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spatstat (version 1.22-1)

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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Version

Install

install.packages('spatstat')

Monthly Downloads

18,534

Version

1.22-1

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

May 19th, 2011

Functions in spatstat (1.22-1)

Extract.splitppp

Extract or Replace Sub-Patterns

Multitype K Function (Cross-type)

The Soft Core Point Process Model

Calculate four standard summary functions of a point pattern.

Point and Click Interface for Displaying a Point Pattern

Extract Original Data from a Fitted Point Process Model

Pairwise distances between two different point patterns

as.data.frame.im

Convert Pixel Image to Data Frame

Apply a Function to a Point Pattern Broken Down by Factor

Kernel Smoothed Intensity of Point Pattern

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Berman-Huntington points and lines data

Extract Subset of Signed or Vector Measure

Inhomogeneous Cross K Function

Convert Polygonal Region into Different Format

Test Whether Marks Are Present

Bronze gradient filter data

Inhomogeneous Multitype L Dot Function

Crossing Points of Two Line Segment Patterns

Distance Map of Line Segment Pattern

Convert Data To Class owin

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Murchison gold deposits

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Simulate Matern Cluster Process

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Extract Subset of Function Values

The Piecewise Constant Pairwise Interaction Point Process Model

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Geyer's Saturation Point Process Model

Extract Subset of Function Array

Apply Affine Transformation To Window

The Area Interaction Point Process Model

Poisson Point Process Model

bounding.box.xy

Convex Hull of Points

Beadlet Anemones Data

Combine Two Line Segment Patterns

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Geometrical Calculations for Multi-Dimensional Box

Generic Ord Interaction model

Biological Cells Point Pattern

Convert Data To Class psp

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Evaluate Expression Involving Function Arrays

Multitype K Function (i-to-any)

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Hughes' Amacrine Cell Data

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Compute Expansion Window for Simulation

Expand Window By Factor

Diggle's Heather Data

Convert Data to Hyperframe

Midpoints of Line Segment Pattern

Diggle-Gratton model

Aherne's hamster tumour data

Spherical Contact Distribution Function

Beta Ganglion Cells in Cat Retina, Old Version

Reduced Second Moment Measure

Areas of Morphological Dilations

Multi-Dimensional Box

Distance to Boundary of Window

K-function using FFT

Intersection of Two Tessellations

Classify Points in a Point Pattern

Extract Subset of Line Segment Pattern

Multitype L-function (i-to-any)

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Kernel Smoothing of Line Segment Pattern

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

Methods for Linear Networks

Perfect Simulation of the Strauss Process

Estimate the J-function

spatstat-deprecated

Deprecated spatstat functions

Level Set of a Pixel Image

Plot a linear network

Convert a Window to a Polygonal Window

Nearest neighbours in three dimensions

Intersection, Union or Set Subtraction of Two Windows

Identify Segments in a Line Segment Pattern

Subset of Quadrature Scheme

Analysis of Deviance for Spatial Logistic Regression Models

Plot a List of Point Patterns

Create a Pixel Image Object

Nearest Neighbour Clutter Removal

Extract or Replace Subset of Point Pattern

Nearest-Neighbour Correlation Indices of Marked Point Pattern

The Strauss Point Process Model

Inhomogeneous Cross Type L Function

Artificial Data Point Pattern

Area of a Window

Test Whether Points Are Inside A Window

Number of Points in a Point Pattern

Place Points Evenly Along Specified Lines

Print News About Latest Version of Package

Convert Data to Three-Dimensional Box

Berman's Tests for Point Process Model

Convert to Pixel Image

pairwise.family

Pairwise Interaction Process Family

Distance to Boundary of Window

Create a Window

Multitype pair correlation function (cross-type)

Generate a Default Pattern of Dummy Points

Pairwise distances between two different three-dimensional point patterns

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

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

Multitype L-function (cross-type)

Fry Plot of Point Pattern

Fit Point Process Model to Data

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

The Lennard-Jones Potential

Pixel Image Approximation of a Window

Contour plot of pixel image

Summarise Marks in Every Neighbourhood in a Point Pattern

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Test Whether A Point Pattern is Marked

Interactively join vertices on a plot

plot.hyperframe

Plot Entries in a Hyperframe

Generic Pairwise Interaction model

Methods for Multidimensional Space-Time Point Patterns

Inhomogeneous Multitype K Dot Function

Estimate the I-function

Saturated Pairwise Interaction Point Process Family

Pine saplings in Finland.

