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spatstat (version 1.23-2)

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

18,534

Version

1.23-2

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

August 11th, 2011

Functions in spatstat (1.23-2)

Spherical Contact Distribution Function

Extract.splitppp

Extract or Replace Sub-Patterns

K-function using FFT

Model Compensator of K Function

Reduced Second Moment Measure

Extract or Replace Subset of Point Pattern

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

Residual G Function

Extract Subset of Function Values

Model Compensator of Nearest Neighbour Function

Marked J Function

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Beta Ganglion Cells in Cat Retina

Calculate four standard summary functions of a point pattern.

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Residual K Function

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Nearest Neighbour Distance Function G

Distance to Boundary of Window

Berman's Tests for Point Process Model

The Multitype Hard Core Point Process Model

Extract Subset of Line Segment Pattern

Pairwise distances

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Convert Line Segment Pattern to Binary Pixel Mask

Pixel Image Approximation of a Window

Extract Subset of Function Array

Convert Data to Hyperframe

Colour Lookup Tables

Convert a Window to a Polygonal Window

Extract Subset of Signed or Vector Measure

Three-Dimensional Box

The Piecewise Constant Pairwise Interaction Point Process Model

Kernel Smoothing of Line Segment Pattern

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Tropical rain forest trees

Circumradius and Diameter of a Linear Network

Diagnostics for random marking

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

The Fiksel Interaction

Estimate the empty space function F

Estimate the J-function

Convert Pixel Image from Numeric to Factor

Generic Pairwise Interaction model

Extract Subset of Image

Marked K-Function

Beta Ganglion Cells in Cat Retina, Old Version

The Soft Core Point Process Model

Diggle-Gratton model

Generic Ord Interaction model

Pine saplings in Finland.

Crossing Points of Two Line Segment Patterns

Berman-Huntington points and lines data

Locally Scaled K-function

Ord's Interaction model

crossdist.default

Pairwise distances between two different sets of points

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Extract Original Data from a Fitted Point Process Model

Analysis of Deviance for Spatial Logistic Regression Models

Hughes' Amacrine Cell Data

Inhomogeneous Multitype L Dot Function

Morphological Closing

Multitype K Function (i-to-any)

ANOVA for Fitted Point Process Models

complement.owin

Take Complement of a Window

Subdivide a Window or Tessellation using a Set of Lines

Reset Values in Subset of Image

as.data.frame.im

Convert Pixel Image to Data Frame

Convert Data To Class ppp

Compute Expansion Window for Simulation

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Test Whether Marks Are Present

Concatenate x,y Coordinate Vectors

spatstat-deprecated

Deprecated spatstat functions

Safely Convert Point Pattern Window to Binary Mask

Artificial Data Point Pattern

Convert Polygonal Region into Different Format

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Determine Duplicated Points in a Spatial Point Pattern

Convert Data To Class owin

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Fry Plot of Point Pattern

Endpoints of Line Segment Pattern

pairdist.default

Pairwise distances

Japanese Pines Point Pattern

Linear Pair Correlation Function

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Simulation Envelopes of Summary Function

ANOVA for Fitted Point Process Models on Linear Network

Create a Point Pattern

Bronze gradient filter data

Chicago Street Crime Data

Interactively Define a Polygon

clarkevans.test

Clark and Evans Test

matclust.estpcf

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

Centroid of a window

Convert Data To Tessellation

Harkness-Isham ants' nests data

Contour plot of pixel image

Evaluate Expression Involving Functions

Convert Data to Three-Dimensional Box

Apply Gaussian Blur to a Pixel Image

Interpolate a Pixel Image

Divide Region into Quadrats

Diameter of an Object

Model Formulae for Gibbs Point Process Models

Recognise Stationary and Poisson Point Process Models

Stoyan's Rule of Thumb for Bandwidth Selection

Envelope for Point Patterns on Linear Network

Identify Segments in a Line Segment Pattern

Test Whether a Window is Convex

Convert Pixel Image to Matrix or Array

Distance to Boundary of Window

Hutchings' Bramble Canes data

Evaluate Expression Involving Pixel Images

Test Whether An Object Is A Window

Intersection, Union or Set Subtraction of Two Windows

K function of a model

Inhomogeneous K-function

Intersect Infinite Straight Lines with a Window

Corners of a rectangle

Hyper Data Frame

Empty Space Function of a Three-Dimensional Point Pattern

Create a Pixel Image Object

Perspective Plot of Pixel Image

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Test Whether Points Are Inside A Window

