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spatstat (version 1.17-5)

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

17,668

Version

1.17-5

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

January 6th, 2010

Functions in spatstat (1.17-5)

The Strauss Point Process Model

Biological Cells Point Pattern

Difference of Disc Areas

Extract or Replace Subset of a List of Things

Diggle-Gratton model

Generic Ord Interaction model

K-function of a Three-Dimensional Point Pattern

Diagnostics for random marking

Distance Map of Line Segment Pattern

Distance to Boundary of Window

Combine Two Line Segment Patterns

Fry Plot of Point Pattern

Diameter of a Window

Marked J Function

Distance Map of Window

Apply Function to Every Neighbourhood in a Point Pattern

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Delaunay Triangulation of Point Pattern

Convert to Pixel Image

Apply Affine Transformation To Point Pattern

K-function using FFT

Test Whether An Object Is A Point Pattern

ANOVA for Fitted Point Process Models

Estimate the empty space function F

Pixel Image Approximation of a Window

Test Whether Marks Are Present

Saturated Pairwise Interaction model

Marked Nearest Neighbour Distance Function

Subset of Quadrature Scheme

Inhomogeneous Cross Type L Function

Extract Original Data from a Fitted Point Process Model

Geyer's Saturation Point Process Model

Aherne's hamster tumour data

The Piecewise Constant Pairwise Interaction Point Process Model

Apply Affine Transformation To Line Segment Pattern

Generic Pairwise Interaction model

Extract Subset of Image

Interactively Define a Polygon

Inhomogeneous Multitype K Dot Function

Convert Pixel Image to Matrix

Multitype pair correlation function (cross-type)

Convert Data to Three-Dimensional Box

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

Calculate four standard summary functions of a point pattern.

Poisson Point Process Model

Multitype K Function (Cross-type)

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Circular Window

Interpolate a Pixel Image

Interactively Add Points

Apply Function to Image Broken Down by Factor

Inhomogeneous Multitype L Dot Function

Morphological Dilation

The Multitype Strauss Point Process Model

Pairwise distances

Lurking variable plot

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

Convert Data to Hyperframe

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

Extract Subset of Function Array

Plot a tessellation

Safely Convert Point Pattern Window to Binary Mask

Extract or Replace Subset of Tessellation

Convert a Window to a Polygonal Window

Apply a Function to a Point Pattern Broken Down by Factor

Areas of Morphological Erosions

Hughes' Amacrine Cell Data

Convert Data To Class psp

Empty Space Function of a Three-Dimensional Point Pattern

Convert Pixel Image from Numeric to Factor

Concatenate x,y Coordinate Vectors

Artificial Data Point Pattern

Multitype J Function (i-to-j)

Test Whether An Object Is Empty

Fit the Matern Cluster Point Process by Minimum Contrast

Area of a Window

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Extract Dummy Points Used to Fit a Point Process Model

Convert Data To Tessellation

Test Whether a Window is Convex

Orientation Angles of Line Segments

Harkness-Isham ants' nests data

Apply Affine Transformation To Window

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Test Whether Two Pixel Images Are Compatible

Midpoints of Line Segment Pattern

Hybrid Geyer Point Process Model

Connected components of an image or window

Reset Values in Subset of Image

Evaluate Expression Involving Pixel Images

Beta Ganglion Cells in Cat Retina, Old Version

Estimate the I-function

Berman's Tests for Point Process Model

Methods for Three-Dimensional Box

Coefficients of Fitted Point Process Model

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Fitted Conditional Intensity for Point Process Model

Fit Point Process Model to Data

Area of Part of Disc

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

Level Set of a Pixel Image

Ord's Interaction model

Bounding Box of a Window or Point Pattern

Colour Lookup Tables

Marked K-Function

Generate a Default Pattern of Dummy Points

Convert Data To Class owin

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Extract Subset of Function Values

Create a Pixel Image Object

Pairwise distances between two different three-dimensional point patterns

The Area Interaction Point Process Model

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Distance to Boundary of Window

