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spatstat (version 1.21-4)

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

1.21-4

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

January 20th, 2011

Functions in spatstat (1.21-4)

Coefficients of Fitted Spatial Logistic Regression Model

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

bounding.box.xy

Convex Hull of Points

The Multitype Hard Core Point Process Model

Distance to Boundary of Window

Bounding Box of a Window or Point Pattern

Convert Data to Hyperframe

Test Whether Two Function Objects Are Compatible

Berman-Huntington points and lines data

crossdist.default

Pairwise distances between two different sets of points

Pairwise distances

The Strauss / Hard Core Point Process Model

The Strauss Point Process Model

Circular Window

Determine Duplicated Points in a Spatial Point Pattern

Test Whether A Point Process Model is Marked

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Distance Map as a Function

Convert Data To Class psp

Difference of Disc Areas

Humberside Data on Childhood Leukaemia and Lymphoma

Simulation Envelopes of Summary Function for 3D Point Pattern

Create a Function Value Table

Interactively Add Points

Multitype L-function (i-to-any)

clarkevans.test

Clark and Evans Test

Local pair correlation function

Inhomogeneous Multitype L Dot Function

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Convex Hull of Points

Crossing Points of Two Line Segment Patterns

Distance to Boundary of Window

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

inforder.family

Infinite Order Interaction Family

Corners of a rectangle

Delaunay Triangulation of Point Pattern

Difference of Disc Areas

Print a Quadrature Scheme

Fitted Probabilities for Spatial Logistic Regression

Compute Images of Constructed Covariates

Pairwise distances between two different line segment patterns

Infinite Straight Lines

Test whether Object is Multitype

Log Likelihood for Poisson Point Process Model

Determine Whether One Window is Contained In Another

Perimeter Length of Window

Test Whether An Object Is Empty

Pairwise distances between two different three-dimensional point patterns

Plot a plotppm Object Created by plot.ppm

Dirichlet Tessellation of Point Pattern

Plot a Spatial Kolmogorov-Smirnov Test

Apply a Function to a Point Pattern Broken Down by Factor

Contour plot of pixel image

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Apply Affine Transformation To Line Segment Pattern

Morphological Dilation

Saturated Pairwise Interaction model

Generic Ord Interaction model

Nearest neighbour distances in three dimensions

Midpoints of Line Segment Pattern

Class of Images

Plot a three-dimensional point pattern

model.frame.ppm

Extract the Environment of a Point Process Model

Convert Data To Tessellation

Apply Function to Every Neighbourhood in a Point Pattern

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Test Whether Points Are Inside A Window

Apply Gaussian Blur to a Pixel Image

Piecewise Constant Saturated Pairwise Interaction Point Process Model

The Multitype Strauss Point Process Model

plot a Spatial Quadrature Scheme

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

Plot a Pixel Image

Morishita Index Plot

Concatenate x,y Coordinate Vectors

Perspective Plot of Pixel Image

Rotate a Window

Subdivide a Window or Tessellation using a Set of Lines

Coefficients of Fitted Point Process Model

Scatterplot Matrix for Pixel Images

Evaluate Expression Involving Functions

Clark and Evans Aggregation Index

Orientation Angles of Line Segments

Convert to Pixel Image

Find Largest Circle Inside Window

Plot a Function Array

Pairwise distances between two different point patterns

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Evaluate Expression Involving Function Arrays

Collapse Several Function Tables into One

Biological Cells Point Pattern

Multi-Dimensional Box

Colour Lookup Tables

Classify Points in a Point Pattern

Aherne's hamster tumour data

Extract Original Data from a Fitted Point Process Model

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Diagnostic Plots for Fitted Point Process Model

Compute Quadrature Weights Based on Grid Counts

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Generate grid of parallel lines with random displacement

New Zealand Trees Point Pattern

Evaluate Expression Involving Pixel Images

Connected components of an image or window

Combine Two Line Segment Patterns

Level Set of a Pixel Image

Test Whether Marks Are Present

Define Point Process Model for Metropolis-Hastings Simulation.

