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spatstat (version 1.18-2)

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. Also supports three-dimensional point patterns. 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, pixel images and tessellations. 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

16,015

Version

1.18-2

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

April 10th, 2010

Functions in spatstat (1.18-2)

Harkness-Isham ants' nests data

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Clark and Evans Aggregation Index

Estimate the J-function

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

The Strauss / Hard Core Point Process Model

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Classify Points in a Point Pattern

Diagnostics for random marking

Convert Data To Class psp

Estimate the empty space function F

Class of Images

Evaluate Expression Involving Function Arrays

Interpolate a Pixel Image

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

Centroid of a window

Multitype J Function (i-to-any)

Pairwise distances

Intersection of Two Tessellations

Geyer's Saturation Point Process Model

Distance Map of Point Pattern

Inhomogeneous Cross K Function

Multitype K Function (Cross-type)

Convert Data To Class owin

Fitted Conditional Intensity for Point Process Model

New Zealand Trees Point Pattern

complement.owin

Take Complement of a Window

K-function using FFT

Print News About Latest Version of Package

The Strauss Point Process Model

Convert Data to Hyperframe

Pairwise distances

Convert Polygonal Region into Different Format

Prediction from a Fitted Point Process Model

Print Brief Details of an Image

Hyper Data Frame

Convert Data To Tessellation

Multitype L-function (cross-type)

The Multitype Strauss Point Process Model

Diggle-Gratton model

Test Whether A Point Process Model is Marked

Point and Click Interface for Exploratory Analysis of Point Pattern

Chorley-Ribble Cancer Data

Saturated Pairwise Interaction model

Create a Point Pattern

Poisson Point Process Model

Crossing Points of Two Line Segment Patterns

Distance Map of Line Segment Pattern

Pair Correlation Function

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

Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)

The Area Interaction Point Process Model

Extract Subset of Function Values

Extract Subset of Function Array

Convert Line Segment Pattern to Binary Pixel Mask

Reset Values in Subset of Image

Difference of Disc Areas

Nearest Neighbour Distance Function G

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Evaluate Expression Involving Pixel Images

Lengths of Line Segments

Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern

Mark Correlation Function

Inhomogeneous Cross Type L Function

Compute Quadrature Weights Based on Grid Counts

Extract Subset of Image

Spherical Contact Distribution Function

Generic Pairwise Interaction model

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Bounding Box of a Window or Point Pattern

Marked Nearest Neighbour Distance Function

Subdivide a Window or Tessellation using a Set of Lines

Random Re-Labelling of Point Pattern

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Generate N Random Points

Summarise Marks in Every Neighbourhood in a Point Pattern

Apply Affine Transformation

Convert to Pixel Image

Area of a Window

Morishita Index Plot

The Soft Core Point Process Model

Convert Data to Three-Dimensional Box

Foxall's Distance Functions

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Multitype L-function (i-to-any)

Generic Ord Interaction model

Method of Minimum Contrast

Simulate systematic random point pattern

Apply Vector Translation To Window

Hutchings' Bramble Canes data

Collapse Several Function Tables into One

Reduced Second Moment Measure

Orientation Angles of Line Segments

Combine Function Value Tables

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Summary of a Point Pattern Dataset

Ord's Interaction model

Nearest neighbour distances in three dimensions

Contour plot of pixel image

Distance to Boundary of Window

Inhomogeneous Pair Correlation Function

Coefficients of Fitted Point Process Model

Apply Function to Image Broken Down by Factor

Geometrical Calculations for Three-Dimensional Box

Delaunay Triangulation of Point Pattern

plot.hyperframe

Plot Entries in a Hyperframe

pairwise.family

Pairwise Interaction Process Family

Convex Hull of Points

Plot a plotppm Object Created by plot.ppm

Plot a Spatial Window

Create a Window

Convert Pixel Image from Numeric to Factor

Inhomogeneous Multitype L Dot Function

Kernel Smoothed Intensity of Point Pattern

Test Whether Two Pixel Images Are Compatible

Interactively Define a Polygon

spatstat-deprecated

Deprecated spatstat functions

Extract Subset of Line Segment Pattern

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Make Periodic Copies of a Spatial Pattern

Apply a Function to a Point Pattern Broken Down by Factor

Beta Ganglion Cells in Cat Retina

Extract Dummy Points Used to Fit a Point Process Model

Determine Duplicated Points in a Spatial Point Pattern

Weighted Empirical Cumulative Distribution Function

Connected components of an image or window

Circular Window

Plot a List of Things

Generate a Default Pattern of Dummy Points

crossdist.default

Pairwise distances between two different sets of points

Simulate point patterns using the Metropolis-Hastings algorithm.

