Learn R Programming

⚠️There's a newer version (3.3-1) of this package.Take me there.

spatstat (version 1.19-1)

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, and space-time point patterns in any number of dimensions. 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).

Copy Link

Version

Install

install.packages('spatstat')

Monthly Downloads

17,668

Version

1.19-1

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

May 25th, 2010

Functions in spatstat (1.19-1)

Multitype J Function (i-to-j)

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Harkness-Isham ants' nests data

Classify Points in a Point Pattern

Convex Hull of Points

Poisson Point Process Model

Distance Map of Window

Method of Minimum Contrast

Summarise Marks in Every Neighbourhood in a Point Pattern

Methods for Three-Dimensional Box

Convert Pixel Image from Numeric to Factor

Spherical Contact Distribution Function

Apply Affine Transformation To Point Pattern

Estimate the I-function

Extract Subset of Function Values

Extract.splitppp

Extract or Replace Sub-Patterns

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

Beta Ganglion Cells in Cat Retina

Multitype L-function (cross-type)

Inhomogeneous Cross Type L Function

Generic Pairwise Interaction model

Chorley-Ribble Cancer Data

Point Patterns of New Brunswick Forest Fires

Test Whether Two Pixel Images Are Compatible

The Multitype Strauss Point Process Model

Calculate four standard summary functions of a point pattern.

The Soft Core Point Process Model

K-function using FFT

pppmatching.object

Class of Point Matchings

The Strauss / Hard Core Point Process Model

Pairwise distances

Marked J Function

Simulate Thomas Process

Fitted Conditional Intensity for Point Process Model

Interactively Define a Polygon

The Hard Core Point Process Model

Convert Line Segment Pattern to Binary Pixel Mask

Multitype K Function (i-to-any)

Convert Pixel Image to Matrix

Extract or Replace Subset of a List of Things

Distance to Boundary of Window

Convert a Window to a Polygonal Window

Centroid of a window

Diggle-Gratton model

Crossing Points of Two Line Segment Patterns

Generate a Default Pattern of Dummy Points

Clark and Evans Aggregation Index

Extract Subset of Image

Generic Ord Interaction model

Berman's Tests for Point Process Model

Convert to Pixel Image

The Strauss Point Process Model

ANOVA for Fitted Point Process Models

Expand Window By Factor

Nearest Neighbour Distance Function G

Pairwise distances between two different line segment patterns

Evaluate Expression Involving Functions

Create a Window

Multitype pair correlation function (cross-type)

Compute Quadrature Weights Based on Grid Counts

Random Re-Labelling of Point Pattern

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

Collapse Several Function Tables into One

Delaunay Triangulation of Point Pattern

Reset Values in Subset of Image

Print Brief Details of a Point Pattern Dataset

California Redwoods Point Pattern (Entire Dataset)

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

Pairwise distances between two different point patterns

Point and Click Interface for Exploratory Analysis of Point Pattern

Kolmogorov-Smirnov Test for Point Process Model

Bounding Box of a Window or Point Pattern

Point and Click Interface for Displaying a Point Pattern

Convert Data To Tessellation

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Evaluate Expression Involving Function Arrays

bounding.box.xy

Convex Hull of Points

Compute Images of Constructed Covariates

Marks of a Point Pattern

Biological Cells Point Pattern

Lansing Woods Point Pattern

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Three-Dimensional Box

Artificial Data Point Pattern

Test Whether An Object Is A Pixel Image

Diagnostics for random marking

Kaplan-Meier and Reduced Sample Estimator using Histograms

Identify Points in a Point Pattern

Difference of Disc Areas

Apply Affine Transformation To Line Segment Pattern

Apply Gaussian Blur to a Pixel Image

Subset of Quadrature Scheme

Convert Spatial Object to Pixel Image

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Inhomogeneous Cross K Function

Areas of Morphological Dilations

Nearest Neighbour Distances in Any Dimensions

Nearest Neighbour Clutter Removal

Make Periodic Copies of a Spatial Pattern

Simulate a Fitted Cluster Point Process Model

Distance Map as a Function

Log Likelihood for Poisson Point Process Model

Apply Vector Translation To Line Segment Pattern

Interpolate a Pixel Image

Geometrical Calculations for Multi-Dimensional Box

Create a Pixel Image Object

Define Point Process Model for Metropolis-Hastings Simulation.