Rotate a Point Pattern

Chorley-Ribble Cancer Data

Areas of Morphological Erosions

model.matrix.ppm

Extract Design Matrix from Point Process Model

Apply Function to Image Broken Down by Factor

plot.bermantest

Plot Result of Berman Test

Summarise Marks in Every Neighbourhood in a Point Pattern

Tropical rain forest trees

Method of Minimum Contrast

Berman's Tests for Point Process Model

Nonparametric Estimate of Spatially-Varying Relative Risk

Convert Line Segment Pattern to Another Unit of Length

Nearest neighbours in three dimensions

Three-Dimensional Box

Convert Window to Another Unit of Length

Distance for a Point Pattern Matching

Exponential Energy Marks

Diameter of an Object

Test Whether An Object Is A Pixel Image

Print News About Latest Version of Package

Ord Interaction Process Family

Neighbourhood density function

Stoyan's Rule of Thumb for Bandwidth Selection

Poisson Point Process Model

Extract Quadrature Scheme Used to Fit a Point Process Model

The Lennard-Jones Potential

Pair Correlation Function obtained from K Function

Point and Click Interface for Exploratory Analysis of Point Pattern

Extract the Interaction from a Fitted Point Process Model

Endpoints of Line Segment Pattern

Function Arrays for Spatial Patterns

Reset Values in Subset of Image

Signed or Vector-Valued Measure

Kaplan-Meier Estimator using Histogram Data

Simulate a Fitted Cluster Point Process Model

plot a Fitted Point Process Model

Test Whether An Object Is A Window

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Nearest Neighbours Between Two Patterns

Apply Affine Transformation To Point Pattern

Estimate window from points alone

Weighted Empirical Cumulative Distribution Function

Convert Polygonal Region into Different Format

Inhomogeneous Pair Correlation Function

Compute Expansion Window for Simulation

Randomly Shift a Point Pattern

Convert Spatial Object to Pixel Image

Beta Ganglion Cells in Cat Retina

Distance Map of Point Pattern

Distance Map of Line Segment Pattern

Ord's Interaction model

Centroid of a window

Point and Click Interface for Displaying a Point Pattern

Simulate point patterns using the Metropolis-Hastings algorithm.

Apply Affine Transformation

Kaplan-Meier and Reduced Sample Estimator using Histograms

Plot a Colour Map

Japanese Pines Point Pattern

Kernel Smoothing of Line Segment Pattern

Calculate four standard summary functions of a point pattern.

plot a Spatial Point Pattern

Generate N Uniform Random Points in a Disc

Place Points Evenly Along Specified Lines

Reduced Sample Estimator using Histogram Data

Pair Correlation Function obtained from array of K functions

Combine Function Value Tables

Morphological Erosion

Simulate Thomas Process

Geometrical Calculations for Multi-Dimensional Box

Pairwise Distances in Any Dimensions

Geometrical Calculations for Three-Dimensional Box

Data Frames of Function Values

Profile Maximum Pseudolikelihood

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Convert dataset to another unit of length

Intersect Infinite Straight Lines with a Window

Expand Window By Factor

The Piecewise Constant Pairwise Interaction Point Process Model

Convert Point Pattern to Another Unit of Length

Beta Ganglion Cells in Cat Retina, Old Version

Nearest neighbour

Apply Vector Translation To Pixel Image

Apply Affine Transformation To Window

Fitted Conditional Intensity for Point Process Model

Convert a Window to a Polygonal Window

Diameter of a Window

pairdist.default

Pairwise distances

ANOVA for Fitted Point Process Models

as.data.frame.im

Convert Pixel Image to Data Frame

Number of Points in a Point Pattern

Diggle's Heather Data

Distance Between Two Point Patterns

Kernel Smoothed Intensity of Point Pattern

Border Region of a Window

Convert Data To Class ppp

Multitype pair correlation function (cross-type)

Area of Part of Disc

Mark Correlation Integral

Mosaic Random Field

Summary of a Spatial Window

Convert Pixel Image to Matrix or Array

Marks of a Point Pattern

Multitype pair correlation function (i-to-any)

Interpolate a Pixel Image

Create a Tessellation

Harkness-Isham ants' nests data

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Cartesian Coordinates for a Pixel Raster

Test Whether a Window is Convex

Lurking variable plot

Hutchings' Bramble Canes data

Nearest neighbour distances

Pairwise distances

Poisson Line Tessellation

Mark Connection Function

Summarizing a Fitted Point Process Model

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Histogram of Pixel Values in an Image

Variance-Covariance Matrix for a Fitted Point Process Model

Set Covariance of a Window

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Create a Line Segment Pattern

spatstat-internal

Internal spatstat functions

plot.hyperframe

Plot Entries in a Hyperframe

The Soft Core Point Process Model

Fit cluster point process model

Set Control Parameters for Metropolis-Hastings Algorithm.

