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spatstat (version 1.21-1)

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

16,590

Version

1.21-1

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

November 11th, 2010

Functions in spatstat (1.21-1)

Estimate the I-function

Diagnostics for random marking

Spherical Contact Distribution Function

Extract or Replace Subset of Point Pattern

Connected components of an image or window

The Area Interaction Point Process Model

Extract Subset of Function Values

Apply Function to Image Broken Down by Factor

Poisson Point Process Model

ANOVA for Fitted Point Process Models

Extract Subset of Function Array

Distance to Boundary of Window

Multitype J Function (i-to-j)

Inhomogeneous Cross K Function

Estimate the empty space function F

Subdivide a Window or Tessellation using a Set of Lines

K-function of a Three-Dimensional Point Pattern

Multitype J Function (i-to-any)

Distance to Boundary of Window

The Soft Core Point Process Model

Centroid of a window

Geyer's Saturation Point Process Model

Difference of Disc Areas

Pairwise distances between two different point patterns

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

bounding.box.xy

Convex Hull of Points

Saturated Pairwise Interaction model

Subset of Quadrature Scheme

The Strauss Point Process Model

Extract Subset of Line Segment Pattern

Inhomogeneous Multitype K Dot Function

Calculate four standard summary functions of a point pattern.

The Lennard-Jones Potential

Inhomogeneous Cross Type L Function

Generate a Default Pattern of Dummy Points

Diggle-Gratton model

Convert to Pixel Image

Berman-Huntington points and lines data

Convert Data To Class owin

Apply Gaussian Blur to a Pixel Image

Extract Original Data from a Fitted Point Process Model

Simulation Envelopes of Summary Function for 3D Point Pattern

Border Region of a Window

Inhomogeneous Multitype L Dot Function

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Clark and Evans Aggregation Index

Marked K-Function

Combine Two Line Segment Patterns

Multitype K Function (Cross-type)

Reset Values in Subset of Image

Marked J Function

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Concatenate x,y Coordinate Vectors

Collapse Several Function Tables into One

Beadlet Anemones Data

Coefficients of Fitted Spatial Logistic Regression Model

Convert and Compare Colours in Different Formats

K-function using FFT

Extract or Replace Subset of Tessellation

Crossing Points of Two Line Segment Patterns

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

The Piecewise Constant Pairwise Interaction Point Process Model

Generic Ord Interaction model

Hutchings' Bramble Canes data

Three-Dimensional Box

Interactively Define a Polygon

Extract or Replace Subset of a List of Things

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Function Arrays for Spatial Patterns

Dirichlet Tessellation of Point Pattern

Multitype K Function (i-to-any)

Test Whether Points Are Inside A Window

Classify Points in a Point Pattern

Convert a Window to a Polygonal Window

Convert Pixel Image from Numeric to Factor

Hughes' Amacrine Cell Data

Area of a Window

Extract Subset of Image

Extract Dummy Points Used to Fit a Point Process Model

Biological Cells Point Pattern

Analysis of Deviance for Spatial Logistic Regression Models

Exponential Energy Marks

Berman's Tests for Point Process Model

Hyper Data Frame

The Hard Core Point Process Model

Area of Part of Disc

Diameter of an Object

Bounding Box of a Window or Point Pattern

Nearest Neighbour Distance Function G

spatstat-internal

Internal spatstat functions

Areas of Morphological Dilations

Distance Map of Line Segment Pattern

Distance Map of Point Pattern

Distance Map of Window

Bronze gradient filter data

Humberside Data on Childhood Leukaemia and Lymphoma

Diameter of a Window

Interactively Add Points

Test Whether Two Function Objects Are Compatible

Hybrid Geyer Point Process Model

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Empty Space Function of a Three-Dimensional Point Pattern

Distance to Boundary of Window

complement.owin

Take Complement of a Window

Morphological Dilation

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Beta Ganglion Cells in Cat Retina, Old Version

Integral of a Pixel Image

plot a Spatial Line Segment Pattern

Pixel Image Approximation of a Window

Kernel Smoothing of Line Segment Pattern

Artificial Data Point Pattern

Apply a Function to a Point Pattern Broken Down by Factor

Create a Function Value Table

Ord's Interaction model

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Point and Click Interface for Exploratory Analysis of Point Pattern

Test Whether Two Pixel Images Are Compatible

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Pine saplings in Finland.

