundary of Window

Apply a Function to a Point Pattern Broken Down by Factor

The Lennard-Jones Potential

Interactively Add Points

Collapse Several Function Tables into One

compatible.fasp

Test Whether Two Function Arrays Are Compatible

The Multitype Hard Core Point Process Model

Distance to Boundary of Window

Extract Original Data from a Fitted Point Process Model

Apply Function to Image Broken Down by Factor

Basis for Harmonic Functions

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Interactively Define a Polygon

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Point and Click Interface for Displaying a Point Pattern

Window in Shape of Letter R

Diameter of a Window

Identify Points in a Point Pattern

Vertices of a Window

Distance for a Point Pattern Matching

Test Whether Marks Are Present

Centroid of a window

Nearest Neighbours in Any Dimensions

Fit cluster point process model

Create a Window

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Distance to Boundary of Window

Hyper Data Frame

Nearest Neighbours Between Two Patterns

Quadrature Scheme Based on Pixel Grid

Stoyan's Rule of Thumb for Bandwidth Selection

Contour plot of pixel image

Apply Affine Transformation To Point Pattern

Generate a Default Pattern of Dummy Points

The Soft Core Point Process Model

as.data.frame.im

Convert Pixel Image to Data Frame

Diagnostic Plots for Fitted Point Process Model

Identify Segments in a Line Segment Pattern

Reset Values in Subset of Image

Perimeter Length of Window

The Strauss / Hard Core Point Process Model

Print Brief Details of a Line Segment Pattern Dataset

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

Calculate four standard summary functions of a point pattern.

Convert and Compare Colours in Different Formats

Nearest neighbours in three dimensions

Convert Pixel Image to Matrix or Array

Pairwise distances between line segments

Weighted Histogram

Biological Cells Point Pattern

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Murchison gold deposits

Convert Line Segment Pattern to Binary Pixel Mask

Test Whether Points Are Inside A Window

Nearest-Neighbour Correlation Indices of Marked Point Pattern

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Plot a tessellation

Make Periodic Copies of a Spatial Pattern

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Pair Correlation Function obtained from K Function

Plot a Fitted Spatial Logistic Regression

bounding.box.xy

Convex Hull of Points

Berman's Tests for Point Process Model

Geometrical Calculations for Multi-Dimensional Box

complement.owin

Take Complement of a Window

Pairwise distances between two different point patterns

Create a Function Value Table

Kaplan-Meier and Reduced Sample Estimator using Histograms

Summarise Marks in Every Neighbourhood in a Point Pattern

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Pair Correlation Function

Loglikelihood of Spatial Logistic Regression

Hughes' Amacrine Cell Data

Test Whether An Object Is A Pixel Image

Generate a Quadrature Scheme from a Point Pattern

Plot a Colour Map

Distance Map as a Function

Japanese Pines Point Pattern

Convert Pixel Image from Numeric to Factor

Pairwise distances

Geometrical Calculations for Three-Dimensional Box

Point Patterns of New Brunswick Forest Fires

Connected components of an image or window

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Scatterplot Matrix for Pixel Images

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Pixel Image Approximation of a Window

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Test Whether An Object Is A Point Pattern

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Morphological Closing

Convert Window to Pixel Image

Create a Line Segment Pattern

Simulation Envelopes of Summary Function for 3D Point Pattern

Cartesian Coordinates for a Pixel Raster

Ord Interaction Process Family

Lansing Woods Point Pattern

Apply Function to Every Neighbourhood in a Point Pattern

Rectangular grid of points

Generic Pairwise Interaction model

Analysis of Deviance for Spatial Logistic Regression Models

Apply Affine Transformation To Window

Kaplan-Meier Estimator using Histogram Data

Convex Hull of Points

Difference of Disc Areas

Set Control Parameters for Metropolis-Hastings Algorithm.

ANOVA for Fitted Point Process Models

Reduced Sample Estimator using Histogram Data

Methods for Three-Dimensional Box

Three Dimensional Point Pattern

multiplicity.ppp

Count Multiplicity of Duplicate Points

Delaunay Triangulation of Point Pattern

Data and Code From JRSS Discussion Paper on Residuals

Define Point Process Model for Metropolis-Hastings Simulation.

