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spatstat (version 1.17-2)

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. Contains 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. Point process models can be fitted to point pattern data. Cluster type models are fitted by the method of minimum contrast. Very general Gibbs point process models can be fitted to point pattern data using a function ppm similar to lm or glm. Models may include dependence on covariates, interpoint interaction 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

1.17-2

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

November 10th, 2009

Functions in spatstat (1.17-2)

Hybrid Geyer Point Process Model

Subdivide a Window or Tessellation using a Set of Lines

Interactively Define a Polygon

Hutchings' Bramble Canes data

Pairwise distances between two different point patterns

Dirichlet Tessellation of Point Pattern

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

Distance Map of Line Segment Pattern

Convert Data to Three-Dimensional Box

Border Region of a Window

Extract Subset of Function Values

Intersect Infinite Straight Lines with a Window

Extract Subset of Image

Multitype L-function (i-to-any)

The Multitype Strauss Point Process Model

Areas of Morphological Erosions

Evaluate Expression Involving Functions

Function Arrays for Spatial Patterns

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Weighted Empirical Cumulative Distribution Function

Pairwise distances

Reduced Second Moment Measure

Convert Pixel Image to Matrix

Extract.splitppp

Extract or Replace Sub-Patterns

Inhomogeneous Multitype L Dot Function

Marked Nearest Neighbour Distance Function

The Soft Core Point Process Model

Apply Function to Every Neighbourhood in a Point Pattern

Apply Affine Transformation To Point Pattern

The Area Interaction Point Process Model

K-function using FFT

Apply Affine Transformation To Line Segment Pattern

Test Whether Two Function Objects Are Compatible

Convert a Window to a Polygonal Window

Beta Ganglion Cells in Cat Retina

Simulation envelopes of summary function

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Apply Affine Transformation

Orientation Angles of Line Segments

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

Subset of Quadrature Scheme

Convert Polygonal Region into Different Format

Convert Data to Hyperframe

Mark Connection Function

K-function of a Three-Dimensional Point Pattern

Estimate the I-function

Area of a Window

Harkness-Isham ants' nests data

The Strauss / Hard Core Point Process Model

Test Whether Two Pixel Images Are Compatible

Methods for Multidimensional Space-Time Point Patterns

Test Whether a Window is Convex

Difference of Disc Areas

complement.owin

Take Complement of a Window

Point Patterns of New Brunswick Forest Fires

Distance to Boundary of Window

Diagnostics for random marking

Artificial Data Point Pattern

Distance to Boundary of Window

Diggle-Gratton model

Extract or Replace Subset of Point Pattern

Inhomogeneous Cross K Function

Multitype L-function (cross-type)

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Marked J Function

Extract or Replace Subset of a List of Things

Convert Data To Tessellation

Morphological Dilation

Inhomogeneous Cross Type L Function

Spherical Contact Distribution Function

Estimate the empty space function F

Reset Values in Subset of Image

Multitype J Function (i-to-j)

Pair Correlation Function

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Expand Window By Factor

plot a Spatial Point Pattern

Empty Space Function of a Three-Dimensional Point Pattern

Estimate the J-function

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Print Brief Details of an Image

Multitype K Function (i-to-any)

Beadlet Anemones Data

Convert Data To Class ppp

Convex Hull of Points

Geyer's Saturation Point Process Model

Test Whether Points Are Inside A Window

Hughes' Amacrine Cell Data

Morphological Opening

Basis for Harmonic Functions

The Strauss Point Process Model

Saturated Pairwise Interaction model

Difference of Disc Areas

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Colour Lookup Tables

Clark and Evans Aggregation Index

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

Test Whether A Point Process Model is Marked

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Convert to Pixel Image

Level Set of a Pixel Image

Morphological Erosion

Generate a Default Pattern of Dummy Points

Marked K-Function

Identify Points in a Point Pattern

The Lennard-Jones Potential

Extract Subset of Line Segment Pattern

Bronze gradient filter data

Intersection of Two Tessellations

Histogram of Pixel Values in an Image

Apply Gaussian Blur to a Pixel Image

Mark Correlation Function

Nearest Neighbour Distance Function G

Calculate Summary Statistic for All Types in a Multitype Point Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Bounding Box of a Window or Point Pattern