Class of Quadrature Schemes

Generate N Uniform Random Points in Three Dimensions

Print Brief Details of a Line Segment Pattern Dataset

Generate Multitype Poisson Point Pattern

methods.distfun

Methods for Distance Functions

Generate N Uniform Random Points in Any Dimensions

Pairwise distances in Three Dimensions

Morphological Closing

Identify Points in a Point Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Area of a Window

Distance to Boundary of Window

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

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

Three Dimensional Point Pattern

Pairwise distances between line segments

Convert Point Pattern to Pixel Image

spatstat-deprecated

Deprecated spatstat functions

Test Whether A Point Pattern is Marked

Print Brief Details of an Image

Convert and Compare Colours in Different Formats

Smooth a Signed or Vector-Valued Measure

Print Brief Details of a Spatial Window

Simulate Neyman-Scott Process

Convert Data to Three-Dimensional Box

Analysis of Deviance for Spatial Logistic Regression Models

Simulate Stratified Random Point Pattern

Kolmogorov-Smirnov Test for Point Process Model

Test Whether An Object Is A Fitted Point Process Model

Plot a Spatial Window

Cut margins from rectangle

Summarizing a Pixel Image

Plot a fitted cluster point process

Class of Point Patterns

Point Patterns of New Brunswick Forest Fires

Saturated Pairwise Interaction Point Process Family

Nearest Neighbour Clutter Removal

Convert Data To Class owin

Smoothing Estimate of Covariate Transformation

Prediction from a Fitted Point Process Model

Simulate Baddeley-Silverman Cell Process

Plot a tessellation

nearest.raster.point

Find Pixel Nearest to a Given Point

multiplicity.ppp

Count Multiplicity of Duplicate Points

plot a Spatial Line Segment Pattern

Summarizing a Quadrature Scheme

pppmatching.object

Class of Point Matchings

Generate N Random Multitype Points

Print a Fitted Point Process Model

Q-Q Plot of Residuals from Fitted Point Process Model

California Redwoods Point Pattern (Entire Dataset)

Nearest Neighbour Distances in Any Dimensions

Data and Code From JRSS Discussion Paper on Residuals

Integral of a Pixel Image

pairwise.family

Pairwise Interaction Process Family

Extract List of Tiles in a Tessellation

Ponderosa Pine Tree Point Pattern

Generate Poisson Random Line Process

Simulate Matern Cluster Process

Interactively Define a Polygon

Lansing Woods Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Update a Fitted Cluster Point Process Model

Nearest neighbour distances between line segments

Window in Shape of Letter R

Morphological Opening

Lengths of Line Segments

Simulate Gauss-Poisson Process

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Mosaic Random Set

Methods for Multi-Dimensional Box

Print Brief Details of a Point Pattern Dataset

Convert Window to Pixel Image

Test Whether Two Pixel Images Are Compatible

Generate N Uniform Random Points

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Fit Point Process Model to Data

Summary of a List of Things

Loglikelihood of Spatial Logistic Regression

Apply Vector Translation To Point Pattern

Class of Fitted Point Process Models

Mark Correlation Function

Simulate Matern Model I

Make Periodic Copies of a Spatial Pattern

Create a Window

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

Volume of an Object

Create a Pixel Image Object

Determine Initial State for Metropolis-Hastings Simulation.

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Sample Quantiles of Pixel Image

Rotate a Line Segment Pattern

Data Sharpening of Point Pattern

Pairwise distances

Apply Vector Translation

rshift.splitppp

Randomly Shift a List of Point Patterns

Theoretical Distribution of Nearest Neighbour Distance

California Redwoods Point Pattern (Ripley's Subset)

Generate Poisson Point Pattern on Line Segments

Murchison gold deposits

Sufficient Statistic of Point Process Model

Apply Smoothing to Function Values

Create a Point Matching

Fry Plot of Point Pattern

Hyper Data Frame

Generic Pairwise Interaction model

Pair Correlation Function

Areas of Morphological Dilations

Name for Unit of Length

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

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

Generate Poisson Point Pattern in Any Dimensions

Pair Correlation Function of a Three-Dimensional Point Pattern

Convert Line Segment Pattern to Pixel Image

Quadrature Scheme Based on Pixel Grid

Generate Poisson Point Pattern in Three Dimensions

Summary of a Line Segment Pattern Dataset

Compute Areas of Tiles in a Tessellation

Superimpose Several Point Patterns

Random Re-Labelling of Point Pattern

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

quadratresample

Resample a Point Pattern by Resampling Quadrats

Compute Integral of Function Against Cumulative Distribution

Quadrat counting for a point pattern

Weighted Histogram

Class of Line Segment Patterns

Galaxies in the Shapley Supercluster

Spatial Logistic Regression

Perfect Simulation of the Strauss Process

Create a Point Pattern

Divide Region into Quadrats

Estimate Variance of Summary Statistic by Subdivision

Test Whether An Object Is A Point Pattern

Vertices of a Window

Approximate a Polygon by a Simpler Polygon

Extract Dummy Points Used to Fit a Point Process Model

Intersection, Union or Set Subtraction of Two Windows

Plot a List of Point Patterns

Predicted or Fitted Values from Spatial Logistic Regression

Methods for Three-Dimensional Box

Define Point Process Model for Metropolis-Hastings Simulation.

