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spatstat (version 1.21-0)

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

1.21-0

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

November 5th, 2010

Functions in spatstat (1.21-0)

Pixel Image Approximation of a Window

Inhomogeneous Multitype L Dot Function

Contour plot of pixel image

as.data.frame.im

Convert Pixel Image to Data Frame

Poisson Point Process Model

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Apply Gaussian Blur to a Pixel Image

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

ANOVA for Fitted Point Process Models

Distance to Boundary of Window

bounding.box.xy

Convex Hull of Points

Coefficients of Fitted Point Process Model

Areas of Morphological Erosions

Saturated Pairwise Interaction model

Integral of a Pixel Image

The Piecewise Constant Pairwise Interaction Point Process Model

Hyper Data Frame

Fry Plot of Point Pattern

Cross Validated Bandwidth Selection for Relative Risk Estimation

Subdivide a Window or Tessellation using a Set of Lines

Convert Pixel Image to Matrix

Area of Part of Disc

Border Region of a Window

The Lennard-Jones Potential

Convert to Pixel Image

Combine Function Value Tables

Difference of Disc Areas

Test Whether An Object Is A Fitted Point Process Model

Extract the Interaction from a Fitted Point Process Model

Midpoints of Line Segment Pattern

Centroid of a window

Berman's Tests for Point Process Model

complement.owin

Take Complement of a Window

Methods for Multidimensional Space-Time Point Patterns

Classify Points in a Point Pattern

Create a Function Value Table

Convert Data To Tessellation

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Crossing Points of Two Line Segment Patterns

Ord Interaction Process Family

Intersection of Two Tessellations

Difference of Disc Areas

Convert and Compare Colours in Different Formats

Test Whether Two Pixel Images Are Compatible

Beadlet Anemones Data

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

Mark Correlation Function

Intersect Infinite Straight Lines with a Window

methods.distfun

Methods for Distance Functions

Hughes' Amacrine Cell Data

Pairwise distances between two different line segment patterns

Identify Segments in a Line Segment Pattern

Convex Hull of Points

Exponential Energy Marks

Test Whether A Point Pattern is Marked

Collapse Several Function Tables into One

Method of Minimum Contrast

Expand Window By Factor

Multi-Dimensional Box

Calculate four standard summary functions of a point pattern.

Kernel Smoothed Intensity of Point Pattern

Generic Pairwise Interaction model

Apply Function to Every Neighbourhood in a Point Pattern

Distance to Boundary of Window

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

model.frame.ppm

Extract the Environment of a Point Process Model

Colour Lookup Tables

The Soft Core Point Process Model

Hutchings' Bramble Canes data

Multitype L-function (i-to-any)

Convert Data To Class owin

Function Arrays for Spatial Patterns

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Corners of a rectangle

Basis for Harmonic Functions

crossdist.default

Pairwise distances between two different sets of points

Diggle's Heather Data

Rectangular grid of points

Print Brief Details of an Image

Longleaf Pines Point Pattern

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Simulate Baddeley-Silverman Cell Process

Convert Data to Hyperframe

Endpoints of Line Segment Pattern

Evaluate Expression Involving Functions

Create a Point Pattern

Aherne's hamster tumour data

Apply Affine Transformation To Window

Distance to Boundary of Window

Convert Line Segment Pattern to Another Unit of Length

Inhomogeneous Pair Correlation Function

Distance Map as a Function

spatstat-internal

Internal spatstat functions

Distance for a Point Pattern Matching

Make Periodic Copies of a Spatial Pattern

Pairwise distances between two different point patterns

Distance Map of Point Pattern

Convert Window to Pixel Image

Kaplan-Meier and Reduced Sample Estimator using Histograms

Extract Original Data from a Fitted Point Process Model

Perspective Plot of Pixel Image

Determine Whether One Window is Contained In Another

Circular Window

Marks of a Point Pattern

Harkness-Isham ants' nests data

Level Set of a Pixel Image

Intersection, Union or Set Subtraction of Two Windows

Interactively Define a Polygon

Apply a Function to a Point Pattern Broken Down by Factor

The Multitype Strauss Point Process Model

Window in Shape of Letter R

spatstat-deprecated

Deprecated spatstat functions

Geometrical Calculations for Multi-Dimensional Box

Fitted Conditional Intensity for Point Process Model

Test Whether Two Function Objects Are Compatible

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Diameter of a Window

Test Whether A Point Process Model is Marked

Print Brief Details of a Spatial Window

nearest.raster.point

Find Pixel Nearest to a Given Point

Compute Quadrature Weights Based on Grid Counts

Convert Pixel Image from Numeric to Factor

plot a Spatial Quadrature Scheme

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Dirichlet Tessellation of Point Pattern

