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spatstat (version 1.16-0)

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. 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

17,668

Version

1.16-0

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

July 2nd, 2009

Functions in spatstat (1.16-0)

Reset Values in Subset of Image

Estimate the I-function

Nearest Neighbour Distance Function G

Marked K-Function

Extract Subset of Image

Ord's Interaction model

Reduced Second Moment Measure

Beadlet Anemones Data

The Lennard-Jones Potential

Convert to Pixel Image

Extract Subset of Function Array

Apply Affine Transformation To Line Segment Pattern

ANOVA for Fitted Point Process Models

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

Distance to Boundary of Window

bounding.box.xy

Convex Hull of Points

Multitype J Function (i-to-j)

Convert Data To Tessellation

Multitype K Function (i-to-any)

Subdivide a Window or Tessellation using a Set of Lines

Extract Subset of Function Values

Pairwise distances

complement.owin

Take Complement of a Window

Artificial Data Point Pattern

Circular Window

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Coefficients of Fitted Point Process Model

Subset of Quadrature Scheme

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Distance to Boundary of Window

Estimate the J-function

Extract Dummy Points Used to Fit a Point Process Model

Multitype K Function (Cross-type)

Exponential Energy Marks

Diggle-Gratton model

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Combine Two Line Segment Patterns

Inhomogeneous Multitype K Dot Function

Apply Gaussian Blur to a Pixel Image

Endpoints of Line Segment Pattern

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

The Soft Core Point Process Model

Multitype J Function (i-to-any)

Extract or Replace Subset of a List of Things

Hutchings' Bramble Canes data

Convert Data To Class psp

Multitype L-function (i-to-any)

Morphological Closing of a Window

The Strauss / Hard Core Point Process Model

Pixel Image Approximation of a Window

The Multitype Strauss Point Process Model

Geyer's Saturation Point Process Model

Calculate four standard summary functions of a point pattern.

Generic Ord Interaction model

Evaluate Expression Involving Functions

Apply Function to Every Neighbourhood in a Point Pattern

Colour Lookup Tables

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

Extract Original Data from a Fitted Point Process Model

Clark and Evans Aggregation Index

Test Whether A Point Process Model is Marked

Safely Convert Point Pattern Window to Binary Mask

Inhomogeneous Cross Type L Function

Concatenate x,y Coordinate Vectors

Kaplan-Meier Estimator using Histogram Data

Generate a Default Pattern of Dummy Points

Diagnostics for random marking

Distance Map of Window

Bounding Box of a Window or Point Pattern

Interactively Add Points

Extract or Replace Subset of Point Pattern

Infinite Straight Lines

Hybrid Geyer Point Process Model

Pairwise distances between two different line segment patterns

Distance Map of Line Segment Pattern

Berman-Huntington points and lines data

spatstat-internal

Internal spatstat functions

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Estimate the empty space function F

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Test Whether Marks Are Present

Histogram of Pixel Values in an Image

Interpolate a Pixel Image

Convert Pixel Image to Matrix

Level Set of a Pixel Image

model.matrix.ppm

Extract Design Matrix from Point Process Model

Distance for a Point Pattern Matching

Neighbourhood density function

Test Whether Two Pixel Images Are Compatible

Multitype L-function (cross-type)

Murchison gold deposits

Create a Pixel Image Object

Rectangular grid of points

Point and Click Interface for Displaying a Point Pattern

Kernel Smoothed Intensity of Point Pattern

Convert Pixel Image from Numeric to Factor

Inhomogeneous Multitype L Dot Function

Plot a Colour Map

Weighted Empirical Cumulative Distribution Function

Longleaf Pines Point Pattern

Hughes' Amacrine Cell Data

Pair Correlation Function of Point Pattern

Create a Point Pattern

Biological Cells Point Pattern

Extract Subset of Line Segment Pattern

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

Harkness-Isham ants' nests data

Midpoints of Line Segment Pattern

Lengths of Line Segments

Diggle's Heather Data

Mean, Median and Range of Pixel Values in an Image

Simulation envelopes of summary function

K-function using FFT

Japanese Pines Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

Pairwise distances between two different point patterns

The Piecewise Constant Pairwise Interaction Point Process Model

Area of a Window

Apply Function to Image Broken Down by Factor

Evaluate Expression Involving Pixel Images

The Strauss Point Process Model

Diameter of a Window

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Dirichlet Tessellation of Point Pattern

Determine Whether One Window is Contained In Another

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Kolmogorov-Smirnov Test for Point Process Model

