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spatstat (version 1.17-0)

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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Install

install.packages('spatstat')

Monthly Downloads

16,015

Version

1.17-0

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

October 22nd, 2009

Functions in spatstat (1.17-0)

Marked Nearest Neighbour Distance Function

Multitype K Function (Cross-type)

Multitype K Function (i-to-any)

Estimate the I-function

Diagnostics for random marking

Extract.splitppp

Extract or Replace Sub-Patterns

Hybrid Geyer Point Process Model

Spherical Contact Distribution Function

Inhomogeneous K-function

Multitype L-function (cross-type)

Inhomogeneous Cross K Function

Extract Subset of Image

Saturated Pairwise Interaction model

Extract or Replace Subset of Tessellation

Extract Subset of Function Values

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Nearest Neighbour Distance Function G

Marked K-Function

Inhomogeneous Cross Type L Function

Extract or Replace Subset of a List of Things

Interactively Add Points

Generic Pairwise Interaction model

Multitype J Function (i-to-any)

Convert Pixel Image to Matrix

Estimate the empty space function F

K-function using FFT

Orientation Angles of Line Segments

Inhomogeneous Multitype K Dot Function

Apply Affine Transformation

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

Geyer's Saturation Point Process Model

Extract Subset of Function Array

Multitype J Function (i-to-j)

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

Generic Ord Interaction model

complement.owin

Take Complement of a Window

Convert a Window to a Polygonal Window

Multitype L-function (i-to-any)

Difference of Disc Areas

The Strauss Point Process Model

Artificial Data Point Pattern

Biological Cells Point Pattern

The Area Interaction Point Process Model

Reduced Second Moment Measure

Morphological Closing

Diggle-Gratton model

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Marked J Function

Simulation envelopes of summary function

Convert Data To Tessellation

Apply Affine Transformation To Line Segment Pattern

Beta Ganglion Cells in Cat Retina

ANOVA for Fitted Point Process Models

Evaluate Expression Involving Functions

Hutchings' Bramble Canes data

The Soft Core Point Process Model

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

The Piecewise Constant Pairwise Interaction Point Process Model

The Multitype Strauss Point Process Model

Pixel Image Approximation of a Window

Difference of Disc Areas

Generate a Default Pattern of Dummy Points

bounding.box.xy

Convex Hull of Points

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Subset of Quadrature Scheme

Apply Function to Image Broken Down by Factor

Beadlet Anemones Data

Hughes' Amacrine Cell Data

Apply Affine Transformation To Window

Bronze gradient filter data

The Lennard-Jones Potential

Harkness-Isham ants' nests data

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Colour Lookup Tables

Function Arrays for Spatial Patterns

Expand Window By Factor

Apply Affine Transformation To Point Pattern

Convert to Pixel Image

Ord's Interaction model

Convert Data To Class ppp

Distance to Boundary of Window

Calculate four standard summary functions of a point pattern.

Extract Subset of Line Segment Pattern

Inhomogeneous Multitype L Dot Function

Determine Duplicated Points in a Spatial Point Pattern

The Strauss / Hard Core Point Process Model

Convert Data To Class psp

Extract or Replace Subset of Point Pattern

Estimate the J-function

Intersection of Two Tessellations

Apply Function to Every Neighbourhood in a Point Pattern

Hyper Data Frame

Morphological Dilation

Reset Values in Subset of Image

Distance Map of Point Pattern

Interactively Define a Polygon

Apply a Function to a Point Pattern Broken Down by Factor

Berman-Huntington points and lines data

Tropical rain forest trees

spatstat-internal

Internal spatstat functions

Corners of a rectangle

Area of a Window

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Create a Point Matching

Poisson Point Process Model

Convert Pixel Image from Numeric to Factor

Lengths of Line Segments

Chorley-Ribble Cancer Data

Area of Part of Disc

Contour plot of pixel image

Combine Two Line Segment Patterns

Distance to Boundary of Window

Extract Original Data from a Fitted Point Process Model

Endpoints of Line Segment Pattern

Level Set of a Pixel Image

spatstat-deprecated

Deprecated spatstat functions

Evaluate Expression Involving Function Arrays

crossdist.default

Pairwise distances between two different sets of points

Test Whether Two Function Objects Are Compatible

Diameter of a Window

Convert Data To Class owin

Ord Interaction Process Family

Berman's Tests for Point Process Model

Point and Click Interface for Displaying a Point Pattern

Kernel Smoothed Intensity of Point Pattern

Distance Map of Window

Diagnostic Plots for Fitted Point Process Model

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Compute Quadrature Weights Based on Grid Counts