Poisson Point Process Model

Divide Region into Quadrats

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Test Whether An Object Is A Point Pattern

Berman-Huntington points and lines data

Contour plot of pixel image

model.matrix.ppm

Extract Design Matrix from Point Process Model

Three-Dimensional Box

Test Whether An Object Is A Fitted Point Process Model

Diameter of a Window

Fit the Matern Cluster Point Process by Minimum Contrast

Aherne's hamster tumour data

Perspective Plot of Pixel Image

Apply Vector Translation To Point Pattern

Concatenate x,y Coordinate Vectors

Chorley-Ribble Cancer Data

Inhomogeneous K-function

Multitype J Function (i-to-any)

Morishita Index Plot

Convert Line Segment Pattern to Another Unit of Length

Distance Map as a Function

Combine Two Line Segment Patterns

Evaluate Expression Involving Pixel Images

Point and Click Interface for Exploratory Analysis of Point Pattern

Plot a Pixel Image

Window in Shape of Letter R

Compute Quadrature Weights Based on Grid Counts

Hyper Data Frame

Multitype K Function (Cross-type)

plot a Spatial Line Segment Pattern

Perfect Simulation of the Strauss Process

Define Point Process Model for Metropolis-Hastings Simulation.

New Zealand Trees Point Pattern

Extract or Replace Subset of Tessellation

Endpoints of Line Segment Pattern

Evaluate Expression Involving Function Arrays

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Area of Part of Disc

Interactively Add Points

Inhomogeneous Multitype K Dot Function

California Redwoods Point Pattern (Entire Dataset)

Midpoints of Line Segment Pattern

Apply Function to Image Broken Down by Factor

Delaunay Triangulation of Point Pattern

Update a Fitted Point Process Model

Circular Window

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Crossing Points of Two Line Segment Patterns

ANOVA for Fitted Point Process Models

Multitype pair correlation function

Generic Pairwise Interaction model

Ponderosa Pine Tree Point Pattern

Morphological Closing

Convert Data To Class owin

spatstat-deprecated

Deprecated spatstat functions

crossdist.default

Pairwise distances between two different sets of points

Distance Map of Point Pattern

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Class of Point Patterns

Exponential Energy Marks

Coefficients of Fitted Point Process Model

Safely Convert Point Pattern Window to Binary Mask

Areas of Morphological Dilations

Compute Integral of Function Against Cumulative Distribution

Tropical rain forest trees

Test Whether An Object Is Empty

Pine saplings in Finland.

Test whether Object is Multitype

bounding.box.xy

Convex Hull of Points

multiplicity.ppp

Count Multiplicity of Duplicate Points

Summarizing a Pixel Image

Mark Correlation Integral

Extract Original Data from a Fitted Point Process Model

Find Largest Circle Inside Window

Extract the Interaction from a Fitted Point Process Model

Fit the Thomas Point Process by Minimum Contrast

Pairwise distances

Three Dimensional Point Pattern

Longleaf Pines Point Pattern

inforder.family

Infinite Order Interaction Family

Plot a fitted cluster point process

Plot a Spatial Window

Summarise Marks in Every Neighbourhood in a Point Pattern

Nearest Neighbours Between Two Patterns

Class of Images

Berman's Tests for Point Process Model

Saturated Pairwise Interaction Point Process Family

Interpolate a Pixel Image

Simulate systematic random point pattern

Corners of a rectangle

Rotate a Window

Classify Points in a Point Pattern

Find Line Segment Nearest to Each Point

Plot a Spatial Kolmogorov-Smirnov Test

Plot a Function Array

Spruces Point Pattern

Print a Quadrature Scheme

Plot a plotppm Object Created by plot.ppm

Generate Poisson Random Line Process

Perimeter Length of Window

Point and Click Interface for Displaying a Point Pattern

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Simulate Neyman-Scott Process

