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spatstat (version 1.16-3)

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

16,590

Version

1.16-3

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

October 13th, 2009

Functions in spatstat (1.16-3)

Extract Subset of Function Values

Extract or Replace Subset of a List of Things

The Multitype Strauss Point Process Model

Subset of Quadrature Scheme

Generic Ord Interaction model

Apply Affine Transformation To Point Pattern

Convert Data To Class owin

Multitype L-function (cross-type)

complement.owin

Take Complement of a Window

Test whether Object is Multitype

Inhomogeneous Cross Type L Function

Window in Shape of Letter R

Multitype L-function (i-to-any)

Orientation Angles of Line Segments

Multitype J Function (i-to-j)

Extract.splitppp

Extract or Replace Sub-Patterns

Reduced Second Moment Measure

Difference of Disc Areas

Diagnostics for random marking

Estimate the empty space function F

The Lennard-Jones Potential

The Piecewise Constant Pairwise Interaction Point Process Model

Extract or Replace Subset of Tessellation

Distance to Boundary of Window

Marked K-Function

Generic Pairwise Interaction model

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Marked J Function

Hughes' Amacrine Cell Data

Area of a Window

Coefficients of Fitted Point Process Model

Evaluate Expression Involving Functions

Aherne's hamster tumour data

Convex Hull of Points

The Soft Core Point Process Model

Centroid of a window

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Multitype J Function (i-to-any)

Concatenate x,y Coordinate Vectors

inforder.family

Infinite Order Interaction Family

K-function using FFT

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Pixel Image Approximation of a Window

Convert Pixel Image from Numeric to Factor

Distance for a Point Pattern Matching

Hybrid Geyer Point Process Model

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Saturated Pairwise Interaction model

Convert Window to Pixel Image

Subdivide a Window or Tessellation using a Set of Lines

Create a Point Matching

Biological Cells Point Pattern

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

Kernel Smoothed Intensity of Point Pattern

Extract Subset of Line Segment Pattern

Distance to Boundary of Window

Poisson Point Process Model

Pairwise distances between two different point patterns

Apply Affine Transformation

Apply Affine Transformation To Window

The Strauss Point Process Model

Dirichlet Tessellation of Point Pattern

Inhomogeneous Multitype K Dot Function

Mark Correlation Integral

Apply Affine Transformation To Line Segment Pattern

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

Extract Dummy Points Used to Fit a Point Process Model

Extract or Replace Subset of Point Pattern

Beadlet Anemones Data

Apply Function to Image Broken Down by Factor

Nearest neighbour distances between line segments

Lansing Woods Point Pattern

Extract Subset of Image

Convert Data To Class ppp

Evaluate Expression Involving Function Arrays

Apply Gaussian Blur to a Pixel Image

Corners of a rectangle

Diggle's Heather Data

Generate a Default Pattern of Dummy Points

crossdist.default

Pairwise distances between two different sets of points

Inhomogeneous Multitype L Dot Function

Distance Map of Point Pattern

Marked Nearest Neighbour Distance Function

Intersection or Union of Two Windows

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Ord's Interaction model

Extract Subset of Function Array

Murchison gold deposits

Test Whether An Object Is Empty

Kaplan-Meier Estimator using Histogram Data

plot.hyperframe

Plot Entries in a Hyperframe

Create a Window

Nearest Neighbours Between Two Patterns

Kernel Smoothing of Line Segment Pattern

Multitype K Function (i-to-any)

Mosaic Random Set

Determine Whether One Window is Contained In Another

The Area Interaction Point Process Model

Inhomogeneous Cross K Function

The Strauss / Hard Core Point Process Model

Pair Correlation Function of Point Pattern

Pine saplings in Finland.

Plot a Spatial Window

bounding.box.xy

Convex Hull of Points

Point and Click Interface for Displaying a Point Pattern

Morphological Dilation

Weighted Empirical Cumulative Distribution Function

Clark and Evans Aggregation Index

Determine Initial State for Metropolis-Hastings Simulation.

Mosaic Random Field

Nearest Neighbour Distance Function G

Extract Original Data from a Fitted Point Process Model

ANOVA for Fitted Point Process Models

Test Whether a Window is Convex

Diggle-Gratton model

Beta Ganglion Cells in Cat Retina

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Reset Values in Subset of Image

Circular Window

Convert Data To Tessellation

spatstat-internal

Internal spatstat functions

Distance Map as a Function

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Combine Two Line Segment Patterns

Convert Pixel Image to Matrix

plot a Spatial Point Pattern

Chorley-Ribble Cancer Data

Distance Map of Window

Determine Duplicated Points in a Spatial Point Pattern

Interpret Fitted Model for Metropolis-Hastings Simulation.