Kernel Smoothed Intensity of Point Pattern

Convert Data to Hyperframe

Interpolate a Pixel Image

Morphological Erosion

Convex Hull of Points

Japanese Pines Point Pattern

Distance Map as a Function

Kolmogorov-Smirnov Test for Point Process Model

Apply Affine Transformation To Line Segment Pattern

The Multitype Strauss Point Process Model

Locally Scaled K-function

Harkness-Isham ants' nests data

Foxall's Distance Functions

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Estimate the J-function

Rectangular grid of points

Evaluate Expression Involving Function Arrays

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Combine Function Value Tables

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

Test Whether A Point Process Model is Marked

Find Line Segment Nearest to Each Point

Kaplan-Meier and Reduced Sample Estimator using Histograms

Mark Correlation Integral

Plot a plotppm Object Created by plot.ppm

Fitted Conditional Intensity for Point Process Model

Inhomogeneous K-function

Convert Window to Pixel Image

Three Dimensional Point Pattern

Areas of Morphological Erosions

Identify Points in a Point Pattern

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Multitype L-function (i-to-any)

Plot a Colour Map

Summarise Marks in Every Neighbourhood in a Point Pattern

spatstat-deprecated

Deprecated spatstat functions

Create a Window

Multitype pair correlation function (cross-type)

Local pair correlation function

Geometrical Calculations for Multi-Dimensional Box

Prediction from a Fitted Cluster Point Process Model

Pairwise distances between line segments

Print News About Latest Version of Package

Plot a List of Point Patterns

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

Nearest neighbour distances in three dimensions

Convert Data To Tessellation

Cartesian Coordinates for a Pixel Raster

inforder.family

Infinite Order Interaction Family

Methods for three-dimensional point patterns

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

pairwise.family

Pairwise Interaction Process Family

Difference of Disc Areas

Test Whether An Object Is Empty

Marks of a Point Pattern

Contour plot of pixel image

Test Whether A Point Pattern is Marked

Intersect Infinite Straight Lines with a Window

Mosaic Random Set

Apply Function to Every Neighbourhood in a Point Pattern

Convert Spatial Object to Pixel Image

Mark Correlation Function

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Window in Shape of Letter R

Level Set of a Pixel Image

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Convert Line Segment Pattern to Binary Pixel Mask

Aherne's hamster tumour data

Test Whether a Window is Convex

multiplicity.ppp

Count Multiplicity of Duplicate Points

New Zealand Trees Point Pattern

Nearest Neighbours in Any Dimensions

Longleaf Pines Point Pattern

Diagnostic Plots for Fitted Point Process Model

Fit the Matern Cluster Point Process by Minimum Contrast

Generate N Uniform Random Points in Any Dimensions

Morphological Opening

Lurking variable plot

Plot a Spatial Kolmogorov-Smirnov Test

Determine Duplicated Points in a Spatial Point Pattern

Determine Whether One Window is Contained In Another

Pairwise distances between two different three-dimensional point patterns

Compute Expansion Window for Simulation

Apply Affine Transformation To Point Pattern

Methods for Three-Dimensional Box

Test Whether An Object Is A Fitted Point Process Model

Extract the Interaction from a Fitted Point Process Model

Neighbourhood density function

Pairwise Distances in Any Dimensions

Test Whether An Object Is A Window

Nearest Neighbour Clutter Removal

Create a Line Segment Pattern

Pairwise distances

Convert Point Pattern to Pixel Image

pppmatching.object

Class of Point Matchings

model.frame.ppm

Extract the Environment of a Point Process Model

Make Periodic Copies of a Spatial Pattern

Test Whether Marks Are Present

Circular Window

Simulate Matern Model I

spatstat.options

Internal Options in Spatstat Package

Pair Correlation Function obtained from K Function

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Plot a tessellation

Multitype pair correlation function (i-to-any)

Pairwise distances

Simulate Thomas Process

plot a Spatial Point Pattern

Print Brief Details of an Image

Test whether Object is Multitype

Delaunay Triangulation of Point Pattern

Generic Pairwise Interaction model

Fit the Thomas Point Process by Minimum Contrast

Test Whether An Object Is A Point Pattern

Pairwise distances in Three Dimensions

Simulate Gauss-Poisson Process

Spokes pattern of dummy points

rshift.splitppp

Randomly Shift a List of Point Patterns

Simulate systematic random point pattern

Geometrical Calculations for Three-Dimensional Box

Generate grid of parallel lines with random displacement

Evaluate an Expression in a Function Table

Generate Poisson Point Pattern on Line Segments

Plot a Pixel Image

Nearest Neighbour Distances in Any Dimensions

Intersection of Two Tessellations

Spatial smoothing of observations at irregular points

Number of Points in a Point Pattern

The Strauss / Hard Core Point Process Model

Poisson Line Tessellation

Class of Line Segment Patterns

Pair Correlation Function obtained from array of K functions

Methods for Multidimensional Space-Time Point Patterns

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Simulate point patterns using the Metropolis-Hastings algorithm.

