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spatstat (version 1.16-1)

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. 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, and pixel images. 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

18,161

Version

1.16-1

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

July 27th, 2009

Functions in spatstat (1.16-1)

Extract or Replace Subset of Tessellation

Estimate the J-function

Multitype L-function (i-to-any)

Diagnostics for random marking

Diggle-Gratton model

Extract Subset of Image

Extract Subset of Function Array

Marked Nearest Neighbour Distance Function

Estimate the empty space function F

Inhomogeneous Cross K Function

Apply Affine Transformation To Window

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Ord's Interaction model

ANOVA for Fitted Point Process Models

Extract or Replace Subset of a List of Things

Marked K-Function

The Spatstat Package

Inhomogeneous Multitype K Dot Function

Area of a Window

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Intersect Infinite Straight Lines with a Window

Beadlet Anemones Data

The Area Interaction Point Process Model

Marked J Function

Apply Affine Transformation

Extract or Replace Subset of Point Pattern

Convert Data To Class ppp

Distance to Boundary of Window

Inhomogeneous K-function

Calculate four standard summary functions of a point pattern.

complement.owin

Take Complement of a Window

Inhomogeneous Multitype L Dot Function

Multitype K Function (i-to-any)

Convert to Pixel Image

Inhomogeneous Cross Type L Function

Delaunay Triangulation of Point Pattern

Hughes' Amacrine Cell Data

Corners of a rectangle

Orientation Angles of Line Segments

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Connected components of an image or window

Beta Ganglion Cells in Cat Retina

Hybrid Geyer Point Process Model

Reduced Second Moment Measure

Interactively Add Points

Apply Gaussian Blur to a Pixel Image

Subset of Quadrature Scheme

K-function using FFT

Convert Data To Class owin

The Piecewise Constant Pairwise Interaction Point Process Model

Convert Pixel Image from Numeric to Factor

Multitype K Function (Cross-type)

Extract Subset of Function Values

Pine saplings in Finland.