Class of Fitted Point Process Models

Randomly Shift a Point Pattern

quadratresample

Resample a Point Pattern by Resampling Quadrats

Plot a Signed or Vector-Valued Measure

California Redwoods Point Pattern (Entire Dataset)

Plot a fitted cluster point process

Apply Affine Transformation To Line Segment Pattern

Convert Pixel Image from Numeric to Factor

Multitype J Function (i-to-j)

Collapse Several Function Tables into One

Pairwise distances between two different line segment patterns

Apply Vector Translation

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

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

Rectangular grid of points

Diameter of an Object

Ponderosa Pine Tree Point Pattern

Distance Map as a Function

The Strauss / Hard Core Point Process Model

Ord Interaction Process Family

Simulate Gauss-Poisson Process

Print a Fitted Point Process Model

Create Colour-Valued Pixel Image

Interactively Add Points

Marked J Function

Multitype pair correlation function (i-to-any)

Inhomogeneous Pair Correlation Function

Orientation Angles of Line Segments

Mosaic Random Field

Kaplan-Meier and Reduced Sample Estimator using Histograms

Random Thinning

Extract the Interaction from a Fitted Point Process Model

Reduced Sample Estimator using Histogram Data

plot a Spatial Point Pattern

Morphological Dilation

Pairwise distances

Basis for Harmonic Functions

Compute Quadrature Weights Based on Grid Counts

Diagnostic Plots for Fitted Point Process Model

Evaluate Expression Involving Pixel Images

Apply Affine Transformation To Point Pattern

Randomly Shift a Line Segment Pattern

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Convert Data To Tessellation

Morphological Erosion

The Fiksel Interaction

Ord's Interaction model

clarkevans.test

Clark and Evans Test

Humberside Data on Childhood Leukaemia and Lymphoma

Point Patterns of New Brunswick Forest Fires

Apply Function to Every Neighbourhood in a Point Pattern

Spatial smoothing of observations at irregular points

rshift.splitppp

Randomly Shift a List of Point Patterns

Weighted Empirical Cumulative Distribution Function

Galaxies in the Shapley Supercluster

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Multidimensional Space-Time Point Pattern

Convert Spatial Object to Pixel Image

Beta Ganglion Cells in Cat Retina

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Summarizing a Fitted Point Process Model

Local pair correlation function

Apply Function to Image Broken Down by Factor

Circular Window

Generate Poisson Random Line Process

Hybrid Geyer Point Process Model

Cross Validated Bandwidth Selection for Relative Risk Estimation

Pairwise distances

Apply Affine Transformation

Q-Q Plot of Residuals from Fitted Point Process Model

Summary of a Point Pattern Dataset

Plot a List of Things

Exponential Energy Marks

Print Brief Details of a Line Segment Pattern Dataset

Print Brief Details of a Spatial Window

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Nearest Neighbour Distance Function G

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

Connected components of an image or window

Infinite Straight Lines

Interpret Fitted Model for Metropolis-Hastings Simulation.

Determine Whether One Window is Contained In Another

Define Point Process Model for Metropolis-Hastings Simulation.

spatstat-internal

Internal spatstat functions

Divide Point Pattern into Sub-patterns

Inhomogeneous K-function

Generate N Uniform Random Points

Test Whether An Object Is A Pixel Image

Generate Poisson Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

Simulated Point Pattern

Marked Nearest Neighbour Distance Function

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Method of Minimum Contrast

Harkness-Isham ants' nests data

Test Whether An Object Is A Point Pattern

Fit the Thomas Point Process by Minimum Contrast

Generate Poisson Point Pattern in Any Dimensions

Apply Gaussian Blur to a Pixel Image

Determine Duplicated Points in a Spatial Point Pattern

Subdivide a Window or Tessellation using a Set of Lines

Prediction from a Fitted Cluster Point Process Model

Window in Shape of Letter R

Identify Points in a Point Pattern

Prediction from a Fitted Point Process Model

Border Region of a Window

Simulate Matern Model II

Fitted Conditional Intensity for Point Process Model

Difference of Disc Areas

Three-Dimensional Box

Bounding Box of a Window or Point Pattern

K-function of a Three-Dimensional Point Pattern

Convert Pixel Image to Matrix or Array

Function Arrays for Spatial Patterns

Nearest neighbour distances between line segments

Pairwise Distances in Any Dimensions

Residuals for Fitted Point Process Model

Perspective Plot of Pixel Image

Create Point Pattern on Linear Network

summary.splitppp

Summary of a Split Point Pattern

Scatterplot Matrix for Pixel Images

Pairwise distances between line segments

Generate N Random Points

Identify Pixelwise Maximum of Several Pixel Images

The Multitype Hard Core Point Process Model

Class of Line Segment Patterns

Extract Subset of Image

Chorley-Ribble Cancer Data

Concatenate x,y Coordinate Vectors

Convert and Compare Colours in Different Formats

Compute Areas of Tiles in a Tessellation

Create a Function Value Table

Superimpose Several Geometric Patterns

Generate N Uniform Random Points in a Disc

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

complement.owin

Take Complement of a Window

Rotate a Line Segment Pattern

Methods for Three-Dimensional Box

Locally Scaled K-function

Simulation Envelopes of Summary Function for 3D Point Pattern

Endpoints of Line Segment Pattern

Divide Image Into Sub-images

Hyper Data Frame

Profile Maximum Pseudolikelihood

Pair Correlation Function obtained from K Function

Diameter of a Window

Fitted Probabilities for Spatial Logistic Regression

Sample Quantiles of Pixel Image

Foxall's Distance Functions

Test Whether a Window is Convex

scaletointerval

Rescale Data to Lie Between Specified Limits

Set Control Parameters for Metropolis-Hastings Algorithm.