Corners of a rectangle

Tropical rain forest trees

Diagnostic Plots for Fitted Point Process Model

The Area Interaction Point Process Model

Apply Affine Transformation

Fit cluster point process model

Extract.splitppp

Extract or Replace Sub-Patterns

Nearest Neighbours Between Two Patterns

Connected components of an image or window

Class of Images

Intersect Infinite Straight Lines with a Window

Nearest neighbour distances

Nearest neighbour distances between line segments

Generic Pairwise Interaction model

Poisson Point Process Model

Convex Hull of Points

Test Whether Two Function Objects Are Compatible

Apply Affine Transformation To Window

Evaluate Expression Involving Function Arrays

Test whether Object is Multitype

Humberside Data on Childhood Leukaemia and Lymphoma

Print a Fitted Point Process Model

pairdist.default

Pairwise distances

Saturated Pairwise Interaction model

Fitted Conditional Intensity for Point Process Model

Find Largest Circle Inside Window

Test Whether Points Are Inside A Window

Plot a List of Things

Create a Window

Method of Minimum Contrast

Fry Plot of Point Pattern

Pairwise distances between line segments

Compute Quadrature Weights Based on Grid Counts

Mark Connection Function

Class of Line Segment Patterns

spatstat-deprecated

Deprecated spatstat functions

Simulate Gauss-Poisson Process

pppmatching.object

Class of Point Matchings

Convert Data To Class owin

Create a Point Matching

Perspective Plot of Pixel Image

Test Whether An Object Is A Pixel Image

Mosaic Random Field

Hyper Data Frame

Class of Quadrature Schemes

Quadrature Scheme Based on Pixel Grid

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

New Zealand Trees Point Pattern

Plot a tessellation

crossdist.default

Pairwise distances between two different sets of points

Nearest neighbour

Pair Correlation Function

Pine saplings in Finland.

inforder.family

Infinite Order Interaction Family

Fit Point Process Model to Data

Ord Interaction Process Family

Plot a plotppm Object Created by plot.ppm

plot.hyperframe

Plot Entries in a Hyperframe

plot a Spatial Quadrature Scheme

Sample Quantiles of Pixel Image

Compute Images of Constructed Covariates

multiplicity.ppp

Count Multiplicity of Duplicate Points

Pair Correlation Function obtained from K Function

Morphological Opening of a Window

Delaunay Triangulation of Point Pattern

Centroid of a window

Extract or Replace Subset of Tessellation

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Prediction from a Fitted Point Process Model

project2segment

Move Point To Nearest Line

Pairwise distances

Determine Duplicated Points in a Spatial Point Pattern

Convert Window to Another Unit of Length

Cartesian Coordinates for a Pixel Raster

Convert Point Pattern to Another Unit of Length

Quadrat counting for a point pattern

Distance Map of Point Pattern

Function Arrays for Spatial Patterns

Intersection or Union of Two Windows

Kernel Smoothing of Line Segment Pattern

Apply Vector Translation To Pixel Image

Extract List of Tiles in a Tessellation

Window in Shape of Letter R

Evaluate an Expression in Each Row of a Hyperframe

Extract the Interaction from a Fitted Point Process Model

Intersection of Two Tessellations

Log Likelihood for Poisson Point Process Model

Multitype pair correlation function

Convert Polygonal Region into Different Format

Create a Line Segment Pattern

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Test Whether A Point Pattern is Marked

quadratresample

Resample a Point Pattern by Resampling Quadrats

Ponderosa Pine Tree Point Pattern

Aherne's hamster tumour data

Data and Code From JRSS Discussion Paper on Residuals

Identify Points in a Point Pattern

Spherical Contact Distribution Function

Approximate a Polygon by a Simpler Polygon

Basis for Harmonic Functions

Place Points Evenly Along Specified Lines

Data Frames of Function Values

Residuals for Fitted Point Process Model

Beta Ganglion Cells in Cat Retina, Old Version

Saturated Pairwise Interaction Point Process Family

Plot a Pixel Image

Plot a List of Point Patterns

Inhomogeneous Cross K Function

Summary of a Spatial Window

Marked J Function

plot a Spatial Point Pattern

Variance-Covariance Matrix for a Fitted Point Process Model

Print Brief Details of an Image

Generate grid of parallel lines with random displacement

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Print a Quadrature Scheme

Summary of a Point Pattern Dataset

Determine Initial State for Metropolis-Hastings Simulation.