Test Whether An Object Is A Window

Prediction from a Fitted Cluster Point Process Model

Print Brief Details of an Image

Inhomogeneous K-function

Nearest neighbour distances in three dimensions

Coefficients of Fitted Point Process Model

Weighted Empirical Cumulative Distribution Function

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Area of a Window

Difference of Disc Areas

Contour plot of pixel image

Summarizing a Fitted Point Process Model

Foxall's Distance Functions

Mark Connection Function

Morphological Closing

Pairwise Distances in Any Dimensions

Estimate the J-function

Test Whether a Window is Convex

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Perspective Plot of Pixel Image

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Area of Part of Disc

Midpoints of Line Segment Pattern

Estimate window from points alone

Level Set of a Pixel Image

Pixel Image Approximation of a Window

Three Dimensional Point Pattern

Multitype K Function (Cross-type)

Simulation Envelopes of Summary Function for 3D Point Pattern

Perimeter Length of Window

Diggle's Heather Data

The Piecewise Constant Pairwise Interaction Point Process Model

Extract Original Data from a Fitted Point Process Model

Distance Map of Line Segment Pattern

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Extract or Replace Subset of Tessellation

Convert Polygonal Region into Different Format

Hybrid Geyer Point Process Model

The Area Interaction Point Process Model

Extract Dummy Points Used to Fit a Point Process Model

Sample Quantiles of Pixel Image

Plot a List of Point Patterns

Class of Point Patterns

Test Whether An Object Is A Point Pattern

Estimate the empty space function F

Evaluate Expression Involving Pixel Images

Convert Line Segment Pattern to Pixel Image

spatstat-internal

Internal spatstat functions

Hutchings' Bramble Canes data

Diagnostic Plots for Fitted Point Process Model

Geyer's Saturation Point Process Model

Combine Function Value Tables

California Redwoods Point Pattern (Ripley's Subset)

Spatial smoothing of observations at irregular points

Diameter of an Object

Mark Correlation Integral

Simulate Matern Model II

Convert Data To Class psp

Geometrical Calculations for Three-Dimensional Box

Print a Quadrature Scheme

Convert Window to Pixel Image

Test Whether Marks Are Present

Apply a Function to a Point Pattern Broken Down by Factor

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

Lurking variable plot

Plot a Pixel Image

Multidimensional Space-Time Point Pattern

Print News About Latest Version of Package

Apply Vector Translation

Subdivide a Window or Tessellation using a Set of Lines

Humberside Data on Childhood Leukaemia and Lymphoma

Combine Two Line Segment Patterns

crossdist.default

Pairwise distances between two different sets of points

Create a Function Value Table

Murchison gold deposits

Interactively Add Points

Test Whether A Point Process Model is Marked

Plot a tessellation

Convert Data To Class owin

Spruces Point Pattern

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Aherne's hamster tumour data

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Convert Line Segment Pattern to Another Unit of Length

Infinite Straight Lines

Nearest Neighbours Between Two Patterns

Summary of a Point Pattern Dataset

project2segment

Move Point To Nearest Line

Neighbourhood density function

Tropical rain forest trees

Methods for Multi-Dimensional Box

Methods for Multidimensional Space-Time Point Patterns

Generate N Uniform Random Points in Three Dimensions

Bronze gradient filter data

Apply Affine Transformation

Distance Between Two Point Patterns

Plot a Colour Map

Kaplan-Meier Estimator using Histogram Data

Simulate Simple Sequential Inhibition

Generate N Uniform Random Points in a Disc

Summary of a Spatial Window

Profile Maximum Pseudolikelihood

Distance to Boundary of Window

Distance for a Point Pattern Matching

Extract Subset of Line Segment Pattern

Intersect Infinite Straight Lines with a Window

Convert Data to Three-Dimensional Box

Distance Map of Point Pattern

Concatenate x,y Coordinate Vectors

Simulate Matern Model I

Multitype L-function (i-to-any)

Lengths of Line Segments

Apply Function to Image Broken Down by Factor

Colour Lookup Tables

The Lennard-Jones Potential

Saturated Pairwise Interaction model

Pine saplings in Finland.