Mean, Median and Range of Pixel Values in an Image

Centroid of a window

Clark and Evans Aggregation Index

Test Whether An Object Is A Window

Weighted Empirical Cumulative Distribution Function

Diggle's Heather Data

Pairwise distances

Delaunay Triangulation of Point Pattern

Class of Line Segment Patterns

Kaplan-Meier and Reduced Sample Estimator using Histograms

plot a Fitted Point Process Model

Convert Polygonal Region into Different Format

Evaluate Expression Involving Pixel Images

Bounding Box of a Window or Point Pattern

Perfect Simulation of the Strauss Process

Test Whether Two Pixel Images Are Compatible

Distance Map of Line Segment Pattern

Log Likelihood for Poisson Point Process Model

plot.hyperframe

Plot Entries in a Hyperframe

Nearest neighbour distances

Nearest Neighbours Between Two Patterns

Exponential Energy Marks

Subdivide a Window or Tessellation using a Set of Lines

Safely Convert Point Pattern Window to Binary Mask

Quadrat counting for a point pattern

Test Whether An Object Is Empty

Pine saplings in Finland.

Pair Correlation Function obtained from array of K functions

Crossing Points of Two Line Segment Patterns

Test Whether Points Are Inside A Window

Pair Correlation Function of Point Pattern

Concatenate x,y Coordinate Vectors

Evaluate an Expression in Each Row of a Hyperframe

Plot a Colour Map

Intersect Infinite Straight Lines with a Window

Nearest neighbour distances between line segments

Random Thinning

Perspective Plot of Pixel Image

Plot a Pixel Image

Simulate Simple Sequential Inhibition

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Infinite Straight Lines

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Connected components of an image or window

Dirichlet Tessellation of Point Pattern

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Kernel Smoothing of Line Segment Pattern

Plot a Function Array

Basis for Harmonic Functions

Morphological Erosion

Fit cluster point process model

Lurking variable plot

Window in Shape of Letter R

Poisson Line Tessellation

Print a Fitted Point Process Model

Kaplan-Meier Estimator using Histogram Data

Fry Plot of Point Pattern

Profile Maximum Pseudolikelihood

Pair Correlation Function

Pairwise distances

Aherne's hamster tumour data

Test Whether a Window is Convex

Test Whether Marks Are Present

Japanese Pines Point Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Test Whether An Object Is A Fitted Point Process Model

Generate Multitype Poisson Point Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

pairdist.default

Pairwise distances

Humberside Data on Childhood Leukaemia and Lymphoma

Test Whether A Point Pattern is Marked

Midpoints of Line Segment Pattern

Plot a Spatial Window

Histogram of Pixel Values in an Image

Fit Point Process Model to Data

Coefficients of Fitted Point Process Model

Create a Pixel Image Object

Test Whether An Object Is A Pixel Image

Test Whether A Point Process Model is Marked

spatstat.options

Internal Options in Spatstat Package

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

Pair Correlation Function obtained from K Function

Extract Quadrature Scheme Used to Fit a Point Process Model

Intersection or Union of Two Windows

Distance Map as a Function

Compute Images of Constructed Covariates

Simulate systematic random point pattern

Create a Tessellation

Rectangular grid of points

Apply Gaussian Blur to a Pixel Image

Data Frames of Function Values

Identify Points in a Point Pattern

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Ponderosa Pine Tree Point Pattern

inforder.family

Infinite Order Interaction Family

Fitted Conditional Intensity for Point Process Model

Convex Hull of Points

Plot a fitted cluster point process

Create a Point Pattern

Summarizing a Quadrature Scheme

Extract Dummy Points Used to Fit a Point Process Model

Murchison gold deposits

Interaction Distance of a Point Process

Galaxies in the Shapley Supercluster

Point Patterns of New Brunswick Forest Fires

New Zealand Trees Point Pattern

Determine Whether One Window is Contained In Another

Generate Poisson Random Line Process

Interpolate a Pixel Image

plot a Spatial Quadrature Scheme

Classify Points in a Point Pattern

Mosaic Random Set

Circular Window

Pairwise distances between two different point patterns

model.matrix.ppm

Extract Design Matrix from Point Process Model

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Test whether Object is Multitype

Generate N Uniform Random Points in a Disc

Saturated Pairwise Interaction Point Process Family

Class of Point Patterns

Place Points Evenly Along Specified Lines

Extract the Interaction from a Fitted Point Process Model

Mark Correlation Function

Simulate Gauss-Poisson Process

Simulate Thomas Process

Divide Region into Quadrats

Areas of Morphological Dilations

Generate a Quadrature Scheme from a Point Pattern

Randomly Shift a Point Pattern

nearest.raster.point

Find Pixel Nearest to a Given Point

Method of Minimum Contrast

Prediction from a Fitted Point Process Model

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Kolmogorov-Smirnov Test for Point Process Model

Simulate Baddeley-Silverman Cell Process

Pairwise distances between two different line segment patterns

Pairwise distances

Set Control Parameters for Metropolis-Hastings Algorithm.

