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spatstat (version 1.15-4)

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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Install

install.packages('spatstat')

Monthly Downloads

16,015

Version

1.15-4

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

June 16th, 2009

Functions in spatstat (1.15-4)

Nearest Neighbour Distance Function G

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Determine Whether One Window is Contained In Another

Multitype K Function (i-to-any)

Lurking variable plot

Calculate four standard summary functions of a point pattern.

Saturated Pairwise Interaction model

Estimate the empty space function F

Convert to Pixel Image

The Lennard-Jones Potential

Poisson Point Process Model

Multitype J Function (i-to-j)

Extract Subset of Line Segment Pattern

Distance to Boundary of Window

Subset of Quadrature Scheme

Combine Two Line Segment Patterns

The Piecewise Constant Pairwise Interaction Point Process Model

Extract Subset of Function Values

Berman-Huntington points and lines data

Corners of a rectangle

Compute Images of Constructed Covariates

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

Convert Data To Class owin

Inhomogeneous K-function

Multitype J Function (i-to-any)

Diagnostics for random marking

plot a Spatial Point Pattern

Dirichlet Tessellation of Point Pattern

spatstat-deprecated

Deprecated spatstat functions

Extract or Replace Subset of Point Pattern

Extract Subset of Image

Extract or Replace Subset of Tessellation

Pairwise distances

Convert Data To Class psp

Test Whether Two Pixel Images Are Compatible

Test Whether A Point Pattern is Marked

Harkness-Isham ants' nests data

crossdist.default

Pairwise distances between two different sets of points

Extract the Interaction from a Fitted Point Process Model

Identify Points in a Point Pattern

Test Whether An Object Is A Pixel Image

Ord's Interaction model

Mark Correlation Integral

Kernel Smoothed Intensity of Point Pattern

Diagnostic Plots for Fitted Point Process Model

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Exponential Energy Marks

Convert Pixel Image to Another Unit of Length

Convert Window to Another Unit of Length

Diameter of a Window

Convert Data To Class ppp

bounding.box.xy

Convex Hull of Points

Contour plot of pixel image

Estimate the J-function

The Strauss Point Process Model

plot a Spatial Line Segment Pattern

Colour Lookup Tables

Log Likelihood for Poisson Point Process Model

Reset Values in Subset of Image

Biological Cells Point Pattern

Aherne's hamster tumour data

Extract Subset of Function Array

Spherical Contact Distribution Function

Ponderosa Pine Tree Point Pattern

rescue.rectangle

Convert Window Back To Rectangle

Method of Minimum Contrast

Generate a Default Pattern of Dummy Points

Test Whether Points Are Inside A Window

Print Brief Details of a Point Pattern Dataset

Morphological Opening of a Window

Pair Correlation Function

Nearest Neighbours Between Two Patterns

ANOVA for Fitted Point Process Models

Plot a Pixel Image

Endpoints of Line Segment Pattern

project2segment

Move Point To Nearest Line

Generate Poisson Random Line Process

Apply Affine Transformation To Line Segment Pattern

plot a Spatial Quadrature Scheme

Nearest neighbour distances between line segments

Test Whether A Point Process Model is Marked

Beta Ganglion Cells in Cat Retina

Midpoints of Line Segment Pattern

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Convert Point Pattern to Pixel Image

Convert Pixel Image from Numeric to Factor

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Perfect Simulation of the Strauss Process

Generate Multitype Poisson Point Pattern

Multitype K Function (Cross-type)

Area of a Window

Pairwise distances

Pairwise distances

Approximate a Polygon by a Simpler Polygon

Plot a Spatial Window

Define Point Process Model for Metropolis-Hastings Simulation.

Print Brief Details of an Image

Simulated Point Pattern

Evaluate Expression Involving Pixel Images

Apply Function to Every Neighbourhood in a Point Pattern

Simulate Matern Cluster Process

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Concatenate x,y Coordinate Vectors