Kolmogorov-Smirnov Test for Point Process Model

Test Whether An Object Is A Fitted Point Process Model

Perimeter Length of Window

Data Sharpening of Point Pattern

Distance Map of Window

Loglikelihood of Spatial Logistic Regression

Pair Correlation Function obtained from array of K functions

Simulate from a Fitted Point Process Model

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Colour Lookup Tables

Methods for Point Patterns on a Linear Network

Saturated Pairwise Interaction model

Dirichlet Tessellation of Point Pattern

Print Brief Details of an Image

Nearest Neighbours in Any Dimensions

Quadrat counting for a point pattern

Plot a Colour Map

plot.bermantest

Plot Result of Berman Test

Quadrature Scheme Based on Pixel Grid

Generate Poisson Point Pattern on Line Segments

Summarizing a Quadrature Scheme

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Find Line Segment Nearest to Each Point

nearest.raster.point

Find Pixel Nearest to a Given Point

Cut margins from rectangle

Marks of a Point Pattern

Apply Vector Translation To Window

Point and Click Interface for Exploratory Analysis of Point Pattern

Estimate Variance of Summary Statistic by Subdivision

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Pair Correlation Function of Point Pattern

Morphological Opening

Intersect Infinite Straight Lines with a Window

spatstat.options

Internal Options in Spatstat Package

Areas of Morphological Erosions

Summarizing a Pixel Image

Data Frames of Function Values

Extract List of Tiles in a Tessellation

Test Whether Two Function Objects Are Compatible

Create a Linear Network

Generate a Quadrature Scheme from a Point Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

Plot a Fitted Spatial Logistic Regression

Theoretical Distribution of Nearest Neighbour Distance

Coefficients of Fitted Spatial Logistic Regression Model

Generate N Uniform Random Points in Three Dimensions

Pairwise distances in Three Dimensions

Nearest Neighbour Distances in Any Dimensions

Compute Images of Constructed Covariates

Plot a Simulation Envelope

Rotate a Window

Signed or Vector-Valued Measure

Mark Correlation Function

Make Periodic Copies of a Spatial Pattern

Simulate Matern Model I

Japanese Pines Point Pattern

Morishita Index Plot

plot a Spatial Quadrature Scheme

Print Brief Details of a Point Pattern Dataset

plot a Fitted Point Process Model

methods.distfun

Methods for Distance Functions

Rotate a Point Pattern

Spruces Point Pattern

Fit cluster point process model

Create a Point Matching

Generate Multitype Poisson Point Pattern

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

Update a Fitted Point Process Model

multiplicity.ppp

Count Multiplicity of Duplicate Points

Pair Correlation Function of a Three-Dimensional Point Pattern

Plot a tessellation

plot a Spatial Line Segment Pattern

Smooth a Signed or Vector-Valued Measure

Predicted or Fitted Values from Spatial Logistic Regression

Divide Region into Quadrats

Simple Example of Linear Network

Smoothing Estimate of Covariate Transformation

Simulate a Fitted Cluster Point Process Model

Print a Quadrature Scheme

Integral of a Pixel Image

Plot a Spatial Window

Convert Point Pattern to Another Unit of Length

spatstat-package

The Spatstat Package

Plot a plotppm Object Created by plot.ppm

Distance Between Two Point Patterns

Convert Point Pattern to Pixel Image

Extract or Replace Subset of Tessellation

Marked K-Function

Pairwise distances

Simulate Baddeley-Silverman Cell Process

Diagnostics for random marking

Nearest Neighbours Between Two Patterns

Extract Quadrature Scheme Used to Fit a Point Process Model

Simulate Simple Sequential Inhibition

Morphological Closing

rescue.rectangle

Convert Window Back To Rectangle

Generate N Random Multitype Points

Random Perturbation of a Point Pattern

Find Largest Circle Inside Window

Test Whether An Object Is Empty

Class of Point Patterns

Convert Window to Pixel Image

Summary of a Spatial Window

Plot a Function Array

Read Point Pattern From Data File

Plot Function Values

Convert Pixel Image to Another Unit of Length

Distance for a Point Pattern Matching

Apply Vector Translation To Line Segment Pattern

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Fit the Thomas Point Process by Minimum Contrast