Reset Values in Subset of Image

Tropical rain forest trees

Concatenate x,y Coordinate Vectors

Morphological Erosion

The Soft Core Point Process Model

Test Whether Two Pixel Images Are Compatible

Spherical Contact Distribution Function

Estimate the I-function

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

Pairwise distances between two different point patterns

The Lennard-Jones Potential

Pairwise distances between two different line segment patterns

Crossing Points of Two Line Segment Patterns

Generic Ord Interaction model

Geyer's Saturation Point Process Model

Diagnostic Plots for Fitted Point Process Model

Test Whether a Window is Convex

Pairwise distances

The Strauss / Hard Core Point Process Model

Convert Data To Tessellation

Difference of Disc Areas

Extract Subset of Line Segment Pattern

Diameter of a Window

Distance Map of Line Segment Pattern

Apply Function to Every Neighbourhood in a Point Pattern

Nearest Neighbour Distance Function G

Convert Data To Class psp

Harkness-Isham ants' nests data

Evaluate Expression Involving Pixel Images

Extract.splitppp

Extract or Replace Sub-Patterns

Apply Function to Image Broken Down by Factor

Apply Affine Transformation To Point Pattern

Safely Convert Point Pattern Window to Binary Mask

Combine Two Line Segment Patterns

Berman's Tests for Point Process Model

Generic Pairwise Interaction model

crossdist.default

Pairwise distances between two different sets of points

The Strauss Point Process Model

Clark and Evans Aggregation Index

Test Whether Marks Are Present

Basis for Harmonic Functions

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Create a Window

Hutchings' Bramble Canes data

Fit the Matern Cluster Point Process by Minimum Contrast

Beta Ganglion Cells in Cat Retina, Old Version

Poisson Point Process Model

Bounding Box of a Window or Point Pattern

Interactively Define a Polygon

The Multitype Strauss Point Process Model

Distance to Boundary of Window

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

Convex Hull of Points

bounding.box.xy

Convex Hull of Points

Convert Polygonal Region into Different Format

Pair Correlation Function obtained from K Function

Evaluate Expression Involving Functions

Morphological Closing

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Morphological Dilation

Exponential Energy Marks

Convert Pixel Image to Matrix

Residuals for Fitted Point Process Model

Data Frames of Function Values

Aherne's hamster tumour data

Kernel Smoothing of Line Segment Pattern

Test Whether An Object Is A Window

Evaluate Expression Involving Function Arrays

Level Set of a Pixel Image

Interpolate a Pixel Image

Kolmogorov-Smirnov Test for Point Process Model

Convert Point Pattern to Another Unit of Length

spatstat-deprecated

Deprecated spatstat functions

Berman-Huntington points and lines data

Determine Duplicated Points in a Spatial Point Pattern

Fitted Conditional Intensity for Point Process Model

Plot a Spatial Window

Print Brief Details of a Spatial Window

Classify Points in a Point Pattern

Endpoints of Line Segment Pattern

Pairwise distances

Class of Images

Test Whether An Object Is A Point Pattern

Class of Point Patterns

Test Whether Points Are Inside A Window

Intersection or Union of Two Windows

spatstat-internal

Internal spatstat functions

Nearest neighbour distances between line segments

Print Brief Details of a Line Segment Pattern Dataset

Apply a Function to a Point Pattern Broken Down by Factor

Distance Between Two Point Patterns

inforder.family

Infinite Order Interaction Family

Biological Cells Point Pattern

Plot a Spatial Kolmogorov-Smirnov Test

Artificial Data Point Pattern

Pair Correlation Function

Pixel Image Approximation of a Window

Saturated Pairwise Interaction model

Plot a Pixel Image

Chorley-Ribble Cancer Data

Convert a Window to a Polygonal Window

Determine Whether One Window is Contained In Another

Prediction from a Fitted Cluster Point Process Model

Lengths of Line Segments

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Kaplan-Meier and Reduced Sample Estimator using Histograms

Find Largest Circle Inside Window

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

Centroid of a window

Fit Point Process Model to Data

Function Arrays for Spatial Patterns

Saturated Pairwise Interaction Point Process Family

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Mean, Median and Range of Pixel Values in an Image

Areas of Morphological Erosions

Diggle's Heather Data

Weighted Empirical Cumulative Distribution Function

Summarise Marks in Every Neighbourhood in a Point Pattern

Kernel Smoothed Intensity of Point Pattern

Test whether Object is Multitype

Expand Window By Factor

Compute Quadrature Weights Based on Grid Counts

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Create a Point Pattern

nearest.raster.point

Find Pixel Nearest to a Given Point

Hyper Data Frame

Histogram of Pixel Values in an Image

Dirichlet Tessellation of Point Pattern

Plot a Function Array

Rectangular grid of points

Pairwise distances

Plot a plotppm Object Created by plot.ppm

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Japanese Pines Point Pattern

Ponderosa Pine Tree Point Pattern

Morishita Index Plot

Colour Lookup Tables

Murchison gold deposits

Test Whether An Object Is Empty

Identify Points in a Point Pattern

Create a Point Matching

Fit cluster point process model

Generate grid of parallel lines with random displacement

Simulate Gauss-Poisson Process

plot a Fitted Point Process Model

Random Re-Labelling of Point Pattern

Mosaic Random Field

Humberside Data on Childhood Leukaemia and Lymphoma

is.multitype.ppm

Test Whether A Point Process Model is Multitype

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

New Zealand Trees Point Pattern

Plot a List of Things

Print Brief Details of an Image

Longleaf Pines Point Pattern

plot a Spatial Quadrature Scheme

Quadrat counting for a point pattern

Point and Click Interface for Exploratory Analysis of Point Pattern

Generate Poisson Random Line Process

Intersection of Two Tessellations

Mark Correlation Function

Simulate Neyman-Scott Process

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Randomly Shift a Line Segment Pattern

Q-Q Plot of Residuals from Fitted Point Process Model

Place Points Evenly Along Specified Lines

Simulate Thomas Process

Print Brief Details of a Point Pattern Dataset

Generate Multitype Poisson Point Pattern

Simulate a Fitted Cluster Point Process Model

Simulate Matern Model I

pppmatching.object

Class of Point Matchings

Fry Plot of Point Pattern

Morphological Opening

Generate Poisson Point Pattern

Nearest neighbour

Fit the Thomas Point Process by Minimum Contrast

Convert Point Pattern to Pixel Image

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Set Control Parameters for Metropolis-Hastings Algorithm.

Random Thinning

Rotate a Window

Point and Click Interface for Displaying a Point Pattern

Test Whether A Point Process Model is Marked

Point Patterns of New Brunswick Forest Fires

Random Perturbation of a Point Pattern

Mosaic Random Set

Print a Quadrature Scheme

Generate N Uniform Random Points in a Disc

Rotate a Point Pattern

Sample Quantiles of Pixel Image

Reduced Sample Estimator using Histogram Data

Circular Window

Generate a Quadrature Scheme from a Point Pattern

Set or Reset the Marks in a Point Pattern

Randomly Shift a Point Pattern

Extract Dummy Points Used to Fit a Point Process Model

Determine Initial State for Metropolis-Hastings Simulation.

Simulate from a Fitted Point Process Model

plot.hyperframe

Plot Entries in a Hyperframe

pairdist.default

Pairwise distances

Ord Interaction Process Family

Sufficient Statistic of Point Process Model

Prediction from a Fitted Point Process Model

Convert Pixel Image to Another Unit of Length

Create a Line Segment Pattern

Extract the Interaction from a Fitted Point Process Model

Infinite Straight Lines

rescue.rectangle

Convert Window Back To Rectangle

Window in Shape of Letter R

Pairwise distances between line segments

Plot a tessellation

Simulate Matern Model II

summary.splitppp

Summary of a Split Point Pattern

Apply Vector Translation To Window

Simulate point patterns using the Metropolis-Hastings algorithm.