Concatenate x,y Coordinate Vectors

Interactively Add Points

Berman-Huntington points and lines data

Kernel Smoothing of Line Segment Pattern

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

Safely Convert Point Pattern Window to Binary Mask

Diameter of a Window

Three Dimensional Point Pattern

Extract Original Data from a Fitted Point Process Model

Three-Dimensional Box

Simulation Envelopes of Summary Function for 3D Point Pattern

Area of Part of Disc

Generate Poisson Random Line Process

Fit cluster point process model

Simulation Envelopes of Summary Function

Create a Function Value Table

Morphological Erosion

Endpoints of Line Segment Pattern

Pairwise distances between two different line segment patterns

model.matrix.ppm

Extract Design Matrix from Point Process Model

Expand Window By Factor

Areas of Morphological Dilations

Function Arrays for Spatial Patterns

inforder.family

Infinite Order Interaction Family

Extract the Interaction from a Fitted Point Process Model

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Methods for Three-Dimensional Box

Test Whether An Object Is A Fitted Point Process Model

Plot a fitted cluster point process

Ord Interaction Process Family

Histogram of Pixel Values in an Image

Find Largest Circle Inside Window

Kaplan-Meier and Reduced Sample Estimator using Histograms

Longleaf Pines Point Pattern

Mean, Median and Range of Pixel Values in an Image

Print Brief Details of a Point Pattern Dataset

Data Frames of Function Values

nearest.raster.point

Find Pixel Nearest to a Given Point

Find Line Segment Nearest to Each Point

Point and Click Interface for Displaying a Point Pattern

Print Brief Details of a Spatial Window

Prediction from a Fitted Cluster Point Process Model

Multidimensional Space-Time Point Pattern

Print a Fitted Point Process Model

multiplicity.ppp

Count Multiplicity of Duplicate Points

Murchison gold deposits

Lansing Woods Point Pattern

Nearest Neighbour Clutter Removal

Determine Whether One Window is Contained In Another

Distance for a Point Pattern Matching

Identify Points in a Point Pattern

Pairwise distances between line segments

Generate a Quadrature Scheme from a Point Pattern

Quadrature Scheme Based on Pixel Grid

Quadrat counting for a point pattern

Test Whether An Object Is A Window

Rectangular grid of points

Pair Correlation Function of Point Pattern

Evaluate Expression Involving Functions

Plot a Function Array

Neighbourhood density function

Hybrid Geyer Point Process Model

Nearest neighbour distances between line segments

Lurking variable plot

Convert Line Segment Pattern to Pixel Image

quadratresample

Resample a Point Pattern by Resampling Quadrats

Japanese Pines Point Pattern

Mark Connection Function

Perimeter Length of Window

Simulate Matern Model II

Level Set of a Pixel Image

Pairwise distances in Three Dimensions

Perfect Simulation of the Strauss Process

Simulate from a Fitted Point Process Model

plot.bermantest

Plot Result of Berman Test

Class of Fitted Point Process Models

Place Points Evenly Along Specified Lines

Convert Spatial Object to Pixel Image

Mosaic Random Field

Create a Point Matching

Randomly Shift a Point Pattern

Ponderosa Pine Tree Point Pattern

Empty Space Function of a Three-Dimensional Point Pattern

Morphological Opening

Plot a Spatial Kolmogorov-Smirnov Test

Plot a three-dimensional point pattern

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

The Hard Core Point Process Model

Generate Poisson Point Pattern on Line Segments

Convert Window to Pixel Image

Determine Initial State for Metropolis-Hastings Simulation.