Generate a Quadrature Scheme from a Point Pattern

Apply a Function to a Point Pattern Broken Down by Factor

Distance for a Point Pattern Matching

Prediction from a Fitted Point Process Model

Create a Tessellation

Lansing Woods Point Pattern

Convert Pixel Image from Numeric to Factor

Rectangular grid of points

Create a Pixel Image Object

Data Frames of Function Values

Swedish Pines Point Pattern

Sample Quantiles of Pixel Image

Residuals for Fitted Point Process Model

Simulate Matern Model II

Kernel Smoothed Intensity of Point Pattern

Union of Data and Dummy Points

Apply Vector Translation To Pixel Image

Approximate a Polygon by a Simpler Polygon

California Redwoods Point Pattern (Ripley's Subset)

Fry Plot of Point Pattern

Test Whether Marks Are Present

Distance Map of Window

plot.bermantest

Plot Result of Berman Test

Determine Duplicated Points in a Spatial Point Pattern

Method of Minimum Contrast

Infinite Straight Lines

Summary of a List of Things

Humberside Data on Childhood Leukaemia and Lymphoma

Biological Cells Point Pattern

Neighbourhood density function

Fit cluster point process model

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

Kaplan-Meier and Reduced Sample Estimator using Histograms

Create a Window

spatstat-internal

Internal spatstat functions

Pairwise distances between line segments

Determine Whether One Window is Contained In Another

Intersection, Union or Set Subtraction of Two Windows

Japanese Pines Point Pattern

Kernel Smoothing of Line Segment Pattern

Print Progress Reports

Test Whether An Object Is A Pixel Image

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

Extract Dummy Points Used to Fit a Point Process Model

Class of Line Segment Patterns

Randomly Shift a Line Segment Pattern

Lengths of Line Segments

project2segment

Move Point To Nearest Line

Methods for Three-Dimensional Box

Class of Quadrature Schemes

Plot a List of Things

Apply Vector Translation To Window

Extract List of Tiles in a Tessellation

Plot Function Values

Spatial smoothing of observations at irregular points

Methods for three-dimensional point patterns

Print a Fitted Point Process Model

Cartesian Coordinates for a Pixel Raster

Rotate a Point Pattern

Class of Fitted Point Process Models

nearest.raster.point

Find Pixel Nearest to a Given Point

Convert Point Pattern to Another Unit of Length

Convert dataset to another unit of length

Pairwise distances

Urkiola Woods Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Quadrat counting for a point pattern

rescue.rectangle

Convert Window Back To Rectangle

plot.hyperframe

Plot Entries in a Hyperframe

Q-Q Plot of Residuals from Fitted Point Process Model

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Plot a List of Point Patterns

Fitted Conditional Intensity for Point Process Model

Beta Ganglion Cells in Cat Retina, Old Version

Simulate Gauss-Poisson Process

Generate N Random Multitype Points

Diggle's Heather Data

Generate N Random Points

Generate Multitype Poisson Point Pattern

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Kaplan-Meier Estimator using Histogram Data

Test Whether An Object Is A Window

Log Likelihood for Poisson Point Process Model

Mean, Median and Range of Pixel Values in an Image

Apply Vector Translation

Galaxies in the Shapley Supercluster

Prediction from a Fitted Cluster Point Process Model

Sufficient Statistic of Point Process Model

plot a Spatial Quadrature Scheme

Convert Point Pattern to Pixel Image

Murchison gold deposits

Extract Unique Points from a Spatial Point Pattern

Pair Correlation Function obtained from K Function

Place Points Evenly Along Specified Lines

Print Brief Details of a Line Segment Pattern Dataset

Simulate Stratified Random Point Pattern

spatstat.options

Internal Options in Spatstat Package

pairdist.default

Pairwise distances

Determine Initial State for Metropolis-Hastings Simulation.