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Reduced Second Moment Measure

Pairwise distances between two different point patterns

Estimate the J-function

Diagnostic Plots for Fitted Point Process Model

Simulation envelopes of summary function

Endpoints of Line Segment Pattern

Nearest neighbour distances

Crossing Points of Two Line Segment Patterns

Kaplan-Meier and Reduced Sample Estimator using Histograms

Nearest Neighbour Distance Function G

Pairwise distances

Pair Correlation Function of Point Pattern

Difference of Disc Areas

Rectangular grid of points

Exponential Energy Marks

plot a Spatial Point Pattern

Multitype K Function (i-to-any)

Intersect Infinite Straight Lines with a Window

Multitype L-function (cross-type)

Kernel Smoothing of Line Segment Pattern

Kernel Smoothed Intensity of Point Pattern

Subdivide a Window or Tessellation using a Set of Lines

Bronze gradient filter data

Test whether Object is Multitype

Multitype J Function (i-to-any)

Simulate Gauss-Poisson Process

Test Whether A Point Process Model is Marked

Compute Quadrature Weights Based on Grid Counts

Distance Map as a Function

spatstat-deprecated

Deprecated spatstat functions

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Mosaic Random Set

Window in Shape of Letter R

Define Point Process Model for Metropolis-Hastings Simulation.

Method of Minimum Contrast

Convert Data To Class ppp

Test Whether An Object Is A Pixel Image

nearest.raster.point

Find Pixel Nearest to a Given Point

Neighbourhood density function

Intersection of Two Tessellations

Point and Click Interface for Exploratory Analysis of Point Pattern

Fit cluster point process model

Test Whether An Object Is A Window

Data Frames of Function Values

Hyper Data Frame

Create a Point Matching

Generate grid of parallel lines with random displacement

The Lennard-Jones Potential

Lengths of Line Segments

Multitype L-function (i-to-any)

Pair Correlation Function obtained from K Function

Find Line Segment Nearest to Each Point

Three-Dimensional Box

plot.hyperframe

Plot Entries in a Hyperframe

Kolmogorov-Smirnov Test for Point Process Model

Summarise Marks in Every Neighbourhood in a Point Pattern

Longleaf Pines Point Pattern

Plot a Spatial Kolmogorov-Smirnov Test

Inhomogeneous Cross K Function

Apply Gaussian Blur to a Pixel Image

Mark Connection Function

Centroid of a window

Expand Window By Factor

Convert Polygonal Region into Different Format

Test Whether Two Function Objects Are Compatible

Distance to Boundary of Window

Extract.splitppp

Extract or Replace Sub-Patterns

Inhomogeneous K-function

Extract Subset of Line Segment Pattern

Beta Ganglion Cells in Cat Retina

Test Whether Points Are Inside A Window

crossdist.default

Pairwise distances between two different sets of points

Nearest neighbour distances in three dimensions

Theoretical Distribution of Nearest Neighbour Distance

Test Whether An Object Is A Fitted Point Process Model

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

project2segment

Move Point To Nearest Line

Determine Whether One Window is Contained In Another

Morphological Closing

Corners of a rectangle

complement.owin

Take Complement of a Window

Prediction from a Fitted Cluster Point Process Model

Integral of a Pixel Image

Extract Quadrature Scheme Used to Fit a Point Process Model

Morphological Opening

Convert Spatial Object to Pixel Image

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Weighted Empirical Cumulative Distribution Function

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Log Likelihood for Poisson Point Process Model

Pairwise distances between two different line segment patterns

Evaluate Expression Involving Functions

Sample Quantiles of Pixel Image

The Strauss / Hard Core Point Process Model

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Cartesian Coordinates for a Pixel Raster

Contour plot of pixel image

bounding.box.xy

Convex Hull of Points

Evaluate Expression Involving Function Arrays

Convert Window to Pixel Image

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Extract the Interaction from a Fitted Point Process Model

Perfect Simulation of the Strauss Process

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Spherical Contact Distribution Function

Nearest Neighbours Between Two Patterns

Three Dimensional Point Pattern

Class of Images

Nearest neighbours in three dimensions

Geometrical Calculations for Three-Dimensional Box

inforder.family

Infinite Order Interaction Family

Perimeter Length of Window

Morishita Index Plot

Inhomogeneous Pair Correlation Function

Plot a Function Array

The Soft Core Point Process Model

Mark Correlation Function

Apply Affine Transformation

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Nearest neighbour

Print Brief Details of a Line Segment Pattern Dataset

Pine saplings in Finland.