Rotate a Point Pattern

Area of Part of Disc

Connected components of an image or window

Bounding Box of a Window or Point Pattern

Interactively Add Points

Test Whether Two Pixel Images Are Compatible

Divide Image Into Sub-images

Set or Reset the Marks in a Point Pattern

Identify Points in a Point Pattern

plot.bermantest

Plot Result of Berman Test

Multitype K Function (Cross-type)

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Estimate the I-function

Convert to Pixel Image

Nearest neighbour distances

Crossing Points of Two Line Segment Patterns

Delaunay Triangulation of Point Pattern

Mean, Median and Range of Pixel Values in an Image

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Fit cluster point process model

Harkness-Isham ants' nests data

Apply Function to Every Neighbourhood in a Point Pattern

Distance Map of Line Segment Pattern

Areas of Morphological Dilations

Class of Line Segment Patterns

Hutchings' Bramble Canes data

Compute Images of Constructed Covariates

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

Classify Points in a Point Pattern

Print Brief Details of an Image

project2segment

Move Point To Nearest Line

Perspective Plot of Pixel Image

Fry Plot of Point Pattern

Convert Spatial Object to Pixel Image

Convert Point Pattern to Pixel Image

Inhomogeneous K-function

pairwise.family

Pairwise Interaction Process Family

Fit the Matern Cluster Point Process by Minimum Contrast

Plot a Colour Map

Difference of Disc Areas

Ord Interaction Process Family

Diameter of a Window

Convert a Window to a Polygonal Window

Infinite Straight Lines

Tropical rain forest trees

Print a Fitted Point Process Model

Simulate Gauss-Poisson Process

summary.splitppp

Summary of a Split Point Pattern

Prediction from a Fitted Point Process Model

Diagnostic Plots for Fitted Point Process Model

pppmatching.object

Class of Point Matchings

Intersection of Two Tessellations

Endpoints of Line Segment Pattern

Function Arrays for Spatial Patterns

Longleaf Pines Point Pattern

Simulate Neyman-Scott Process

Mark Connection Function

Generate grid of parallel lines with random displacement

Rectangular grid of points

Summarizing a Fitted Point Process Model

Summary of a Spatial Window

Histogram of Pixel Values in an Image

Beta Ganglion Cells in Cat Retina, Old Version

Find Largest Circle Inside Window

Pairwise distances

Test Whether Points Are Inside A Window

Sample Quantiles of Pixel Image

Exponential Energy Marks

Kaplan-Meier and Reduced Sample Estimator using Histograms

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Method of Minimum Contrast

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Saturated Pairwise Interaction Point Process Family

Compute Integral of Function Against Cumulative Distribution

Convert Pixel Image to Another Unit of Length

Plot a tessellation

Japanese Pines Point Pattern

Test Whether A Point Process Model is Marked

Humberside Data on Childhood Leukaemia and Lymphoma

Set Control Parameters for Metropolis-Hastings Algorithm.

Pairwise distances

Mark Correlation Function

Morphological Erosion

Spherical Contact Distribution Function

Ponderosa Pine Tree Point Pattern

Summary of a List of Things

Areas of Morphological Erosions

Q-Q Plot of Residuals from Fitted Point Process Model

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Pairwise distances between line segments

Berman's Tests for Point Process Model

Update a Fitted Cluster Point Process Model

Plot Function Values

Vertices of a Window

Log Likelihood for Poisson Point Process Model

Pairwise distances between two different line segment patterns

Plot a List of Things

Convert Point Pattern to Another Unit of Length

Convert Data To Class psp

Lurking variable plot

Quadrat counting for a point pattern

spatstat-deprecated

Deprecated spatstat functions

Class of Images

Random Re-Labelling of Point Pattern

Summarise Marks in Every Neighbourhood in a Point Pattern

Apply a Function to a Point Pattern Broken Down by Factor

rescue.rectangle

Convert Window Back To Rectangle

Pairwise distances

Point and Click Interface for Exploratory Analysis of Point Pattern

Test Whether Marks Are Present

Plot a Pixel Image

Simulation envelopes of summary function

Define Point Process Model for Metropolis-Hastings Simulation.