Weighted Empirical Cumulative Distribution Function

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Morphological Erosion

Kolmogorov-Smirnov Test for Point Process Model

Area of a Window

Distance Between Two Point Patterns

Test Whether Marks Are Present

Class of Images

Local pair correlation function

Berman-Huntington points and lines data

Test Whether An Object Is A Point Pattern

Delaunay Triangulation of Point Pattern

Clark and Evans Aggregation Index

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

Quadrature Scheme Based on Pixel Grid

Class of Line Segment Patterns

Simulate Gauss-Poisson Process

Inhomogeneous Cross Type L Function

Test Whether a Window is Convex

Coefficients of Fitted Spatial Logistic Regression Model

Diagnostic Plots for Fitted Point Process Model

Geometrical Calculations for Three-Dimensional Box

California Redwoods Point Pattern (Entire Dataset)

Test Whether Points Are Inside A Window

Divide Point Pattern into Sub-patterns

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Murchison gold deposits

Distance Map of Window

Histogram of Pixel Values in an Image

Three Dimensional Point Pattern

Nearest Neighbour Distances in Any Dimensions

inforder.family

Infinite Order Interaction Family

Multitype L-function (cross-type)

Interaction Distance of a Point Process

New Zealand Trees Point Pattern

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Nearest neighbours in three dimensions

plot a Spatial Point Pattern

Ord's Interaction model

Nearest Neighbour Clutter Removal

Tropical rain forest trees

Japanese Pines Point Pattern

Convert Window to Another Unit of Length

The Strauss / Hard Core Point Process Model

Determine Duplicated Points in a Spatial Point Pattern

Identify Points in a Point Pattern

Plot a Simulation Envelope

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Safely Convert Point Pattern Window to Binary Mask

Convert Line Segment Pattern to Pixel Image

Methods for Three-Dimensional Box

Extract Dummy Points Used to Fit a Point Process Model

Nearest neighbour distances between line segments

Methods for three-dimensional point patterns

Pairwise distances

Plot a Spatial Window

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Reset Values in Subset of Image

model.matrix.ppm

Extract Design Matrix from Point Process Model

Summary of a List of Things

Convert Point Pattern to Pixel Image

Interpolate a Pixel Image

Plot a List of Point Patterns

California Redwoods Point Pattern (Ripley's Subset)

rescue.rectangle

Convert Window Back To Rectangle

Print Brief Details of a Point Pattern Dataset

Generate grid of parallel lines with random displacement

Apply Affine Transformation To Point Pattern

Areas of Morphological Dilations

Orientation Angles of Line Segments

Evaluate Expression Involving Function Arrays

Distance Map of Line Segment Pattern

Profile Maximum Pseudolikelihood

Predicted or Fitted Values from Spatial Logistic Regression

Vertices of a Window

matclust.estpcf

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

Pairwise distances between two different three-dimensional point patterns

Pair Correlation Function

Simulate point patterns using the Metropolis-Hastings algorithm.

Lurking variable plot

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Simulated Point Pattern

Kaplan-Meier Estimator using Histogram Data

plot a Spatial Line Segment Pattern

Pairwise distances in Three Dimensions

Summary of a Spatial Window

Lansing Woods Point Pattern

Print News About Latest Version of Package

spatstat.options

Internal Options in Spatstat Package

Randomly Shift a Point Pattern

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

Name for Unit of Length

Morishita Index Plot

Point and Click Interface for Exploratory Analysis of Point Pattern

Print Progress Reports

Beta Ganglion Cells in Cat Retina, Old Version

Estimate window from points alone

Evaluate Expression Involving Pixel Images

Convert Spatial Object to Pixel Image

Plot Function Values

Plot a Colour Map

Swedish Pines Point Pattern

Data and Code From JRSS Discussion Paper on Residuals

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Simulation Envelopes of Summary Function for 3D Point Pattern

Nearest Neighbours in Any Dimensions

Print a Quadrature Scheme

Nearest Neighbours Between Two Patterns

Generate a Quadrature Scheme from a Point Pattern

Kernel Smoothing of Line Segment Pattern

Convert a Window to a Polygonal Window

Pairwise distances between line segments

Generic Ord Interaction model

Class of Fitted Point Process Models

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Plot a Fitted Spatial Logistic Regression