Plot a Fitted Spatial Logistic Regression

Inhomogeneous Cross K Function

Fitted Conditional Intensity for Point Process Model

Inhomogeneous Cross Type L Function

Biological Cells Point Pattern

Multitype L-function (cross-type)

Apply Affine Transformation

Bounding Box of a Window or Point Pattern

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

Create Point Pattern on Linear Network

Multitype J Function (i-to-any)

Window in Shape of Letter R

Coefficients of Fitted Spatial Logistic Regression Model

Fitted Probabilities for Spatial Logistic Regression

Extract Interaction Structure

Mark Correlation Integral

Intersection of Two Tessellations

Dummy Function Returns Number of Points

Apply Affine Transformation To Point Pattern

Fit Cluster or Cox Point Process Model

Inhomogeneous Neighbourhood Density Function

Nearest neighbour distances between line segments

Class of Quadrature Schemes

Nearest Neighbours Between Two Patterns

Geometrical Calculations for Three-Dimensional Box

Generate Poisson Point Pattern

Pairwise distances between two different three-dimensional point patterns

Pairwise distances

Apply Affine Transformation To Window

Geometrical Calculations for Multi-Dimensional Box

Number of Line Segments in a Line Segment Pattern

Dirichlet Tessellation of Point Pattern

Morphological Opening

Connected components of an image or window

Distance Map of Point Pattern

K-function of a Three-Dimensional Point Pattern

Marks of a Line Segment Pattern

Distance Map as a Function

Loglikelihood of Spatial Logistic Regression

Areas of Morphological Erosions

Delaunay Triangulation of Point Pattern

Interactively join vertices on a plot

Determine Whether One Window is Contained In Another

plot.hyperframe

Plot Entries in a Hyperframe

Uniform Random Points on a Linear Network

Mark Correlation Function

Diagnostic Plots for Fitted Point Process Model

Class of Images

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

Test whether Object is Multitype

Plot a Pixel Image

Circular Window

Quadrature Scheme Based on Pixel Grid

Multidimensional Space-Time Point Pattern

Expand Window By Factor

Kaplan-Meier and Reduced Sample Estimator using Histograms

Distance Between Two Point Patterns

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

Convert Function Value Table to Function

Inhomogeneous Linear Pair Correlation Function

Estimate the I-function

Methods for Point Patterns on a Linear Network

Print Brief Details of an Image

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Summary of a Line Segment Pattern Dataset

Border Region of a Window

plot a Spatial Point Pattern

Place Points Evenly Along Specified Lines

Methods for Multi-Dimensional Box

Integral of a Pixel Image

The Lennard-Jones Potential

Cross Validated Bandwidth Selection for Relative Risk Estimation

Summary of a List of Things

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

Signed or Vector-Valued Measure

Print Progress Reports

bounding.box.xy

Convex Hull of Points

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Coefficients of Fitted Point Process Model

Pairwise distances between two different point patterns

Influenza Virus Proteins

quadratresample

Resample a Point Pattern by Resampling Quadrats

Plot a plotppm Object Created by plot.ppm

Print Brief Details of a Point Pattern Dataset

Convert Pixel Image to Another Unit of Length

Chorley-Ribble Cancer Data

Lengths of Line Segments

Print Brief Details of a Line Segment Pattern Dataset

Test Whether An Object Is Empty

Pseudoscore Diagnostic For Fitted Model against Saturation Alternative

Inhomogeneous Pair Correlation Function

Convert to Pixel Image

Estimate window from points alone

Convert Line Segment Pattern to Another Unit of Length

Neighbourhood density function

Apply a Function to a Point Pattern Broken Down by Factor

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Test Whether Two Function Objects Are Compatible