Empty Space Function of a Three-Dimensional Point Pattern

Fit the Thomas Point Process by Minimum Contrast

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

Extract the Interaction from a Fitted Point Process Model

Beadlet Anemones Data

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Nearest neighbours in three dimensions

Apply Function to Every Neighbourhood in a Point Pattern

nearest.raster.point

Find Pixel Nearest to a Given Point

Marked Nearest Neighbour Distance Function

Plot a plotppm Object Created by plot.ppm

Convert Pixel Image to Another Unit of Length

Summarizing a Pixel Image

complement.owin

Take Complement of a Window

Plot a three-dimensional point pattern

Summary of a List of Things

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Class of Fitted Point Process Models

Methods for three-dimensional point patterns

Volume of an Object

Number of Points in a Point Pattern

Function Arrays for Spatial Patterns

Reduced Second Moment Measure

Ord's Interaction model

Plot a Spatial Kolmogorov-Smirnov Test

as.data.frame.im

Convert Pixel Image to Data Frame

Multitype pair correlation function (i-to-any)

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Nearest neighbour distances between line segments

rescue.rectangle

Convert Window Back To Rectangle

Generate Multitype Poisson Point Pattern

Pairwise distances

Extract Quadrature Scheme Used to Fit a Point Process Model

Class of Line Segment Patterns

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Convert Point Pattern to Pixel Image

Extract Unique Points from a Spatial Point Pattern

Simulate from a Fitted Point Process Model

Kernel Smoothing of Line Segment Pattern

Mark Correlation Function

Nearest neighbour

plot.bermantest

Plot Result of Berman Test

Simulate Gauss-Poisson Process

Saturated Pairwise Interaction Point Process Family

Find Line Segment Nearest to Each Point

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Integral of a Pixel Image

quadratresample

Resample a Point Pattern by Resampling Quadrats

Convert Data to Hyperframe

Border Region of a Window

Pairwise distances between two different three-dimensional point patterns

Fry Plot of Point Pattern

spatstat-deprecated

Deprecated spatstat functions

Apply Vector Translation To Window

Morphological Dilation

The Fiksel Interaction

Generate N Random Points

Apply Affine Transformation To Window

Generate a Quadrature Scheme from a Point Pattern

Rotate a Point Pattern

Set Covariance of a Window

Pairwise distances in Three Dimensions

Simulate Matern Cluster Process

Extract Subset of Function Array

Perfect Simulation of the Strauss Process

Union of Data and Dummy Points

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

spatstat.options

Internal Options in Spatstat Package

Connected components of an image or window

Compute Integral of Function Against Cumulative Distribution

Japanese Pines Point Pattern

multiplicity.ppp

Count Multiplicity of Duplicate Points

Poisson Line Tessellation

Generate grid of parallel lines with random displacement

Test whether Object is Multitype

Orientation Angles of Line Segments

Kernel Smoothed Intensity of Point Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Fit the Matern Cluster Point Process by Minimum Contrast

Multitype J Function (i-to-any)

Class of Images

Interpret Fitted Model for Metropolis-Hastings Simulation.

Cartesian Coordinates for a Pixel Raster

Randomly Shift a Line Segment Pattern

Quadrat counting for a point pattern

Plot a fitted cluster point process

summary.splitppp

Summary of a Split Point Pattern

Berman-Huntington points and lines data

Simulate point patterns using the Metropolis-Hastings algorithm.

Data and Code From JRSS Discussion Paper on Residuals

Data Frames of Function Values

plot.hyperframe

Plot Entries in a Hyperframe

Nearest Neighbours in Any Dimensions

Simulate a Fitted Gibbs Point Process Model

plot a Fitted Point Process Model

Convert Point Pattern to Another Unit of Length

Beta Ganglion Cells in Cat Retina, Old Version

Generate Poisson Point Pattern in Any Dimensions

Corners of a rectangle

Vertices of a Window

Hughes' Amacrine Cell Data

Define Point Process Model for Metropolis-Hastings Simulation.