Class of Point Patterns

Interaction Distance of a Point Process

Convert dataset to another unit of length

Print Brief Details of a Point Pattern Dataset

Morishita Index Plot

Find Line Segment Nearest to Each Point

Randomly Shift a Line Segment Pattern

plot a Spatial Line Segment Pattern

Simulate Baddeley-Silverman Cell Process

Simulate Matern Cluster Process

Divide Image Into Sub-images

Print Brief Details of a Spatial Window

Generate N Random Multitype Points

Kaplan-Meier and Reduced Sample Estimator using Histograms

Test Whether An Object Is A Window

Convert Point Pattern to Pixel Image

Divide Region into Quadrats

Poisson Line Tessellation

California Redwoods Point Pattern (Entire Dataset)

Plot Function Values

plot a Fitted Point Process Model

Name for Unit of Length

Random Thinning

Inhomogeneous K-function

Test Whether An Object Is A Point Pattern

Simulate Matern Model II

Simulate Stratified Random Point Pattern

Summarizing a Fitted Point Process Model

Superimpose Several Point Patterns

Profile Maximum Pseudolikelihood

Mark Correlation Function

summary.splitppp

Summary of a Split Point Pattern

Lansing Woods Point Pattern

Orientation Angles of Line Segments

Interpret Fitted Model for Metropolis-Hastings Simulation.

Generate Poisson Random Line Process

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Q-Q Plot of Residuals from Fitted Point Process Model

Point and Click Interface for Exploratory Analysis of Point Pattern

Lurking variable plot

Generate Multitype Poisson Point Pattern

Point Patterns of New Brunswick Forest Fires

Simulate from a Fitted Point Process Model

Spatial smoothing of observations at irregular points

Swedish Pines Point Pattern

Randomly Shift a Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

spatstat.options

Internal Options in Spatstat Package

Print Brief Details of a Line Segment Pattern Dataset

Mark Correlation Integral

Distance Between Two Point Patterns

Simulate Neyman-Scott Process

Extract Quadrature Scheme Used to Fit a Point Process Model

Rotate a Window

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

Apply Vector Translation To Window

Pairwise distances

Plot a Function Array

Simulate Thomas Process

Mosaic Random Set

Estimate window from points alone

Create a Tessellation

Convert Line Segment Pattern to Another Unit of Length

Marked Nearest Neighbour Distance Function

Summary of a Line Segment Pattern Dataset

Generate N Uniform Random Points

Simulate a fitted cluster point process model.

Perfect Simulation of the Strauss Process

Update a Fitted Point Process Model

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Set Control Parameters for Metropolis-Hastings Algorithm.

Apply Vector Translation

Urkiola Woods Point Pattern

Superimpose Several Line Segment Patterns

Apply Vector Translation To Point Pattern

Fit the Thomas Point Process by Minimum Contrast

Simulate systematic random point pattern

Pair Correlation Function obtained from array of K functions

Plot a fitted cluster point process

Convert Pixel Image to Another Unit of Length

Contour plot of pixel image

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Apply Vector Translation To Line Segment Pattern

Random Perturbation of a Point Pattern

Simulate point patterns using the Metropolis-Hastings algorithm.

Compute Integral of Function Against Cumulative Distribution

Generate Poisson Point Pattern

Cut margins from rectangle

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Class of Fitted Point Process Models

Divide Point Pattern into Sub-patterns

Test Whether a Window is Convex

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Spruces Point Pattern

Rotate a Point Pattern

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

Random Re-Labelling of Point Pattern

Generate N Random Points

Update a Fitted Cluster Point Process Model

rshift.splitppp

Randomly Shift a List of Point Patterns

Generate N Uniform Random Points in a Disc

rescue.rectangle

Convert Window Back To Rectangle

Simulated Point Pattern

Union of Data and Dummy Points

Galaxies in the Shapley Supercluster

Prediction from a Fitted Cluster Point Process Model

Spokes pattern of dummy points

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Read Point Pattern From Data File

Vertices of a Window

Summary of a List of Things

California Redwoods Point Pattern (Ripley's Subset)

Set Covariance of a Window

Reduced Sample Estimator using Histogram Data

Define Point Process Model for Metropolis-Hastings Simulation.

Generate a Quadrature Scheme from a Point Pattern

Evaluate an Expression in a Function Table

Summarizing a Quadrature Scheme

Extract Unique Points from a Spatial Point Pattern

Apply Affine Transformation To Point Pattern

Apply a Function to a Point Pattern Broken Down by Factor

Chorley-Ribble Cancer Data

Beta Ganglion Cells in Cat Retina

Interactively Define a Polygon

Classify Points in a Point Pattern

Crossing Points of Two Line Segment Patterns

Test Whether An Object Is A Fitted Point Process Model

Summarise Marks in Every Neighbourhood in a Point Pattern

Plot a Spatial Window

Print Progress Reports

Simulate Matern Model I

Rotate a Line Segment Pattern

Generate Poisson Point Pattern on Line Segments

Set or Reset the Marks in a Point Pattern

Summarizing a Pixel Image

The Spatstat Package

Difference of Disc Areas

Convert Data To Class ppp

Dilate a Window

Areas of Morphological Erosions

Expand Window By Factor

nearest.raster.point

Find Pixel Nearest to a Given Point

pairwise.family

Pairwise Interaction Process Family

Simulate Simple Sequential Inhibition

Sufficient Statistic of Point Process Model