Class of Images

Simulate Matern Model II

Neighbourhood density function

Summary of a Spatial Window

Simulate Neyman-Scott Process

pppmatching.object

Class of Point Matchings

Nearest-Neighbour Correlation Indices of Marked Point Pattern

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Print Progress Reports

Find Largest Circle Inside Window

Class of Fitted Point Process Models

Morishita Index Plot

Cartesian Coordinates for a Pixel Raster

Beta Ganglion Cells in Cat Retina, Old Version

Lansing Woods Point Pattern

Print Brief Details of a Spatial Window

Print Brief Details of a Line Segment Pattern Dataset

Create a Window

Plot a tessellation

California Redwoods Point Pattern (Ripley's Subset)

Areas of Morphological Erosions

project2segment

Move Point To Nearest Line

Plot a List of Things

Spokes pattern of dummy points

Find Line Segment Nearest to Each Point

Superimpose Several Line Segment Patterns

Extract Unique Points from a Spatial Point Pattern

Simulate a Fitted Cluster Point Process Model

Rotate a Point Pattern

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Test Whether An Object Is A Point Pattern

Distance for a Point Pattern Matching

Distance Between Two Point Patterns

plot a Spatial Line Segment Pattern

Print Brief Details of a Point Pattern Dataset

Variance-Covariance Matrix for a Fitted Point Process Model

Apply Vector Translation To Line Segment Pattern

Generate Poisson Point Pattern on Line Segments

Print Brief Details of an Image

Morphological Opening

Summary of a Line Segment Pattern Dataset

Convert Window to Another Unit of Length

Point and Click Interface for Exploratory Analysis of Point Pattern

Convert Window to Pixel Image

plot a Spatial Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

multiplicity.ppp

Count Multiplicity of Duplicate Points

Simulate point patterns using the Metropolis-Hastings algorithm.

Generate N Random Multitype Points

pairwise.family

Pairwise Interaction Process Family

Perimeter Length of Window

Longleaf Pines Point Pattern

plot.bermantest

Plot Result of Berman Test

Print a Quadrature Scheme

Reduced Sample Estimator using Histogram Data

Mark Correlation Integral

Apply Vector Translation To Point Pattern

Union of Data and Dummy Points

Residuals for Fitted Point Process Model

Convert Pixel Image to Another Unit of Length

Multitype pair correlation function

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

Quadrature Scheme Based on Pixel Grid

Simulate a Fitted Gibbs Point Process Model

Estimate window from points alone

Simulate Stratified Random Point Pattern

Rotate a Window

Create a Line Segment Pattern

Mosaic Random Field

Nearest neighbour

Summarise Marks in Every Neighbourhood in a Point Pattern

Generate grid of parallel lines with random displacement

Data and Code From JRSS Discussion Paper on Residuals

rescue.rectangle

Convert Window Back To Rectangle

Generate N Random Points

Plot a List of Point Patterns

Simulate Matern Cluster Process

Generate Poisson Point Pattern

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Random Perturbation of a Point Pattern

Set or Reset the Marks in a Point Pattern

Compute Integral of Function Against Cumulative Distribution

Name for Unit of Length

Spruces Point Pattern

Approximate a Polygon by a Simpler Polygon

Fit the Thomas Point Process by Minimum Contrast

Sample Quantiles of Pixel Image

Mark Connection Function

Read Point Pattern From Data File

Simulate from a Fitted Point Process Model

Convert Point Pattern to Another Unit of Length

Summarizing a Fitted Point Process Model

Randomly Shift a Line Segment Pattern

Convert Point Pattern to Pixel Image

summary.splitppp

Summary of a Split Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Random Re-Labelling of Point Pattern

Divide Point Pattern into Sub-patterns

Convert Spatial Object to Pixel Image

quadratresample

Resample a Point Pattern by Resampling Quadrats

Generate N Uniform Random Points

Apply Vector Translation To Window

Apply Vector Translation

Extract List of Tiles in a Tessellation

Swedish Pines Point Pattern

Evaluate an Expression in a Function Table

Q-Q Plot of Residuals from Fitted Point Process Model

Plot a plotppm Object Created by plot.ppm

Interpret Fitted Model for Metropolis-Hastings Simulation.

Pairwise distances between line segments

Prediction from a Fitted Cluster Point Process Model

California Redwoods Point Pattern (Entire Dataset)

rshift.splitppp

Randomly Shift a List of Point Patterns

Plot a Spatial Kolmogorov-Smirnov Test

Divide Image Into Sub-images

Rotate a Line Segment Pattern

Summary of a Point Pattern Dataset

Convert Line Segment Pattern to Another Unit of Length

Cut margins from rectangle

spatstat-package

The Spatstat Package

Apply Vector Translation To Pixel Image

Simulated Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Set Covariance of a Window

Summarizing a Pixel Image

Superimpose Several Point Patterns

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

Summary of a List of Things

Sufficient Statistic of Point Process Model

Update a Fitted Point Process Model

Update a Fitted Cluster Point Process Model

Urkiola Woods Point Pattern

Plot Function Values

Class of Quadrature Schemes

Simulate Matern Model I

Convert dataset to another unit of length

Spatial smoothing of observations at irregular points

Vertices of a Window