Class of Fitted Point Process Models

summary.splitppp

Summary of a Split Point Pattern

Fit cluster point process model

Convert Line Segment Pattern to Another Unit of Length

Stoyan's Rule of Thumb for Bandwidth Selection

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

spatstat-package

The Spatstat Package

Lansing Woods Point Pattern

Print a Fitted Point Process Model

Q-Q Plot of Residuals from Fitted Point Process Model

Nearest neighbours in three dimensions

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Convert Line Segment Pattern to Pixel Image

Class of Point Patterns

Galaxies in the Shapley Supercluster

Print Brief Details of a Line Segment Pattern Dataset

Pairwise distances

pairdist.default

Pairwise distances

Mark Connection Function

quadratresample

Resample a Point Pattern by Resampling Quadrats

Point and Click Interface for Displaying a Point Pattern

Summarizing a Quadrature Scheme

Plot a fitted cluster point process

Distance for a Point Pattern Matching

Extract Quadrature Scheme Used to Fit a Point Process Model

Theoretical Distribution of Nearest Neighbour Distance

Compute Integral of Function Against Cumulative Distribution

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

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

Data Frames of Function Values

Simulate Baddeley-Silverman Cell Process

Find Largest Circle Inside Window

Create a Tessellation

Union of Data and Dummy Points

crossdist.default

Pairwise distances between two different sets of points

project2segment

Move Point To Nearest Line

Apply Affine Transformation To Window

Random Perturbation of a Point Pattern

Convert Data To Class psp

Read Point Pattern From Data File

California Redwoods Point Pattern (Entire Dataset)

nearest.raster.point

Find Pixel Nearest to a Given Point

Extract List of Tiles in a Tessellation

Nearest neighbour distances

Divide Image Into Sub-images

Sufficient Statistic of Point Process Model

Midpoints of Line Segment Pattern

plot a Fitted Point Process Model

Chorley-Ribble Cancer Data

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

Rotate a Line Segment Pattern

Convert Window to Another Unit of Length

Randomly Shift a Point Pattern

Generate N Uniform Random Points

Murchison gold deposits

Convert Polygonal Region into Different Format

Prediction from a Fitted Point Process Model

Generate Poisson Point Pattern in Any Dimensions

Perfect Simulation of the Strauss Process

Perspective Plot of Pixel Image

Variance-Covariance Matrix for a Fitted Point Process Model

Nonparametric Estimate of Spatially-Varying Relative Risk

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Pairwise distances between two different line segment patterns

Update a Fitted Cluster Point Process Model

Create a Pixel Image Object

Plot a List of Things

Convert Pixel Image to Matrix or Array

Pair Correlation Function of Point Pattern

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Name for Unit of Length

plot.bermantest

Plot Result of Berman Test

Interaction Distance of a Point Process

Plot Function Values

Colour Lookup Tables

Nearest neighbour distances between line segments

Kaplan-Meier Estimator using Histogram Data

Randomly Shift a Line Segment Pattern

Apply Vector Translation

Nearest neighbour

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

The Fiksel Interaction

Apply Smoothing to Function Values

Fit Point Process Model to Data

Set Control Parameters for Metropolis-Hastings Algorithm.

Print a Quadrature Scheme

Histogram of Pixel Values in an Image

Summary of a Point Pattern Dataset

Simulate Neyman-Scott Process

Distance Between Two Point Patterns

Generate Multitype Poisson Point Pattern

Identify Pixelwise Maximum of Several Pixel Images

Predicted or Fitted Values from Spatial Logistic Regression

Generate Poisson Point Pattern

Plot a three-dimensional point pattern

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Fitted Probabilities for Spatial Logistic Regression

Class of Images

Convert Data To Class ppp

Sample Quantiles of Pixel Image

Spatial Logistic Regression

Multitype L-function (cross-type)

Residuals for Fitted Point Process Model

Ord Interaction Process Family

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Convert dataset to another unit of length

runifpointOnLines

Generate N Uniform Random Points On Line Segments

methods.distfun

Methods for Distance Functions

Apply Vector Translation To Line Segment Pattern

Corners of a rectangle

Ponderosa Pine Tree Point Pattern

Rotate a Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Plot a Function Array

Coefficients of Fitted Point Process Model

Random Thinning

Superimpose Several Line Segment Patterns

Summary of a Line Segment Pattern Dataset

Point Patterns of New Brunswick Forest Fires

Summarizing a Fitted Point Process Model

Print Brief Details of a Spatial Window

Test Whether An Object Is A Pixel Image

Update a Fitted Point Process Model

Generate a Quadrature Scheme from a Point Pattern

Summarizing a Pixel Image

Simulated Point Pattern

Interpret Fitted Model for Metropolis-Hastings Simulation.