Convert Pixel Image to Matrix

Centroid of a window

Determine Duplicated Points in a Spatial Point Pattern

Kolmogorov-Smirnov Test for Point Process Model

pairwise.family

Pairwise Interaction Process Family

Find Line Segment Nearest to Each Point

Residuals for Fitted Point Process Model

Extract Unique Points from a Spatial Point Pattern

Simulate Matern Model II

Distance to Boundary of Window

Summarizing a Quadrature Scheme

The Area Interaction Point Process Model

Simulate Matern Model I

Simulate systematic random point pattern

Cartesian Coordinates for a Pixel Raster

Extract.splitppp

Extract or Replace Sub-Patterns

inforder.family

Infinite Order Interaction Family

Chorley-Ribble Cancer Data

Orientation Angles of Line Segments

Name for Unit of Length

Coefficients of Fitted Point Process Model

Bounding Box of a Window or Point Pattern

Apply Affine Transformation To Window

Inhomogeneous Multitype K Dot Function

Class of Point Patterns

Histogram of Pixel Values in an Image

Rotate a Point Pattern

Mosaic Random Set

Extract Quadrature Scheme Used to Fit a Point Process Model

Apply a Function to a Point Pattern Broken Down by Factor

Pairwise distances between line segments

Extract Original Data from a Fitted Point Process Model

Reduced Sample Estimator using Histogram Data

Morphological Closing of a Window

Beadlet Anemones Data

Evaluate Expression Involving Functions

quadratresample

Resample a Point Pattern by Resampling Quadrats

California Redwoods Point Pattern (Entire Dataset)

Hybrid Geyer Point Process Model

Intersection or Union of Two Windows

Point Patterns of New Brunswick Forest Fires

Convert dataset to another unit of length

Pair Correlation Function obtained from K Function

Mosaic Random Field

complement.owin

Take Complement of a Window

Crossing Points of Two Line Segment Patterns

Interactively Define a Polygon

Marked J Function

Test Whether Marks Are Present

Distance Map of Window

Apply Vector Translation To Point Pattern

Hyper Data Frame

Evaluate an Expression in a Function Table

Level Set of a Pixel Image

Simulate Stratified Random Point Pattern

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

plot a Fitted Point Process Model

Convert Point Pattern to Another Unit of Length

Marked Nearest Neighbour Distance Function

Distance Map of Point Pattern

Marked K-Function

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Divide Image Into Sub-images

Rotate a Line Segment Pattern

Rotate a Window

Intersect Infinite Straight Lines with a Window

Summary of a List of Things

Reduced Second Moment Measure

Create a Point Matching

Mean, Median and Range of Pixel Values in an Image

Pairwise distances between two different line segment patterns

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

New Zealand Trees Point Pattern

Apply Affine Transformation

Simulate from a Fitted Point Process Model

Multitype L-function (i-to-any)

Diggle's Heather Data

Spatial smoothing of observations at irregular points

Tropical rain forest trees

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

Test Whether An Object Is A Point Pattern

Hutchings' Bramble Canes data

Japanese Pines Point Pattern

Pine saplings in Finland.

Class of Images

Cut margins from rectangle

Apply Gaussian Blur to a Pixel Image

Print Brief Details of a Line Segment Pattern Dataset

Generic Ord Interaction model

Inhomogeneous Cross K Function

Difference of Disc Areas

Areas of Morphological Erosions

Test Whether An Object Is A Fitted Point Process Model

Multitype L-function (cross-type)

Intersection of Two Tessellations

rshift.splitppp

Randomly Shift a List of Point Patterns

Test whether Object is Multitype

Extract List of Tiles in a Tessellation

Prediction from a Fitted Cluster Point Process Model

Kernel Smoothing of Line Segment Pattern

The Soft Core Point Process Model

Artificial Data Point Pattern

Plot a Colour Map

Plot a List of Things

Plot a Function Array

Test Whether Two Function Objects Are Compatible

Classify Points in a Point Pattern

spatstat.options

Internal Options in Spatstat Package

Simulate a fitted cluster point process model.

Expand Window By Factor

Variance-Covariance Matrix for a Fitted Point Process Model

Apply Vector Translation

Beta Ganglion Cells in Cat Retina, Old Version

Print a Quadrature Scheme

K-function using FFT

Profile Maximum Pseudolikelihood

The Spatstat Package

Generate N Uniform Random Points in a Disc

Lansing Woods Point Pattern

Generate Poisson Point Pattern

Delaunay Triangulation of Point Pattern

Kaplan-Meier Estimator using Histogram Data

Find Largest Circle Inside Window

Geyer's Saturation Point Process Model

Update a Fitted Cluster Point Process Model

Infinite Straight Lines

Mark Correlation Function

Circular Window

Function Arrays for Spatial Patterns

Pairwise distances between two different point patterns

Print Progress Reports

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Diggle-Gratton model

Nearest neighbour

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Generate N Uniform Random Points

Vertices of a Window

Sufficient Statistic of Point Process Model

Rectangular grid of points

Subdivide a Window or Tessellation using a Set of Lines

Interactively Add Points

Superimpose Several Line Segment Patterns

Spokes pattern of dummy points

Convex Hull of Points

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Fit Point Process Model to Data

Apply Vector Translation To Pixel Image

Plot Function Valuesn

Generic Pairwise Interaction model

Saturated Pairwise Interaction Point Process Family

Urkiola Woods Point Pattern

Class of Line Segment Patterns

Extract or Replace Subset of a List of Things

Ord Interaction Process Family

Simulate point patterns using the Metropolis-Hastings algorithm.