Pair Correlation Function obtained from array of K functions

Plot Function Values

Chorley-Ribble Cancer Data

Distance for a Point Pattern Matching

Compute Images of Constructed Covariates

Plot a Colour Map

California Redwoods Point Pattern (Ripley's Subset)

Function Arrays for Spatial Patterns

Print Brief Details of an Image

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

Ponderosa Pine Tree Point Pattern

Basis for Harmonic Functions

Multidimensional Space-Time Point Pattern

Hutchings' Bramble Canes data

Convert Line Segment Pattern to Another Unit of Length

Class of Fitted Point Process Models

Kaplan-Meier Estimator using Histogram Data

Plot a Spatial Window

Areas of Morphological Dilations

Superimpose Several Point Patterns

plot a Fitted Point Process Model

Print a Quadrature Scheme

Point and Click Interface for Displaying a Point Pattern

Morphological Erosion

rescue.rectangle

Convert Window Back To Rectangle

Murchison gold deposits

Generate a Quadrature Scheme from a Point Pattern

Plot a fitted cluster point process

Japanese Pines Point Pattern

Simulate Matern Model I

Set or Reset the Marks in a Point Pattern

Infinite Straight Lines

Tropical rain forest trees

Generate Poisson Point Pattern in Three Dimensions

Humberside Data on Childhood Leukaemia and Lymphoma

spatstat-internal

Internal spatstat functions

Beadlet Anemones Data

Dirichlet Tessellation of Point Pattern

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Diggle's Heather Data

Mean, Median and Range of Pixel Values in an Image

Histogram of Pixel Values in an Image

Convert Window to Another Unit of Length

Distance Map of Point Pattern

Simulate Matern Model II

Simulate Simple Sequential Inhibition

Create a Point Pattern

pairwise.family

Pairwise Interaction Process Family

Plot a List of Things

Spruces Point Pattern

Saturated Pairwise Interaction Point Process Family

Set Covariance of a Window

Multitype pair correlation function (i-to-any)

Generate Multitype Poisson Point Pattern

Convex Hull of Points

Methods for three-dimensional point patterns

Randomly Shift a Point Pattern

Estimate window from points alone

Poisson Line Tessellation

Class of Point Patterns

Apply Vector Translation

Print Brief Details of a Point Pattern Dataset

pppmatching.object

Class of Point Matchings

Make Periodic Copies of a Spatial Pattern

Distance Between Two Point Patterns

Quadrature Scheme Based on Pixel Grid

Classify Points in a Point Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Quadrat counting for a point pattern

multiplicity.ppp

Count Multiplicity of Duplicate Points

Ord Interaction Process Family

Q-Q Plot of Residuals from Fitted Point Process Model

Plot a three-dimensional point pattern

Pairwise distances in Three Dimensions

Berman-Huntington points and lines data

Place Points Evenly Along Specified Lines

Simulate Neyman-Scott Process

Reduced Sample Estimator using Histogram Data

Intersection, Union or Set Subtraction of Two Windows

Simulate Baddeley-Silverman Cell Process

Class of Quadrature Schemes

Data and Code From JRSS Discussion Paper on Residuals

Divide Region into Quadrats

Profile Maximum Pseudolikelihood

Methods for Multidimensional Space-Time Point Patterns

California Redwoods Point Pattern (Entire Dataset)