Delaunay Triangulation of Point Pattern

Cartesian Coordinates for a Pixel Raster

Name for Unit of Length

Apply Smoothing to Function Values

Centroid of a window

Uniform Random Points on a Linear Network

crossdist.default

Pairwise distances between two different sets of points

Geometrical Calculations for Three-Dimensional Box

Summary of a List of Things

Apply Vector Translation To Point Pattern

Update a Fitted Cluster Point Process Model

Simulation Envelopes of Summary Function

Evaluate an Expression in a Function Table

Volume of an Object

Poisson Line Tessellation

Simulate a Fitted Gibbs Point Process Model

Mosaic Random Set

California Redwoods Point Pattern (Ripley's Subset)

Data and Code From JRSS Discussion Paper on Residuals

Test Whether A Point Process Model is Marked

Summary of a Line Segment Pattern Dataset

Create a Line Segment Pattern

Methods for Multi-Dimensional Box

Random Re-Labelling of Point Pattern

Neighbourhood density function

Create a Point Pattern

Combine Function Value Tables

Simulate Neyman-Scott Process

The Multitype Strauss Point Process Model

Union of Data and Dummy Points

Weighted Histogram

Reset Values in Subset of Image

Corners of a rectangle

Test Whether Two Pixel Images Are Compatible

Convert dataset to another unit of length

Plot a Pixel Image

Safely Convert Point Pattern Window to Binary Mask

Convert Line Segment Pattern to Binary Pixel Mask

Convert Line Segment Pattern to Pixel Image

Print Progress Reports

Generate grid of parallel lines with random displacement

Lurking variable plot

Spatial Logistic Regression

Stoyan's Rule of Thumb for Bandwidth Selection

pairdist.default

Pairwise distances

Define Point Process Model for Metropolis-Hastings Simulation.

Tropical rain forest trees

Mark Correlation Integral

Create a Tessellation

Area of Part of Disc

Compute Integral of Function Against Cumulative Distribution

ANOVA for Fitted Point Process Models

Poisson Point Process on a Linear Network

Simulate Stratified Random Point Pattern

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Empty Space Function of a Three-Dimensional Point Pattern

Extract or Replace Subset of a List of Things

Distance Map of Point Pattern

Generate Poisson Point Pattern in Three Dimensions

Sufficient Statistic of Point Process Model

Circumradius and Diameter of a Linear Network

Interactively Define a Polygon

Convex Hull of Points

Set Covariance of a Window

Apply Vector Translation To Pixel Image

Vertices of a Window

Convert Data To Class ppp

Estimate window from points alone

Plot a Spatial Kolmogorov-Smirnov Test

inforder.family

Infinite Order Interaction Family

Extract Unique Points from a Spatial Point Pattern

Spokes pattern of dummy points

Test whether Object is Multitype

model.frame.ppm

Extract the Environment of a Point Process Model

Log Likelihood for Poisson Point Process Model

Difference of Disc Areas

Methods for three-dimensional point patterns

Nearest neighbour distances in three dimensions

model.matrix.ppm

Extract Design Matrix from Point Process Model

Nearest neighbour distances

Kaplan-Meier Estimator using Histogram Data

Marks of a Line Segment Pattern

Number of Line Segments in a Line Segment Pattern

Plot a three-dimensional point pattern

project2segment

Move Point To Nearest Line

pppmatching.object

Class of Point Matchings

Lengths of Line Segments

Interaction Distance of a Point Process

Nonparametric Estimate of Spatially-Varying Relative Risk

Urkiola Woods Point Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Simulate systematic random point pattern

matclust.estpcf

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

Convert Window to Another Unit of Length

The Hard Core Point Process Model

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

Approximate a Polygon by a Simpler Polygon

Multitype J Function (i-to-any)

Clark and Evans Aggregation Index

Coefficients of Fitted Point Process Model

Three Dimensional Point Pattern

Simulate Thomas Process

Distance to Boundary of Window

Evaluate Expression Involving Functions

Histogram of Pixel Values in an Image

Extract Dummy Points Used to Fit a Point Process Model

Estimate the empty space function F

Class of Images

Longleaf Pines Point Pattern

Hutchings' Bramble Canes data

Lansing Woods Point Pattern

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

Interpolate a Pixel Image

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Nearest neighbour

Class of Quadrature Schemes

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Generate N Uniform Random Points in Any Dimensions

Convert Line Segment Pattern to Another Unit of Length

Swedish Pines Point Pattern

New Zealand Trees Point Pattern

Pair Correlation Function

Simulate point patterns using the Metropolis-Hastings algorithm.

Test Whether An Object Is A Window

Mark Connection Function