Plot a Fitted Spatial Logistic Regression

Pine saplings in Finland.

Extract Unique Points from a Spatial Point Pattern

Swedish Pines Point Pattern

Spatial smoothing of observations at irregular points

Generate a Quadrature Scheme from a Point Pattern

Simulate Simple Sequential Inhibition

matclust.estpcf

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

Multidimensional Space-Time Point Pattern

Interpret Fitted Model for Metropolis-Hastings Simulation.

Urkiola Woods Point Pattern

Plot a Signed or Vector-Valued Measure

Longleaf Pines Point Pattern

Simulate Matern Model II

Apply Vector Translation To Window

Cross Validated Bandwidth Selection for Relative Risk Estimation

Simulate from a Fitted Point Process Model

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Convert Pixel Image to Another Unit of Length

Simulate a Fitted Gibbs Point Process Model

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

Spokes pattern of dummy points

Identify Pixelwise Maximum of Several Pixel Images

Random Perturbation of a Point Pattern

Divide Point Pattern into Sub-patterns

Spruces Point Pattern

Prediction from a Fitted Cluster Point Process Model

rescue.rectangle

Convert Window Back To Rectangle

spatstat-package

The Spatstat Package

Plot Function Values

Fit the Thomas Point Process by Minimum Contrast

Summary of a Point Pattern Dataset

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Fit the Thomas Point Process by Minimum Contrast

Generate Poisson Point Pattern

Union of Data and Dummy Points

Apply Vector Translation To Line Segment Pattern

Simulate systematic random point pattern

summary.splitppp

Summary of a Split Point Pattern

Superimpose Several Line Segment Patterns

Pixel Image Approximation of a Window

Hughes' Amacrine Cell Data

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Convert Line Segment Pattern to Binary Pixel Mask

Bronze gradient filter data

Beadlet Anemones Data

Convert Pixel Image from Numeric to Factor

Artificial Data Point Pattern

Identify Segments in a Line Segment Pattern

complement.owin

Take Complement of a Window

Intersection of Two Tessellations

Safely Convert Point Pattern Window to Binary Mask

Generate a Default Pattern of Dummy Points

spatstat.options

Internal Options in Spatstat Package

Simulation Envelopes of Summary Function

Distance Map of Window

Extract Subset of Function Values

Basis for Harmonic Functions

Find Line Segment Nearest to Each Point

Methods for three-dimensional point patterns

Marked K-Function

Pair Correlation Function of Point Pattern

Print Progress Reports

Plot a List of Things

Rectangular grid of points

Inhomogeneous Cross K Function

Methods for Multidimensional Space-Time Point Patterns

Residuals for Fitted Point Process Model

project2segment

Move Point To Nearest Line

Interaction Distance of a Point Process

Plot a Simulation Envelope

Simulated Point Pattern

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

Generate N Random Points

Foxall's Distance Functions

Randomly Shift a Line Segment Pattern

Read Point Pattern From Data File

Marked J Function

Divide Image Into Sub-images

Evaluate an Expression in a Function Table

Extract or Replace Subset of a List of Things

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Update a Fitted Point Process Model

Subset of Quadrature Scheme

Nearest Neighbours in Any Dimensions

Random Thinning

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

Diagnostics for random marking

Extract Subset of Function Array

The Area Interaction Point Process Model

Multitype K Function (Cross-type)

Hybrid Geyer Point Process Model

Marked Nearest Neighbour Distance Function

Extract or Replace Subset of Tessellation

K-function of a Three-Dimensional Point Pattern

Estimate the empty space function F

Extract or Replace Subset of Point Pattern

Diggle-Gratton model

Extract Subset of Signed or Vector Measure

The Fiksel Interaction

Multitype L-function (cross-type)

Extract.splitppp

Extract or Replace Sub-Patterns

K-function using FFT

Extract Subset of Line Segment Pattern

Inhomogeneous Cross Type L Function

Geyer's Saturation Point Process Model

The Hard Core Point Process Model

Locally Scaled K-function

Multitype J Function (i-to-j)

Estimate the J-function

Nearest Neighbour Distance Function G

Reduced Second Moment Measure

Extract Subset of Image

Inhomogeneous Multitype K Dot Function

Estimate the I-function

Multitype K Function (i-to-any)

Spherical Contact Distribution Function

Multitype J Function (i-to-any)

Inhomogeneous K-function

Empty Space Function of a Three-Dimensional Point Pattern

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