Pairwise distances

Divide Point Pattern into Sub-patterns

Create a Window

Convert Point Pattern to Another Unit of Length

Simulate Matern Cluster Process

Plot a List of Point Patterns

Generate Poisson Point Pattern

pairdist.default

Pairwise distances

plot a Spatial Line Segment Pattern

Convert Point Pattern to Pixel Image

Plot a Pixel Image

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Simulate Thomas Process

Test Whether A Point Pattern is Marked

quadratresample

Resample a Point Pattern by Resampling Quadrats

Swedish Pines Point Pattern

Extract or Replace Subset of Point Pattern

Mosaic Random Field

Pairwise distances between line segments

Rotate a Window

Summary of a List of Things

Superimpose Several Line Segment Patterns

Nearest neighbour distances between line segments

Determine Duplicated Points in a Spatial Point Pattern

Identify Points in a Point Pattern

Residuals for Fitted Point Process Model

Interaction Distance of a Point Process

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

Simulate from a Fitted Point Process Model

Interpret Fitted Model for Metropolis-Hastings Simulation.

Galaxies in the Shapley Supercluster

Find Largest Circle Inside Window

Spatial smoothing of observations at irregular points

Point Patterns of New Brunswick Forest Fires

Class of Line Segment Patterns

Perspective Plot of Pixel Image

Prediction from a Fitted Point Process Model

model.matrix.ppm

Extract Design Matrix from Point Process Model

New Zealand Trees Point Pattern

Extract List of Tiles in a Tessellation

Set Control Parameters for Metropolis-Hastings Algorithm.

Clark and Evans Aggregation Index

Convert Pixel Image to Another Unit of Length

Rotate a Line Segment Pattern

Random Thinning

Generate Poisson Point Pattern on Line Segments

Generate N Uniform Random Points

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

Summary of a Point Pattern Dataset

Plot a plotppm Object Created by plot.ppm

Random Perturbation of a Point Pattern

Fit the Thomas Point Process by Minimum Contrast

Name for Unit of Length

Print Brief Details of a Spatial Window

plot.bermantest

Plot Result of Berman Test

Simulate systematic random point pattern

Weighted Histogram

plot a Spatial Quadrature Scheme

Border Region of a Window

Approximate a Polygon by a Simpler Polygon

Simulate a Fitted Gibbs Point Process Model

spatstat-package

The Spatstat Package

Generate N Uniform Random Points in a Disc

Print Progress Reports

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Generate N Random Points

Simulated Point Pattern

Read Point Pattern From Data File

Evaluate an Expression in a Function Table

Convert dataset to another unit of length

Generate N Random Multitype Points

Extract Unique Points from a Spatial Point Pattern

Summarizing a Fitted Point Process Model

Create a Tessellation

Mark Correlation Integral

Simulate point patterns using the Metropolis-Hastings algorithm.

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Compute Integral of Function Against Cumulative Distribution

Update a Fitted Cluster Point Process Model

Summarizing a Pixel Image

Apply Vector Translation To Window

Apply Vector Translation To Line Segment Pattern

Apply Vector Translation To Pixel Image

Union of Data and Dummy Points

Apply Vector Translation To Point Pattern

Create a Line Segment Pattern

Urkiola Woods Point Pattern

Summary of a Spatial Window

Divide Image Into Sub-images

Update a Fitted Point Process Model

rshift.splitppp

Randomly Shift a List of Point Patterns

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

Summarizing a Quadrature Scheme

Print a Fitted Point Process Model

Simulate a Fitted Cluster Point Process Model

Summary of a Line Segment Pattern Dataset

Rotate a Point Pattern

Vertices of a Window

spatstat.options

Internal Options in Spatstat Package

Simulate Stratified Random Point Pattern

Randomly Shift a Line Segment Pattern

Pair Correlation Function

Random Re-Labelling of Point Pattern

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Generate N Uniform Random Points in Three Dimensions

Generate Poisson Random Line Process

Sufficient Statistic of Point Process Model

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Define Point Process Model for Metropolis-Hastings Simulation.

Spokes pattern of dummy points

Cut margins from rectangle

summary.splitppp

Summary of a Split Point Pattern

Lansing Woods Point Pattern