Simulate Baddeley-Silverman Cell Process

Generate grid of parallel lines with random displacement

Nearest neighbour

Create a Point Matching

summary.splitppp

Summary of a Split Point Pattern

Summary of a Spatial Window

Profile Maximum Pseudolikelihood

Summarizing a Fitted Point Process Model

Set Covariance of a Window

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Pair Correlation Function obtained from array of K functions

Interaction Distance of a Point Process

pppmatching.object

Class of Point Matchings

Generate N Uniform Random Points in a Disc

pairwise.family

Pairwise Interaction Process Family

Simulate Matern Cluster Process

Multidimensional Space-Time Point Pattern

Generate Poisson Point Pattern

Poisson Line Tessellation

Pair Correlation Function of Point Pattern

Mosaic Random Set

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Create a Point Pattern

Superimpose Several Point Patterns

Data and Code From JRSS Discussion Paper on Residuals

Convert Spatial Object to Pixel Image

Generate Poisson Point Pattern on Line Segments

Name for Unit of Length

Simulate Simple Sequential Inhibition

Simulate from a Fitted Point Process Model

Ord's Interaction model

Ord Interaction Process Family

Create a Line Segment Pattern

Quadrature Scheme Based on Pixel Grid

Plot a Colour Map

Extract Quadrature Scheme Used to Fit a Point Process Model

plot a Fitted Point Process Model

Randomly Shift a Point Pattern

Read Point Pattern From Data File

Summary of a Line Segment Pattern Dataset

Random Perturbation of a Point Pattern

selfcrossing.psp

Crossing Points in a Line Segment Pattern

The Piecewise Constant Pairwise Interaction Point Process Model

rshift.splitppp

Randomly Shift a List of Point Patterns

Random Thinning

Simulate Thomas Process

Pixel Image Approximation of a Window

Simulate a Fitted Gibbs Point Process Model

Fit Point Process Model to Data

Convert Data To Class psp

Simulate point patterns using the Metropolis-Hastings algorithm.

spatstat-package

The Spatstat Package

Connected components of an image or window

Simulate Matern Model I

Spokes pattern of dummy points

Reduced Sample Estimator using Histogram Data

Evaluate an Expression in a Function Table

Vertices of a Window

Apply Vector Translation To Line Segment Pattern

Random Re-Labelling of Point Pattern

Update a Fitted Cluster Point Process Model

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Set Control Parameters for Metropolis-Hastings Algorithm.

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

Cut margins from rectangle

Generate Poisson Point Pattern in Three Dimensions

Pairwise distances between two different line segment patterns

Simulate a Fitted Cluster Point Process Model

Simulated Point Pattern

Divide Point Pattern into Sub-patterns

Summarizing a Quadrature Scheme

Variance-Covariance Matrix for a Fitted Point Process Model

Geometrical Calculations for Three-Dimensional Box

Generate N Uniform Random Points

Compute Images of Constructed Covariates

Superimpose Several Line Segment Patterns

Lurking variable plot

Nearest neighbour distances

Nearest neighbour distances between line segments

Plot a three-dimensional point pattern

Distance Between Two Point Patterns

Print Brief Details of a Spatial Window

quadratresample

Resample a Point Pattern by Resampling Quadrats

Convert Pixel Image to Another Unit of Length

Estimate window from points alone

Rotate a Line Segment Pattern

Extract Subset of Function Array

Generic Ord Interaction model

Generate N Uniform Random Points in Three Dimensions

Set or Reset the Marks in a Point Pattern

Calculate four standard summary functions of a point pattern.

Apply Affine Transformation To Window

Distance to Boundary of Window

Centroid of a window

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Diagnostic Plots for Fitted Point Process Model

Test Whether A Point Pattern is Marked

Kolmogorov-Smirnov Test for Point Process Model

Convert Window to Pixel Image

Plot a tessellation

Print Brief Details of a Point Pattern Dataset

Mosaic Random Field

Convert Window to Another Unit of Length

Interpret Fitted Model for Metropolis-Hastings Simulation.

Divide Image Into Sub-images

Summary of a Point Pattern Dataset