Compute Expansion Window for Simulation

Convert to Pixel Image

Convert Data To Tessellation

Areas of Morphological Erosions

Saturated Pairwise Interaction model

Kernel Smoothing of Line Segment Pattern

Infinite Straight Lines

Classify Points in a Point Pattern

New Zealand Trees Point Pattern

Nearest Neighbour Clutter Removal

Convert Polygonal Region into Different Format

Convert Line Segment Pattern to Pixel Image

Print a Fitted Point Process Model

Pine saplings in Finland.

plot a Fitted Point Process Model

Bounding Box of a Window or Point Pattern

Create a Point Pattern

Evaluate Expression Involving Functions

Distance Map of Point Pattern

Areas of Morphological Dilations

Convert Data To Class owin

model.matrix.ppm

Extract Design Matrix from Point Process Model

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Chorley-Ribble Cancer Data

Concatenate x,y Coordinate Vectors

Methods for three-dimensional point patterns

Random Perturbation of a Point Pattern

rshift.splitppp

Randomly Shift a List of Point Patterns

Level Set of a Pixel Image

Saturated Pairwise Interaction Point Process Family

Morphological Erosion

Pairwise distances between two different line segment patterns

Perspective Plot of Pixel Image

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Intersection, Union or Set Subtraction of Two Windows

Interpret Fitted Model for Metropolis-Hastings Simulation.

Profile Maximum Pseudolikelihood

Beta Ganglion Cells in Cat Retina, Old Version

Test Whether A Point Pattern is Marked

Perfect Simulation of the Strauss Process

Fitted Conditional Intensity for Point Process Model

Generate Poisson Random Line Process

Print Brief Details of a Spatial Window

Print News About Latest Version of Package

Exponential Energy Marks

Pairwise distances between two different three-dimensional point patterns

Test Whether An Object Is Empty

Pairwise distances

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Generate Poisson Point Pattern in Three Dimensions

Test Whether a Window is Convex

Nearest neighbour

Circular Window

Integral of a Pixel Image

Class of Images

Lengths of Line Segments

Generate N Uniform Random Points

Swedish Pines Point Pattern

Mark Correlation Integral

model.frame.ppm

Extract the Environment of a Point Process Model

Superimpose Several Point Patterns

Methods for Multidimensional Space-Time Point Patterns

Extract the Interaction from a Fitted Point Process Model

Convert Data To Class ppp

Generate N Random Multitype Points

Mark Connection Function

Ponderosa Pine Tree Point Pattern

Apply Vector Translation To Window

plot.hyperframe

Plot Entries in a Hyperframe

Print Brief Details of an Image

Class of Quadrature Schemes

Simulate Matern Cluster Process

spatstat-deprecated

Deprecated spatstat functions

Multitype pair correlation function (cross-type)

Generate N Uniform Random Points in Any Dimensions

Test Whether Two Pixel Images Are Compatible

Generate Poisson Point Pattern on Line Segments

inforder.family

Infinite Order Interaction Family

Predicted or Fitted Values from Spatial Logistic Regression

Interaction Distance of a Point Process

Crossing Points of Two Line Segment Patterns

Intersection of Two Tessellations

Plot a Pixel Image

Marks of a Point Pattern

Random Thinning

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

Distance Map of Line Segment Pattern

Nearest Neighbour Distance Function G

Print Brief Details of a Point Pattern Dataset

Subset of Quadrature Scheme

Determine Duplicated Points in a Spatial Point Pattern

Inhomogeneous K-function

Area of Part of Disc

plot.bermantest

Plot Result of Berman Test

Morphological Dilation

Test whether Object is Multitype

Log Likelihood for Poisson Point Process Model

Apply Vector Translation

methods.distfun

Methods for Distance Functions

Find Largest Circle Inside Window

Plot a Function Array

Fitted Probabilities for Spatial Logistic Regression

Local pair correlation function

Evaluate Expression Involving Pixel Images

Generate grid of parallel lines with random displacement

nearest.raster.point

Find Pixel Nearest to a Given Point

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Endpoints of Line Segment Pattern