Smooth a Signed or Vector-Valued Measure

Number of Points in a Point Pattern

Simulate Matern Cluster Process

Pairwise Distances in Any Dimensions

Compute Images of Constructed Covariates

New Zealand Trees Point Pattern

Murchison gold deposits

Convert dataset to another unit of length

Plot a Function Array

Multitype pair correlation function (i-to-any)

Generate a Quadrature Scheme from a Point Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Simulate Matern Model I

Interactively Add Points

Mosaic Random Field

Simulate a Fitted Cluster Point Process Model

Combine Function Value Tables

Interaction Distance of a Point Process

Convert Window to Another Unit of Length

Exponential Energy Marks

Methods for three-dimensional point patterns

Pairwise shortest-path distances between points on a linear network

Point Patterns of New Brunswick Forest Fires

multiplicity.ppp

Count Multiplicity of Duplicate Points

Simulate point patterns using the Metropolis-Hastings algorithm.

Basis for Harmonic Functions

Three Dimensional Point Pattern

Random Perturbation of a Point Pattern

Extract Dummy Points Used to Fit a Point Process Model

Superimpose Several Geometric Patterns

Exchange X and Y Coordinates

Reduced Sample Estimator using Histogram Data

Generate Multitype Poisson Point Pattern

nearest.raster.point

Find Pixel Nearest to a Given Point

Distance Map of Window

Function Arrays for Spatial Patterns

Pairwise distances in Three Dimensions

Simulation Envelopes of Summary Function for 3D Point Pattern

Test Whether An Object Is A Fitted Point Process Model

Class of Fitted Point Process Models

Humberside Data on Childhood Leukaemia and Lymphoma

Generate Poisson Point Pattern in Any Dimensions

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Methods for Cluster Point Process Models

Evaluate an Expression in a Function Table

Summarizing a Quadrature Scheme

Create a Line Segment Pattern

Simulate Stratified Random Point Pattern

Test Whether A Point Pattern is Marked

Randomly Shift a Point Pattern

Linear K Function

Summary of a Point Pattern Dataset

Convert Spatial Object to Pixel Image

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

spatstat-package

The Spatstat Package

Scatterplot Matrix for Pixel Images

Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative

Quadrat counting for a point pattern

Plot a linear network

Compute Areas of Tiles in a Tessellation

Lansing Woods Point Pattern

The Hard Core Point Process Model

Extract List of Tiles in a Tessellation

project2segment

Move Point To Nearest Line

Test Whether An Object Is A Pixel Image

plot a Fitted Point Process Model

Print News About Latest Version of Package

pppmatching.object

Class of Point Matchings

Multitype J Function (i-to-j)

Create a Tessellation

Apply Vector Translation To Line Segment Pattern

The Strauss Point Process Model

Spruces Point Pattern

Saturated Pairwise Interaction Point Process Family

Convert Line Segment Pattern to Pixel Image

Histogram of Pixel Values in an Image

Simulate from a Fitted Point Process Model

rescue.rectangle

Convert Window Back To Rectangle

Generate N Uniform Random Points

Poisson Point Process Model

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Simulate Baddeley-Silverman Cell Process

scaletointerval

Rescale Data to Lie Between Specified Limits

Fit the Thomas Point Process by Minimum Contrast

Plot a Colour Map

Urkiola Woods Point Pattern

Infinite Straight Lines

Create Pixel Image on Linear Network

Methods for Multidimensional Space-Time Point Patterns

Point and Click Interface for Displaying a Point Pattern

Combine Two Line Segment Patterns

Interpret Fitted Model for Metropolis-Hastings Simulation.

Poisson Point Process on a Linear Network

Plot Function Values

Spokes pattern of dummy points

Plot a fitted cluster point process

Galaxies in the Shapley Supercluster

Inhomogeneous Linear K Function

Log Likelihood and AIC for Point Process Model

Plot a Signed or Vector-Valued Measure

Marks of a Point Pattern

Mark Connection Function

Plot Pixel Image on Linear Network

Simple Example of Linear Network

Method of Minimum Contrast

Generate N Uniform Random Points in Three Dimensions

Ord Interaction Process Family

Prediction from a Fitted Point Process Model

model.frame.ppm

Extract the Environment of a Point Process Model

Variance-Covariance Matrix for a Fitted Point Process Model

California Redwoods Point Pattern (Entire Dataset)

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Set Control Parameters for Metropolis-Hastings Algorithm.