spatstat-package

The Spatstat Package

Evaluate an Expression in Each Row of a Hyperframe

Residuals for Fitted Point Process Model

Profile Maximum Pseudolikelihood

Berman-Huntington points and lines data

Random Thinning

Expand Window By Factor

Apply Vector Translation To Point Pattern

Rotate a Window

Test Whether An Object Is A Point Pattern

Compute Quadrature Weights Based on Grid Counts

Safely Convert Point Pattern Window to Binary Mask

Generate Poisson Point Pattern

Generate a Quadrature Scheme from a Point Pattern

Contour plot of pixel image

Apply Vector Translation To Line Segment Pattern

Data and Code From JRSS Discussion Paper on Residuals

Create a Point Pattern

Test Whether An Object Is A Window

Simulate Stratified Random Point Pattern

Simulate a Fitted Gibbs Point Process Model

Create a Tessellation

Perfect Simulation of the Strauss Process

Neighbourhood density function

Place Points Evenly Along Specified Lines

Lengths of Line Segments

Point Patterns of New Brunswick Forest Fires

Union of Data and Dummy Points

Extract Unique Points from a Spatial Point Pattern

Level Set of a Pixel Image

model.matrix.ppm

Extract Design Matrix from Point Process Model

Variance-Covariance Matrix for a Fitted Point Process Model

Fitted Conditional Intensity for Point Process Model

nearest.raster.point

Find Pixel Nearest to a Given Point

Extract List of Tiles in a Tessellation

Morphological Opening

Read Point Pattern From Data File

Simulate systematic random point pattern

Class of Point Patterns

Pair Correlation Function

Print a Quadrature Scheme

Plot a fitted cluster point process

plot a Spatial Quadrature Scheme

Perimeter Length of Window

Pair Correlation Function obtained from K Function

Plot a Function Array

Summary of a Point Pattern Dataset

Extract Quadrature Scheme Used to Fit a Point Process Model

Define Point Process Model for Metropolis-Hastings Simulation.

Summarizing a Pixel Image

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Print Progress Reports

Print Brief Details of a Point Pattern Dataset

Morishita Index Plot

Simulate Thomas Process

Simulate point patterns using the Metropolis-Hastings algorithm.

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

Create a Line Segment Pattern

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

Convert Polygonal Region into Different Format

Estimate the J-function

rshift.splitppp

Randomly Shift a List of Point Patterns

Poisson Line Tessellation

Generate N Uniform Random Points in a Disc

Set Covariance of a Window

Evaluate Expression Involving Pixel Images

Convert Line Segment Pattern to Another Unit of Length

Print Brief Details of a Spatial Window

Spokes pattern of dummy points

Test Whether An Object Is A Fitted Point Process Model

Interaction Distance of a Point Process

Superimpose Several Line Segment Patterns

Find Line Segment Nearest to Each Point

Data Frames of Function Values

Reduced Sample Estimator using Histogram Data

Kolmogorov-Smirnov Test for Point Process Model

Pair Correlation Function obtained from array of K functions

Nearest neighbour

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Multitype pair correlation function

Basis for Harmonic Functions

plot a Spatial Line Segment Pattern

Create a Pixel Image Object

Plot a Spatial Kolmogorov-Smirnov Test

Random Perturbation of a Point Pattern

Distance Between Two Point Patterns

Estimate window from points alone

Spruces Point Pattern

Test Whether An Object Is A Pixel Image

Generate Poisson Point Pattern on Line Segments

Morphological Closing

California Redwoods Point Pattern (Entire Dataset)

Divide Point Pattern into Sub-patterns

Class of Fitted Point Process Models

Extract the Interaction from a Fitted Point Process Model

Rotate a Line Segment Pattern

Update a Fitted Point Process Model

Urkiola Woods Point Pattern

Artificial Data Point Pattern

Generate Poisson Random Line Process

Test Whether A Point Pattern is Marked

Plot a List of Point Patterns

plot a Fitted Point Process Model

Swedish Pines Point Pattern

Name for Unit of Length

Print Brief Details of a Line Segment Pattern Dataset

Apply Vector Translation To Pixel Image

Apply Vector Translation

Sufficient Statistic of Point Process Model

Simulate Matern Cluster Process

Generate N Uniform Random Points

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Approximate a Polygon by a Simpler Polygon

Generate Multitype Poisson Point Pattern

Summarizing a Quadrature Scheme

Fit the Thomas Point Process by Minimum Contrast

Simulate Simple Sequential Inhibition

Simulated Point Pattern

Intersect Infinite Straight Lines with a Window

Midpoints of Line Segment Pattern

Colour Lookup Tables

quadratresample

Resample a Point Pattern by Resampling Quadrats

Spatial smoothing of observations at irregular points

Summary of a Line Segment Pattern Dataset

Evaluate an Expression in a Function Table

spatstat.options

Internal Options in Spatstat Package

Simulate a Fitted Cluster Point Process Model

pairdist.default

Pairwise distances

Convert dataset to another unit of length

California Redwoods Point Pattern (Ripley's Subset)

Convert Window to Another Unit of Length

Cartesian Coordinates for a Pixel Raster

Simulate from a Fitted Point Process Model

Cut margins from rectangle

Randomly Shift a Point Pattern

Generate N Random Points

Fit Point Process Model to Data

Generate N Random Multitype Points

Apply Vector Translation To Window

Geyer's Saturation Point Process Model

Calculate four standard summary functions of a point pattern.

Interactively Define a Polygon

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Test Whether Two Function Objects Are Compatible

Interpolate a Pixel Image

Hyper Data Frame

New Zealand Trees Point Pattern

multiplicity.ppp

Count Multiplicity of Duplicate Points

Quadrature Scheme Based on Pixel Grid

Plot a plotppm Object Created by plot.ppm

Class of Quadrature Schemes

Simulate Baddeley-Silverman Cell Process

Divide Region into Quadrats

Simulate Matern Model I

Prediction from a Fitted Cluster Point Process Model

Simulate Matern Model II

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Randomly Shift a Line Segment Pattern

Galaxies in the Shapley Supercluster

Superimpose Several Point Patterns