project2segment

Move Point To Nearest Line

Generate Poisson Point Pattern in Three Dimensions

Simulate Simple Sequential Inhibition

Generate N Uniform Random Points in Three Dimensions

Divide Region into Quadrats

Convert Pixel Image to Another Unit of Length

Random Perturbation of a Point Pattern

Simulate Gauss-Poisson Process

Convert Point Pattern to Pixel Image

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Multitype J Function (i-to-j)

Cartesian Coordinates for a Pixel Raster

Class of Line Segment Patterns

Generate N Random Multitype Points

Distance Between Two Point Patterns

Sample Quantiles of Pixel Image

Convert Window to Another Unit of Length

Simulated Point Pattern

Simulate Thomas Process

Apply Affine Transformation To Window

Define Point Process Model for Metropolis-Hastings Simulation.

Randomly Shift a Line Segment Pattern

Convert dataset to another unit of length

Plot a Pixel Image

Union of Data and Dummy Points

Generate N Uniform Random Points in a Disc

Divide Point Pattern into Sub-patterns

Convert Point Pattern to Another Unit of Length

Marked K-Function

Rotate a Line Segment Pattern

as.data.frame.im

Convert Pixel Image to Data Frame

Divide Image Into Sub-images

Multitype K Function (i-to-any)

Sufficient Statistic of Point Process Model

Extract or Replace Subset of Tessellation

Pairwise distances between two different three-dimensional point patterns

Subset of Quadrature Scheme

Border Region of a Window

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Set Covariance of a Window

Generate grid of parallel lines with random displacement

Test Whether Two Function Objects Are Compatible

California Redwoods Point Pattern (Ripley's Subset)

Artificial Data Point Pattern

Summarizing a Quadrature Scheme

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

pppmatching.object

Class of Point Matchings

Poisson Line Tessellation

Apply Function to Every Neighbourhood in a Point Pattern

plot a Spatial Point Pattern

Convert a Window to a Polygonal Window

Hughes' Amacrine Cell Data

Compute Integral of Function Against Cumulative Distribution

Distance Map of Window

Morphological Dilation

Vertices of a Window

Random Thinning

Apply Vector Translation To Point Pattern

Summary of a Line Segment Pattern Dataset

Summarizing a Pixel Image

rshift.splitppp

Randomly Shift a List of Point Patterns

Areas of Morphological Erosions

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Approximate a Polygon by a Simpler Polygon

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Apply Vector Translation

Urkiola Woods Point Pattern

Pairwise distances between two different point patterns

Convert Data To Class ppp

Simulate Neyman-Scott Process

Summary of a Spatial Window

Rotate a Window

Apply Affine Transformation To Point Pattern

Diagnostic Plots for Fitted Point Process Model

Spatial smoothing of observations at irregular points

Difference of Disc Areas

Beta Ganglion Cells in Cat Retina, Old Version

The Piecewise Constant Pairwise Interaction Point Process Model

Test Whether An Object Is A Point Pattern

Pixel Image Approximation of a Window

Variance-Covariance Matrix for a Fitted Point Process Model

Colour Lookup Tables

Nearest neighbours in three dimensions

Swedish Pines Point Pattern

Distance Map as a Function

Summary of a List of Things

pairdist.default

Pairwise distances

Basis for Harmonic Functions

Superimpose Several Point Patterns

Create a Pixel Image Object

Estimate window from points alone

Inhomogeneous Multitype K Dot Function

Tropical rain forest trees

spatstat-internal

Internal spatstat functions

Window in Shape of Letter R

Corners of a rectangle

Saturated Pairwise Interaction Point Process Family

Point Patterns of New Brunswick Forest Fires

Biological Cells Point Pattern

Multitype pair correlation function (cross-type)

Diggle's Heather Data

Extract or Replace Subset of Point Pattern

Test Whether An Object Is Empty

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Intersection, Union or Set Subtraction of Two Windows

Combine Two Line Segment Patterns

Simulate Matern Model I

Multitype pair correlation function (i-to-any)

Exponential Energy Marks

Perspective Plot of Pixel Image

Test Whether Marks Are Present

Humberside Data on Childhood Leukaemia and Lymphoma

Convert Pixel Image to Matrix

Apply Affine Transformation To Line Segment Pattern

Plot a Colour Map

Mark Correlation Integral

Print a Quadrature Scheme

Test Whether A Point Pattern is Marked

Test whether Object is Multitype

Methods for Multidimensional Space-Time Point Patterns

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

bounding.box.xy

Convex Hull of Points

Set Control Parameters for Metropolis-Hastings Algorithm.