Test Whether An Object Is Empty

Data Frames of Function Values

Plot a Function Array

Nearest neighbour distances

Pair Correlation Function obtained from K Function

Test Whether An Object Is A Window

Summarizing a Quadrature Scheme

Infinite Straight Lines

Spruces Point Pattern

Simulate Matern Model II

Test Whether An Object Is A Pixel Image

Analysis of Deviance for Spatial Logistic Regression Models

Humberside Data on Childhood Leukaemia and Lymphoma

Convert Data To Class psp

Convert dataset to another unit of length

Scatterplot Matrix for Pixel Images

Concatenate x,y Coordinate Vectors

Divide Image Into Sub-images

Simulate a Fitted Gibbs Point Process Model

Divide Region into Quadrats

Fit the Thomas Point Process by Minimum Contrast

Theoretical Distribution of Nearest Neighbour Distance

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Biological Cells Point Pattern

Simulation Envelopes of Summary Function

Point Patterns of New Brunswick Forest Fires

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Print Brief Details of a Line Segment Pattern Dataset

Q-Q Plot of Residuals from Fitted Point Process Model

Simulate Simple Sequential Inhibition

Reduced Sample Estimator using Histogram Data

pppmatching.object

Class of Point Matchings

Urkiola Woods Point Pattern

spatstat-package

The Spatstat Package

Cut margins from rectangle

Compute Expansion Window for Simulation

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Find Line Segment Nearest to Each Point

Pair Correlation Function obtained from array of K functions

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Bronze gradient filter data

Loglikelihood of Spatial Logistic Regression

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Saturated Pairwise Interaction Point Process Family

Read Point Pattern From Data File

Spokes pattern of dummy points

Sufficient Statistic of Point Process Model

Convert Data To Class ppp

Apply Vector Translation To Line Segment Pattern

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Create a Point Matching

Create a Window

Mark Connection Function

Superimpose Several Line Segment Patterns

Extract Quadrature Scheme Used to Fit a Point Process Model

Generate Poisson Point Pattern on Line Segments

Data Sharpening of Point Pattern

Compute Images of Constructed Covariates

Lengths of Line Segments

Plot a tessellation

Three-Dimensional Box

Pairwise distances

Plot a three-dimensional point pattern

Poisson Line Tessellation

Generate N Uniform Random Points in Any Dimensions

Beta Ganglion Cells in Cat Retina

Plot a List of Things

quadratresample

Resample a Point Pattern by Resampling Quadrats

Fit the Thomas Point Process by Minimum Contrast

Galaxies in the Shapley Supercluster

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Prediction from a Fitted Point Process Model

Nearest neighbour

Rotate a Point Pattern

Neighbourhood density function

multiplicity.ppp

Count Multiplicity of Duplicate Points

Generate N Random Points

The Strauss Point Process Model

pairwise.family

Pairwise Interaction Process Family

Ponderosa Pine Tree Point Pattern

Convert Point Pattern to Another Unit of Length

Simulate from a Fitted Point Process Model

Create a Pixel Image Object

Pair Correlation Function of a Three-Dimensional Point Pattern

Plot a plotppm Object Created by plot.ppm

Apply Vector Translation To Point Pattern

Print a Fitted Point Process Model

Fitted Probabilities for Spatial Logistic Regression

Point and Click Interface for Displaying a Point Pattern

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Methods for Multi-Dimensional Box

plot.bermantest

Plot Result of Berman Test

Generate Multitype Poisson Point Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

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

Apply Affine Transformation

Place Points Evenly Along Specified Lines

Diameter of an Object

Apply Vector Translation To Pixel Image

Rotate a Window

Cartesian Coordinates for a Pixel Raster

Summary of a Point Pattern Dataset

Simulate systematic random point pattern

Summary of a Line Segment Pattern Dataset

Define Point Process Model for Metropolis-Hastings Simulation.

Generate Poisson Point Pattern in Any Dimensions

Convert Line Segment Pattern to Binary Pixel Mask

Sample Quantiles of Pixel Image

Summarizing a Pixel Image

Prediction from a Fitted Cluster Point Process Model

Class of Point Patterns

Generate Poisson Point Pattern

Pairwise Distances in Any Dimensions

Interpret Fitted Model for Metropolis-Hastings Simulation.