Generate Poisson Point Pattern in Three Dimensions

Generate N Uniform Random Points in a Disc

Multitype pair correlation function (cross-type)

Spatial smoothing of observations at irregular points

Kernel Smoothed Intensity of Point Pattern

Plot a Simulation Envelope

Extract or Replace Subset of a List of Things

The Area Interaction Point Process Model

Test Whether Two Pixel Images Are Compatible

The Multitype Strauss Point Process Model

The Strauss / Hard Core Point Process Model

Rotate a Line Segment Pattern

Summarise Marks in Every Neighbourhood in a Point Pattern

Q-Q Plot of Residuals from Fitted Point Process Model

Plot a three-dimensional point pattern

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Simulate Thomas Process

Extract the Interaction from a Fitted Point Process Model

Sample Quantiles of Pixel Image

Midpoints of Line Segment Pattern

Inverse-distance weighted smoothing of observations at irregular points

Sufficient Statistic of Point Process Model

Create a Window

Random Re-Labelling of Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Plot a List of Point Patterns

Perimeter Length of Window

Difference of Disc Areas

Create Colour-Valued Pixel Image

Pair Correlation Function

Convert Point Pattern to Pixel Image

California Redwoods Point Pattern (Ripley's Subset)

Plot a Spatial Kolmogorov-Smirnov Test

Fit Point Process Model to Data

Update a Fitted Cluster Point Process Model

Ponderosa Pine Tree Point Pattern

Apply Vector Translation To Pixel Image

Data Sharpening of Point Pattern

Convert Point Pattern to Another Unit of Length

Apply Vector Translation To Point Pattern

Local pair correlation function

Volume of an Object

Weighted Histogram

Summary of a Spatial Window

Level Set of a Pixel Image

Predicted or Fitted Values from Spatial Logistic Regression

Profile Maximum Pseudolikelihood

Difference of Disc Areas

Create a Linear Network

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Simulate Neyman-Scott Process

Convert Data To Class psp

Generate N Uniform Random Points in Any Dimensions

Generate N Random Multitype Points

Find Line Segment Nearest to Each Point

Read Point Pattern From Data File

Smoothing Estimate of Covariate Transformation

Orientation Angles of Line Segments

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Plot a Spatial Window

Create a Point Matching

Random Thinning

Poisson Line Tessellation

Nearest Neighbour Distances in Any Dimensions

Compute Quadratic Forms

Rotate a Window

Pair Correlation Function obtained from array of K functions

Apply Smoothing to Function Values

Nearest Neighbours in Any Dimensions

Simulated Point Pattern

Simulate Gauss-Poisson Process

Swedish Pines Point Pattern

Residual Diagnostics for Multiple Fitted Models

Mosaic Random Set

Generate Poisson Point Pattern on Line Segments

Approximate a Polygon by a Simpler Polygon

Nearest neighbour distances in three dimensions

spatstat-internal

Internal spatstat functions

Spatial Logistic Regression

Nearest neighbour

Identify Pixelwise Maximum of Several Pixel Images

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Pairwise distances

Areas of Morphological Dilations

Pair Correlation Function obtained from K Function

Morphological Erosion

Summarizing a Pixel Image

Create a Function Value Table

Name for Unit of Length

pairwise.family

Pairwise Interaction Process Family

Test Whether An Object Is A Point Pattern

Update a Fitted Point Process Model

spatstat.options

Internal Options in Spatstat Package

Pair Correlation Function of Point Pattern

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Lurking variable plot

Nearest neighbour distances

Define Point Process Model for Metropolis-Hastings Simulation.