Generate Multitype Poisson Point Pattern

Simulate Stratified Random Point Pattern

Compute Images of Constructed Covariates

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Fit the Thomas Point Process by Minimum Contrast

Nearest neighbour

Class of Point Patterns

Extract or Replace Subset of a List of Things

Profile Maximum Pseudolikelihood

Aherne's hamster tumour data

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Extract.splitppp

Extract or Replace Sub-Patterns

Extract Unique Points from a Spatial Point Pattern

Kolmogorov-Smirnov Test for Point Process Model

Galaxies in the Shapley Supercluster

Mosaic Random Set

Estimate the I-function

rescue.rectangle

Convert Window Back To Rectangle

Simulate Baddeley-Silverman Cell Process

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Log Likelihood for Poisson Point Process Model

Weighted Histogram

Inhomogeneous K-function

Marks of a Point Pattern

Print Brief Details of a Line Segment Pattern Dataset

Class of Quadrature Schemes

Plot Function Values

Midpoints of Line Segment Pattern

spatstat-package

The Spatstat Package

Summarizing a Fitted Point Process Model

Evaluate an Expression in a Function Table

Define Point Process Model for Metropolis-Hastings Simulation.

Plot a List of Point Patterns

Interaction Distance of a Point Process

Update a Fitted Cluster Point Process Model

Berman's Tests for Point Process Model

Simulate a Fitted Cluster Point Process Model

Create a Line Segment Pattern

Dirichlet Tessellation of Point Pattern

plot a Fitted Point Process Model

Theoretical Distribution of Nearest Neighbour Distance

plot a Spatial Quadrature Scheme

Create a Tessellation

Nearest Neighbours Between Two Patterns

Cut margins from rectangle

Pine saplings in Finland.

Marked J Function

Test Whether Points Are Inside A Window

Pair Correlation Function obtained from array of K functions

K-function of a Three-Dimensional Point Pattern

Spruces Point Pattern

Residuals for Fitted Point Process Model

Plot a tessellation

Calculate four standard summary functions of a point pattern.

The Lennard-Jones Potential

Beadlet Anemones Data

summary.splitppp

Summary of a Split Point Pattern

Generate N Uniform Random Points

Test Whether An Object Is A Pixel Image

Extract List of Tiles in a Tessellation

Fit Point Process Model to Data

Read Point Pattern From Data File

Rotate a Point Pattern

Update a Fitted Point Process Model

Fry Plot of Point Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

Kaplan-Meier Estimator using Histogram Data

Name for Unit of Length

ANOVA for Fitted Point Process Models

Methods for three-dimensional point patterns

Distance to Boundary of Window

Distance to Boundary of Window

Bronze gradient filter data

Intersect Infinite Straight Lines with a Window

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Pairwise distances

Convert Line Segment Pattern to Another Unit of Length

Apply Vector Translation To Pixel Image

Morphological Closing

Apply Gaussian Blur to a Pixel Image

Apply Vector Translation To Line Segment Pattern

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

spatstat.options

Internal Options in Spatstat Package

Spokes pattern of dummy points

Infinite Straight Lines

Integral of a Pixel Image

Superimpose Several Line Segment Patterns

Data and Code From JRSS Discussion Paper on Residuals

Test Whether a Window is Convex

Number of Points in a Point Pattern

Nearest neighbour distances

Pair Correlation Function obtained from K Function

plot a Spatial Line Segment Pattern

Print Progress Reports

Extract Quadrature Scheme Used to Fit a Point Process Model

Q-Q Plot of Residuals from Fitted Point Process Model

Simulate Matern Cluster Process

Reduced Sample Estimator using Histogram Data

California Redwoods Point Pattern (Entire Dataset)

Interpret Fitted Model for Metropolis-Hastings Simulation.

Simulate a Fitted Gibbs Point Process Model

Generate Poisson Point Pattern