Print a Fitted Point Process Model

plot a Spatial Point Pattern

Lurking variable plot

Class of Line Segment Patterns

Test Whether Two Function Objects Are Compatible

Perspective Plot of Pixel Image

Simulate Simple Sequential Inhibition

Plot a fitted cluster point process

quadratresample

Resample a Point Pattern by Resampling Quadrats

California Redwoods Point Pattern (Entire Dataset)

Plot a List of Point Patterns

Find Line Segment Nearest to Each Point

multiplicity.ppp

Count Multiplicity of Duplicate Points

Convert Window to Another Unit of Length

Neighbourhood density function

Interpret Fitted Model for Metropolis-Hastings Simulation.

Test Whether An Object Is A Pixel Image

Divide Region into Quadrats

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Spatial smoothing of observations at irregular points

Summarizing a Pixel Image

Compute Images of Constructed Covariates

Multitype pair correlation function

Define Point Process Model for Metropolis-Hastings Simulation.

Update a Fitted Cluster Point Process Model

Class of Quadrature Schemes

Update a Fitted Point Process Model

Log Likelihood for Poisson Point Process Model

Simulation envelopes of summary function

Nearest neighbour distances

Divide Image Into Sub-images

Mark Correlation Integral

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Pair Correlation Function of Point Pattern

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Class of Fitted Point Process Models

Data and Code From JRSS Discussion Paper on Residuals

Midpoints of Line Segment Pattern

Set Covariance of a Window

Print Progress Reports

Simulated Point Pattern

Rotate a Line Segment Pattern

rshift.splitppp

Randomly Shift a List of Point Patterns

Galaxies in the Shapley Supercluster

Extract Unique Points from a Spatial Point Pattern

Generate N Random Multitype Points

Extract Quadrature Scheme Used to Fit a Point Process Model

Approximate a Polygon by a Simpler Polygon

Apply Vector Translation To Pixel Image

Poisson Line Tessellation

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Summarizing a Fitted Point Process Model

Simulate Stratified Random Point Pattern

Method of Minimum Contrast

project2segment

Move Point To Nearest Line

Mark Connection Function

plot a Spatial Line Segment Pattern

Divide Point Pattern into Sub-patterns

Perfect Simulation of the Strauss Process

Create a Tessellation

pairwise.family

Pairwise Interaction Process Family

Generate N Uniform Random Points

Interaction Distance of a Point Process

Apply Vector Translation

Estimate window from points alone

Perimeter Length of Window

Vertices of a Window

Generate N Random Points

Spokes pattern of dummy points

Superimpose Several Point Patterns

Generate Poisson Point Pattern on Line Segments

Name for Unit of Length

Apply Vector Translation To Point Pattern

Simulate systematic random point pattern

Summary of a Line Segment Pattern Dataset

Quadrature Scheme Based on Pixel Grid

Urkiola Woods Point Pattern

Test Whether A Point Pattern is Marked

Compute Integral of Function Against Cumulative Distribution

Convert dataset to another unit of length

Summary of a Point Pattern Dataset

Plot Function Values

Convert Line Segment Pattern to Another Unit of Length

Extract List of Tiles in a Tessellation

Profile Maximum Pseudolikelihood

Define Point Process Model for Metropolis-Hastings Simulation.

Summary of a List of Things

Read Point Pattern From Data File

Summarizing a Quadrature Scheme

California Redwoods Point Pattern (Ripley's Subset)

Cartesian Coordinates for a Pixel Raster

Swedish Pines Point Pattern

Apply Vector Translation To Line Segment Pattern

Spruces Point Pattern

Cut margins from rectangle

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

Union of Data and Dummy Points

Superimpose Several Line Segment Patterns

Multitype J Function (i-to-any)

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

Coefficients of Fitted Point Process Model

Apply Affine Transformation To Line Segment Pattern

Generate a Default Pattern of Dummy Points

Distance Map of Point Pattern

Kaplan-Meier Estimator using Histogram Data

Lansing Woods Point Pattern

Distance for a Point Pattern Matching

model.matrix.ppm

Extract Design Matrix from Point Process Model

Summary of a Spatial Window

Nearest Neighbours Between Two Patterns

Simulate a Fitted Gibbs Point Process Model

Multitype J Function (i-to-j)

Multitype L-function (cross-type)

Subdivide a Window or Tessellation using a Set of Lines

Extract Original Data from a Fitted Point Process Model

Contour plot of pixel image

Distance Map of Window

Evaluate an Expression in Each Row of a Hyperframe

Create a Pixel Image Object

Plot a Colour Map

Test Whether An Object Is A Fitted Point Process Model

Pair Correlation Function obtained from array of K functions

Simulate Baddeley-Silverman Cell Process

Simulate Matern Cluster Process

Variance-Covariance Matrix for a Fitted Point Process Model

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Evaluate an Expression in a Function Table

spatstat.options

Internal Options in Spatstat Package