Summary of a Line Segment Pattern Dataset

Generate N Uniform Random Points in Three Dimensions

Clark and Evans Aggregation Index

Plot a fitted cluster point process

Generate Poisson Point Pattern in Any Dimensions

Nearest neighbour distances in three dimensions

Test Whether An Object Is A Window

Nearest neighbour distances

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Simulate Thomas Process

Beta Ganglion Cells in Cat Retina

Plot Function Values

Compute Images of Constructed Covariates

Convert Window to Another Unit of Length

pairwise.family

Pairwise Interaction Process Family

Print a Quadrature Scheme

Histogram of Pixel Values in an Image

Pair Correlation Function obtained from array of K functions

Find Line Segment Nearest to Each Point

Pair Correlation Function of a Three-Dimensional Point Pattern

Class of Line Segment Patterns

Spatial Logistic Regression

Nearest neighbour distances between line segments

Fit the Matern Cluster Point Process by Minimum Contrast

Extract Dummy Points Used to Fit a Point Process Model

pairdist.default

Pairwise distances

Pair Correlation Function of Point Pattern

Point and Click Interface for Exploratory Analysis of Point Pattern

Simulate Neyman-Scott Process

Morphological Opening

Random Re-Labelling of Point Pattern

Methods for Multi-Dimensional Box

Coefficients of Fitted Point Process Model

Diameter of an Object

Class of Point Patterns

Pairwise Distances in Any Dimensions

Inhomogeneous Pair Correlation Function

Sufficient Statistic of Point Process Model

Simulate Matern Model I

Convert Data to Hyperframe

Place Points Evenly Along Specified Lines

Colour Lookup Tables

Apply Smoothing to Function Values

Plot a List of Point Patterns

Divide Point Pattern into Sub-patterns

Multidimensional Space-Time Point Pattern

Simulated Point Pattern

Midpoints of Line Segment Pattern

Simulate from a Fitted Point Process Model

Simulate a Fitted Gibbs Point Process Model

Generate Multitype Poisson Point Pattern

Class of Fitted Point Process Models

Create a Point Matching

Convert Point Pattern to Pixel Image

Plot a Spatial Kolmogorov-Smirnov Test

Prediction from a Fitted Point Process Model

Residuals for Fitted Point Process Model

Apply Vector Translation To Line Segment Pattern

Poisson Line Tessellation

Simulate systematic random point pattern

Theoretical Distribution of Nearest Neighbour Distance

Update a Fitted Point Process Model

Convert Spatial Object to Pixel Image

Approximate a Polygon by a Simpler Polygon

Simulate Matern Model II

Distance Between Two Point Patterns

Multitype pair correlation function (i-to-any)

Randomly Shift a Point Pattern

Convert Line Segment Pattern to Another Unit of Length

Rotate a Window

Morishita Index Plot

Q-Q Plot of Residuals from Fitted Point Process Model

Humberside Data on Childhood Leukaemia and Lymphoma

Estimate window from points alone

Superimpose Several Line Segment Patterns

Sample Quantiles of Pixel Image

Identify Pixelwise Maximum of Several Pixel Images

Evaluate Expression Involving Function Arrays

Mosaic Random Field

Randomly Shift a Line Segment Pattern

Fit Point Process Model to Data

spatstat.options

Internal Options in Spatstat Package

K-function using FFT

Test Whether An Object Is A Fitted Point Process Model

Data Sharpening of Point Pattern

Smoothing Estimate of Covariate Transformation

Generate N Uniform Random Points in a Disc

Estimate Variance of Summary Statistic by Subdivision

Simulate Baddeley-Silverman Cell Process

Extract List of Tiles in a Tessellation

Summarizing a Quadrature Scheme

project2segment

Move Point To Nearest Line

Pairwise distances in Three Dimensions

pppmatching.object

Class of Point Matchings

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

summary.splitppp

Summary of a Split Point Pattern

Convert Point Pattern to Another Unit of Length

Diggle's Heather Data

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

Data Frames of Function Values

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Summary of a List of Things

Compute Integral of Function Against Cumulative Distribution

Simulate a Fitted Cluster Point Process Model

Simulate point patterns using the Metropolis-Hastings algorithm.