Apply Vector Translation

rshift.splitppp

Randomly Shift a List of Point Patterns

Apply Affine Transformation To Line Segment Pattern

Simulate a Fitted Cluster Point Process Model

Simulate Matern Model I

Superimpose Several Point Patterns

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

project2segment

Move Point To Nearest Line

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Rotate a Line Segment Pattern

Chorley-Ribble Cancer Data

Interactively Add Points

Bounding Box of a Window or Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Generate N Uniform Random Points

Update a Fitted Point Process Model

Convert Polygonal Region into Different Format

Simulate Thomas Process

Generate a Default Pattern of Dummy Points

Find Largest Circle Inside Window

Connected components of an image or window

Convert Pixel Image to Another Unit of Length

Pairwise distances

Random Thinning

Simulate Matern Cluster Process

Summarise Marks in Every Neighbourhood in a Point Pattern

Convert Data to Three-Dimensional Box

Spatial Logistic Regression

Plot a fitted cluster point process

Summarizing a Fitted Point Process Model

Generate N Random Multitype Points

Spatial smoothing of observations at irregular points

Test whether Object is Multitype

Generate Poisson Point Pattern in Three Dimensions

Mosaic Random Set

Artificial Data Point Pattern

Set Control Parameters for Metropolis-Hastings Algorithm.

Weighted Histogram

Create a Tessellation

Simulate Neyman-Scott Process

Class of Quadrature Schemes

Random Perturbation of a Point Pattern

Set Covariance of a Window

pairdist.default

Pairwise distances

Perfect Simulation of the Strauss Process

Extract Unique Points from a Spatial Point Pattern

Pine saplings in Finland.

Apply Vector Translation To Window

Fit cluster point process model

Nearest neighbour distances in three dimensions

Multitype pair correlation function (cross-type)

Nonparametric Estimate of Spatially-Varying Relative Risk

Update a Fitted Cluster Point Process Model

Plot a Spatial Kolmogorov-Smirnov Test

Simulate Stratified Random Point Pattern

Perimeter Length of Window

Morphological Dilation

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Morphological Closing

Evaluate an Expression in a Function Table

Plot a Pixel Image

Randomly Shift a Line Segment Pattern

Create a Line Segment Pattern

plot a Fitted Point Process Model

Pair Correlation Function of Point Pattern

Number of Points in a Point Pattern

Estimate the J-function

Morphological Opening

Fit Point Process Model to Data

Fit the Matern Cluster Point Process by Minimum Contrast

Residuals for Fitted Point Process Model

Combine Two Line Segment Patterns

Inhomogeneous Cross K Function

Determine Initial State for Metropolis-Hastings Simulation.

Multitype pair correlation function (i-to-any)

Generate N Uniform Random Points in a Disc

The Fiksel Interaction

Empty Space Function of a Three-Dimensional Point Pattern

Marked Nearest Neighbour Distance Function

Diggle-Gratton model

Quadrat counting for a point pattern

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Multitype J Function (i-to-j)

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

Multidimensional Space-Time Point Pattern

K-function of a Three-Dimensional Point Pattern

Multitype K Function (i-to-any)

Apply Function to Image Broken Down by Factor

Marked K-Function

The Hard Core Point Process Model

Multitype K Function (Cross-type)

Calculate Summary Statistic for All Types in a Multitype Point Pattern

plot.hyperframe

Plot Entries in a Hyperframe

Geyer's Saturation Point Process Model

K-function using FFT

Foxall's Distance Functions

Spherical Contact Distribution Function

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Mosaic Random Field

Extract.splitppp

Extract or Replace Sub-Patterns

Random Re-Labelling of Point Pattern

Approximate a Polygon by a Simpler Polygon

Marked J Function

Apply Smoothing to Function Values

Extract or Replace Subset of a List of Things

Extract Subset of Function Array

Generate Poisson Random Line Process

Estimate the I-function

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

Locally Scaled K-function

Compute Integral of Function Against Cumulative Distribution

Extract or Replace Subset of Point Pattern

Inhomogeneous Multitype K Dot Function

Mark Correlation Integral

Extract Subset of Image

Extract Subset of Line Segment Pattern

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

The Area Interaction Point Process Model

Inhomogeneous K-function

Generate N Uniform Random Points in Three Dimensions

Subset of Quadrature Scheme

Hybrid Geyer Point Process Model

summary.splitppp

Summary of a Split Point Pattern

Volume of an Object

Extract List of Tiles in a Tessellation

Reduced Second Moment Measure

Extract Subset of Function Values

Nearest Neighbour Distance Function G

Union of Data and Dummy Points

Estimate the empty space function F

Extract or Replace Subset of Tessellation

Multitype J Function (i-to-any)

Log Likelihood for Poisson Point Process Model

Diagnostics for random marking