Generate grid of parallel lines with random displacement

Pairwise distances between line segments

Simulate systematic random point pattern

Test Whether A Point Process Model is Marked

Make Periodic Copies of a Spatial Pattern

Simulate Matern Model II

Simulate a Fitted Gibbs Point Process Model

Print Brief Details of a Spatial Window

Extract Quadrature Scheme Used to Fit a Point Process Model

Class of Line Segment Patterns

Cartesian Coordinates for a Pixel Raster

Randomly Shift a Line Segment Pattern

runifpointOnLines

Generate N Uniform Random Points On Line Segments

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

Apply Vector Translation

summary.splitppp

Summary of a Split Point Pattern

Union of Data and Dummy Points

Hybrid Geyer Point Process Model

Subset of Quadrature Scheme

Multitype K Function (Cross-type)

Saturated Pairwise Interaction model

Apply Function to Image Broken Down by Factor

Clark and Evans Aggregation Index

Convert and Compare Colours in Different Formats

Area of Part of Disc

Diameter of a Window

Extract or Replace Subset of Tessellation

Evaluate Expression Involving Function Arrays

Weighted Empirical Cumulative Distribution Function

Inhomogeneous Multitype K Dot Function

Geyer's Saturation Point Process Model

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Fit Point Process Model to Point Pattern on Linear Network

Distance for a Point Pattern Matching

Apply Affine Transformation To Line Segment Pattern

methods.distfun

Methods for Distance Functions

Methods for Fitted Point Process Models on a Linear Network

Beadlet Anemones Data

plot a Spatial Quadrature Scheme

Plot a List of Things

Theoretical Distribution of Nearest Neighbour Distance

Convex Hull of Points

Generate a Default Pattern of Dummy Points

Morphological Dilation

Generate Poisson Random Line Process

Find Largest Circle Inside Window

rshift.splitppp

Randomly Shift a List of Point Patterns

inforder.family

Infinite Order Interaction Family

Set Covariance of a Window

Summarizing a Fitted Point Process Model

Cut margins from rectangle

Variance-Covariance Matrix for a Fitted Cluster Point Process Model

Methods for Linear Networks

Longleaf Pines Point Pattern

Print a Quadrature Scheme

plot.bermantest

Plot Result of Berman Test

Pseudoscore Diagnostic For Fitted Model against General Alternative

Simulate Log-Gaussian Cox Process

Simulate Simple Sequential Inhibition

Determine Initial State for Metropolis-Hastings Simulation.

Apply Vector Translation To Window

Generate N Random Points

Estimate Variance of Summary Statistic by Subdivision

Marked Nearest Neighbour Distance Function

Foxall's Distance Functions

Multi-Dimensional Box

Collapse Several Function Tables into One

Pairwise distances between two different line segment patterns

Classify Points in a Point Pattern

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

Function Value Table

Compute Quadrature Weights Based on Grid Counts

Identify Points in a Point Pattern

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Kolmogorov-Smirnov Test for Point Process Model

Methods for Intensity Functions of Spatial Covariate

model.matrix.ppm

Extract Design Matrix from Point Process Model

Pair Correlation Function of a Three-Dimensional Point Pattern

Convert Window to Pixel Image

plot a Spatial Line Segment Pattern

Plot a tessellation

Prediction from a Fitted Cluster Point Process Model

Print a Fitted Point Process Model

Data and Code From JRSS Discussion Paper on Residuals

Nonparametric Estimate of Spatially-Varying Relative Risk

Rotate a Point Pattern

Divide Point Pattern into Sub-patterns

Fit the Thomas Point Process by Minimum Contrast

Rounding of Pixel Values

Vertices of a Window

Compute Integral of Function Against Cumulative Distribution

Kaplan-Meier Estimator using Histogram Data

Residuals for Fitted Point Process Model

Distance to Boundary of Window

Extract Unique Points from a Spatial Point Pattern

Class of Point Patterns

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

Area of a Window

Distance Map of Line Segment Pattern

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Point and Click Interface for Exploratory Analysis of Point Pattern

Multitype L-function (i-to-any)

Morishita Index Plot

Aherne's hamster tumour data

Apply Function to Every Neighbourhood in a Point Pattern

Divide Image Into Sub-images

Nearest Neighbour Clutter Removal

Diggle's Heather Data

Methods for Three-Dimensional Box

Compute Disc of Given Radius in Linear Network

Nearest neighbours in three dimensions

Rectangular grid of points

Perfect Simulation of the Strauss Process

Predict Point Process Model on Linear Network