Simulate Simple Sequential Inhibition

Set Covariance of a Window

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

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

Read Point Pattern From Data File

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

Simulate Stratified Random Point Pattern

Extract Subset of Image

Volume of an Object

Apply Vector Translation To Point Pattern

Extract Unique Points from a Spatial Point Pattern

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

Divide Region into Quadrats

California Redwoods Point Pattern (Entire Dataset)

Spatial smoothing of observations at irregular points

Foxall's Distance Functions

Generate N Random Points

California Redwoods Point Pattern (Ripley's Subset)

Create a Tessellation

Multitype K Function (Cross-type)

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Multitype J Function (i-to-j)

Update a Fitted Cluster Point Process Model

Inhomogeneous Cross Type L Function

Urkiola Woods Point Pattern

Generate Poisson Point Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

Fit the Thomas Point Process by Minimum Contrast

Hybrid Geyer Point Process Model

Evaluate an Expression in a Function Table

Reduced Second Moment Measure

Union of Data and Dummy Points

Marked K-Function

Summarizing a Fitted Point Process Model

Geyer's Saturation Point Process Model

Galaxies in the Shapley Supercluster

Divide Image Into Sub-images

Apply Vector Translation To Pixel Image

Summarizing a Pixel Image

Cut margins from rectangle

Summary of a Spatial Window

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Estimate the empty space function F

Extract Subset of Line Segment Pattern

Extract.splitppp

Extract or Replace Sub-Patterns

quadratresample

Resample a Point Pattern by Resampling Quadrats

Multitype L-function (i-to-any)

Multi-Dimensional Box

Plot a Simulation Envelope

Summary of a Point Pattern Dataset

Rotate a Point Pattern

The Fiksel Interaction

Inhomogeneous Cross K Function

Name for Unit of Length

The Hard Core Point Process Model

Multitype L-function (cross-type)

Inhomogeneous Multitype L Dot Function

The Area Interaction Point Process Model

Marked J Function

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

Extract Subset of Function Array

Extract Subset of Function Values

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Marked Nearest Neighbour Distance Function

Inhomogeneous Multitype K Dot Function

K-function of a Three-Dimensional Point Pattern

Estimate the I-function

Estimate the J-function

Spherical Contact Distribution Function

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

Diggle-Gratton model

Locally Scaled K-function

Empty Space Function of a Three-Dimensional Point Pattern

Combine Two Line Segment Patterns

Area of a Window

Convert a Window to a Polygonal Window

Three-Dimensional Box

Hutchings' Bramble Canes data

Extract or Replace Subset of Point Pattern

Diagnostics for random marking

Convert Data To Class psp

Apply Affine Transformation

Berman-Huntington points and lines data

Apply Gaussian Blur to a Pixel Image

Tropical rain forest trees

Safely Convert Point Pattern Window to Binary Mask

Function Arrays for Spatial Patterns

Simulation Envelopes of Summary Function

Test Whether A Point Process Model is Marked

Weighted Empirical Cumulative Distribution Function

Longleaf Pines Point Pattern

Mark Correlation Function

spatstat-internal

Internal spatstat functions

Aherne's hamster tumour data

Number of Points in a Point Pattern

Expand Window By Factor

Plot a three-dimensional point pattern

plot a Spatial Point Pattern

Prediction from a Fitted Cluster Point Process Model

plot a Spatial Quadrature Scheme

plot a Spatial Line Segment Pattern

Plot a plotppm Object Created by plot.ppm

Plot a Spatial Window

Intersect Infinite Straight Lines with a Window

Define Point Process Model for Metropolis-Hastings Simulation.

Nonparametric Estimate of Spatially-Varying Relative Risk

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Fit the Thomas Point Process by Minimum Contrast

spatstat-package

The Spatstat Package

Determine Initial State for Metropolis-Hastings Simulation.

Spokes pattern of dummy points

Rotate a Line Segment Pattern

Spruces Point Pattern

Simulate Gauss-Poisson Process

rescue.rectangle

Convert Window Back To Rectangle

Multitype J Function (i-to-any)

Extract or Replace Subset of Tessellation

Extract or Replace Subset of a List of Things

Multitype K Function (i-to-any)