Marked Nearest Neighbour Distance Function

Volume of an Object

Extract.splitppp

Extract or Replace Sub-Patterns

Generate N Uniform Random Points in a Disc

Plot a Simulation Envelope

Pair Correlation Function of a Three-Dimensional Point Pattern

Plot a Spatial Window

Simulate Matern Cluster Process

Simulate Simple Sequential Inhibition

Morishita Index Plot

Determine Initial State for Metropolis-Hastings Simulation.

Extract Unique Points from a Spatial Point Pattern

Random Re-Labelling of Point Pattern

Fit the Thomas Point Process by Minimum Contrast

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

Inhomogeneous Pair Correlation Function

Print Brief Details of a Point Pattern Dataset

Infinite Straight Lines

Evaluate Expression Involving Pixel Images

Spruces Point Pattern

Apply Vector Translation To Pixel Image

Beta Ganglion Cells in Cat Retina

Apply Affine Transformation

Data and Code From JRSS Discussion Paper on Residuals

plot.hyperframe

Plot Entries in a Hyperframe

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Urkiola Woods Point Pattern

Reduced Sample Estimator using Histogram Data

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Multi-Dimensional Box

Simulate from a Fitted Point Process Model

Lengths of Line Segments

Perimeter Length of Window

Loglikelihood of Spatial Logistic Regression

Print Progress Reports

Pair Correlation Function

matclust.estpcf

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

Quadrature Scheme Based on Pixel Grid

Mosaic Random Field

Data Sharpening of Point Pattern

model.matrix.ppm

Extract Design Matrix from Point Process Model

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Generate N Random Multitype Points

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Vertices of a Window

Estimate Variance of Summary Statistic by Subdivision

Create a Point Pattern

Methods for Multi-Dimensional Box

Create a Point Matching

Expand Window By Factor

Profile Maximum Pseudolikelihood

Tropical rain forest trees

Summary of a Spatial Window

Diggle's Heather Data

Apply Vector Translation To Window

Place Points Evenly Along Specified Lines

Summary of a List of Things

Fry Plot of Point Pattern

Divide Point Pattern into Sub-patterns

Estimate window from points alone

Orientation Angles of Line Segments

Divide Region into Quadrats

Convert Data to Three-Dimensional Box

Intersection, Union or Set Subtraction of Two Windows

Generate N Uniform Random Points in Three Dimensions

Swedish Pines Point Pattern

Simulate Stratified Random Point Pattern

Endpoints of Line Segment Pattern

Weighted Empirical Cumulative Distribution Function

Simulate a Fitted Cluster Point Process Model

Morphological Closing

Apply Vector Translation To Point Pattern

Approximate a Polygon by a Simpler Polygon

Generate Poisson Point Pattern in Three Dimensions

as.data.frame.im

Convert Pixel Image to Data Frame

Identify Segments in a Line Segment Pattern

Cross Validated Bandwidth Selection for Relative Risk Estimation

Evaluate Expression Involving Functions

Simulate a Fitted Gibbs Point Process Model

Saturated Pairwise Interaction Point Process Family

Weighted Histogram

Generate N Random Points

Rotate a Window

Convert Pixel Image to Another Unit of Length

Simulate Matern Model II

Generate Poisson Random Line Process

Nearest Neighbours Between Two Patterns

Multidimensional Space-Time Point Pattern

Class of Quadrature Schemes

Convert Point Pattern to Another Unit of Length

Quadrat counting for a point pattern

Plot a Fitted Spatial Logistic Regression

Cut margins from rectangle

Method of Minimum Contrast

Superimpose Several Point Patterns

rescue.rectangle

Convert Window Back To Rectangle

California Redwoods Point Pattern (Ripley's Subset)

Safely Convert Point Pattern Window to Binary Mask

Compute Quadrature Weights Based on Grid Counts

Compute Images of Constructed Covariates

Scatterplot Matrix for Pixel Images

plot a Spatial Quadrature Scheme

Set Covariance of a Window

Reduced Second Moment Measure

Basis for Harmonic Functions

Simulation Envelopes of Summary Function

Define Point Process Model for Metropolis-Hastings Simulation.

Log Likelihood for Poisson Point Process Model