Clark and Evans Aggregation Index

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Pixel Image Approximation of a Window

The Strauss / Hard Core Point Process Model

pppmatching.object

Class of Point Matchings

Kaplan-Meier and Reduced Sample Estimator using Histograms

Apply Vector Translation To Window

Humberside Data on Childhood Leukaemia and Lymphoma

Fit the Matern Cluster Point Process by Minimum Contrast

Hughes' Amacrine Cell Data

Poisson Line Tessellation

The Multitype Strauss Point Process Model

Apply Function to Image Broken Down by Factor

Morishita Index Plot

Lengths of Line Segments

Distance for a Point Pattern Matching

Simulation envelopes of summary function

multiplicity.ppp

Count Multiplicity of Duplicate Points

Sample Quantiles of Pixel Image

Extract Dummy Points Used to Fit a Point Process Model

nearest.raster.point

Find Pixel Nearest to a Given Point

Class of Quadrature Schemes

Window in Shape of Letter R

Set or Reset the Marks in a Point Pattern

Dilate a Window

Longleaf Pines Point Pattern

Convert Data To Tessellation

Plot a plotppm Object Created by plot.ppm

Summarizing a Pixel Image

Summarizing a Fitted Point Process Model

Plot a tessellation

Mark Connection Function

Test Whether An Object Is A Window

Interaction Distance of a Point Process

Place Points Evenly Along Specified Lines

Safely Convert Point Pattern Window to Binary Mask

Create a Tessellation

Fitted Conditional Intensity for Point Process Model

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Evaluate Expression Involving Function Arrays

Create a Window

Plot a List of Point Patterns

Update a Fitted Point Process Model

Prediction from a Fitted Point Process Model

Data Frames of Function Values

Interpolate a Pixel Image

Distance Map of Line Segment Pattern

Generate a Quadrature Scheme from a Point Pattern

spatstat-internal

Internal spatstat functions

Superimpose Several Point Patterns

California Redwoods Point Pattern (Ripley's Subset)

Simulate Neyman-Scott Process

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

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

Generate grid of parallel lines with random displacement

Class of Fitted Point Process Models

Fry Plot of Point Pattern

Generate N Random Points

model.matrix.ppm

Extract Design Matrix from Point Process Model

Basis for Harmonic Functions

Union of Data and Dummy Points

Determine Initial State for Metropolis-Hastings Simulation.

pairdist.default

Pairwise distances

Compute Integral of Function Against Cumulative Distribution

Create a Point Pattern

Quadrat counting for a point pattern

Create a Line Segment Pattern

Compute Quadrature Weights Based on Grid Counts

Fit cluster point process model

Divide Region into Quadrats

Interpret Fitted Model for Metropolis-Hastings Simulation.

Summarise Marks in Every Neighbourhood in a Point Pattern

Multitype pair correlation function

Set Control Parameters for Metropolis-Hastings Algorithm.

Read Point Pattern From Data File

Weighted Empirical Cumulative Distribution Function

Generate N Random Multitype Points

Summary of a Point Pattern Dataset

Neighbourhood density function

Murchison gold deposits

Simulate Thomas Process

Random Re-Labelling of Point Pattern

Randomly Shift a Point Pattern

Print a Fitted Point Process Model

Pair Correlation Function obtained from array of K functions

Apply Affine Transformation To Point Pattern

Plot a fitted cluster point process

Simulate Baddeley-Silverman Cell Process

Quadrature Scheme Based on Pixel Grid

Connected components of an image or window

Summary of a Line Segment Pattern Dataset

Random Perturbation of a Point Pattern

Divide Point Pattern into Sub-patterns

Simulate Simple Sequential Inhibition

Set Covariance of a Window

Nearest neighbour distances

Estimate the I-function

Perspective Plot of Pixel Image

Generate Poisson Point Pattern on Line Segments

Define Point Process Model for Metropolis-Hastings Simulation.

Fit the Thomas Point Process by Minimum Contrast

Simulate Gauss-Poisson Process

Pair Correlation Function of Point Pattern

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Q-Q Plot of Residuals from Fitted Point Process Model

Apply Vector Translation To Line Segment Pattern

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Evaluate an Expression in Each Row of a Hyperframe

Estimate window from points alone

Swedish Pines Point Pattern

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

Create a Pixel Image Object

Spruces Point Pattern

Random Thinning

Convert Polygonal Region into Different Format

Convert Line Segment Pattern to Another Unit of Length

Galaxies in the Shapley Supercluster

Summary of a Spatial Window

summary.splitppp

Summary of a Split Point Pattern

Print Brief Details of a Spatial Window

Randomly Shift a Line Segment Pattern

Distance Between Two Point Patterns

plot.hyperframe

Plot Entries in a Hyperframe

Data and Code From JRSS Discussion Paper on Residuals