Hyper Data Frame

Create a Tessellation

Endpoints of Line Segment Pattern

Inhomogeneous Pair Correlation Function

Test Whether An Object Is Empty

Theoretical Distribution of Nearest Neighbour Distance

Print Brief Details of a Line Segment Pattern Dataset

Rotate a Window

Summary of a Line Segment Pattern Dataset

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Simulate Stratified Random Point Pattern

Longleaf Pines Point Pattern

Q-Q Plot of Residuals from Fitted Point Process Model

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Multi-Dimensional Box

Determine Duplicated Points in a Spatial Point Pattern

Exponential Energy Marks

Spokes pattern of dummy points

Simulate systematic random point pattern

Pairwise distances

Test Whether An Object Is A Fitted Point Process Model

Sufficient Statistic of Point Process Model

model.matrix.ppm

Extract Design Matrix from Point Process Model

Simulate Baddeley-Silverman Cell Process

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Basis for Harmonic Functions

Generate Poisson Random Line Process

Histogram of Pixel Values in an Image

Superimpose Several Line Segment Patterns

Generate N Uniform Random Points in Any Dimensions

Find Largest Circle Inside Window

Galaxies in the Shapley Supercluster

Test Whether A Point Pattern is Marked

Pair Correlation Function obtained from K Function

Update a Fitted Cluster Point Process Model

Fit cluster point process model

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

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Approximate a Polygon by a Simpler Polygon

Intersection of Two Tessellations

Pair Correlation Function

Convert Data To Class ppp

Test Whether Points Are Inside A Window

Simulated Point Pattern

Plot a Spatial Window

Generate N Uniform Random Points

Place Points Evenly Along Specified Lines

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

inforder.family

Infinite Order Interaction Family

Nearest neighbour distances

Ponderosa Pine Tree Point Pattern

Morphological Opening

pairdist.default

Pairwise distances

Window in Shape of Letter R

Determine Whether One Window is Contained In Another

plot a Spatial Quadrature Scheme

Print Brief Details of a Spatial Window

Inhomogeneous Multitype L Dot Function

Set Control Parameters for Metropolis-Hastings Algorithm.

Test Whether Two Function Objects Are Compatible

Pairwise distances between line segments

Generate Poisson Point Pattern on Line Segments

spatstat-package

The Spatstat Package

Morphological Erosion

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Extract or Replace Subset of Point Pattern

rshift.splitppp

Randomly Shift a List of Point Patterns

Mosaic Random Field

Print a Fitted Point Process Model

Prediction from a Fitted Point Process Model

plot a Spatial Line Segment Pattern

Marked K-Function

Weighted Histogram

Class of Quadrature Schemes

Areas of Morphological Erosions

Cut margins from rectangle

Safely Convert Point Pattern Window to Binary Mask

Apply Vector Translation To Pixel Image

Intersection, Union or Set Subtraction of Two Windows

Plot Function Values

Divide Point Pattern into Sub-patterns

Generate N Random Multitype Points

Simulation Envelopes of Summary Function

Generate Poisson Point Pattern in Three Dimensions

pairwise.family

Pairwise Interaction Process Family

Create a Point Matching

Divide Image Into Sub-images

Convert Window to Another Unit of Length

Read Point Pattern From Data File

Extract List of Tiles in a Tessellation

Extract Coordinates of a Spatial or Spatiotemporal Point Pattern

Random Perturbation of a Point Pattern

Randomly Shift a Point Pattern

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

New Zealand Trees Point Pattern

Residuals for Fitted Point Process Model

Ord Interaction Process Family

plot a Spatial Point Pattern

Inhomogeneous Multitype K Dot Function

Dirichlet Tessellation of Point Pattern

Fit Point Process Model to Data

Superimpose Several Point Patterns

Reduced Sample Estimator using Histogram Data

Swedish Pines Point Pattern

Rotate a Line Segment Pattern

Distance to Boundary of Window

Interaction Distance of a Point Process

Pair Correlation Function of Point Pattern

Urkiola Woods Point Pattern

Create a Line Segment Pattern

Apply Smoothing to Function Values

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Summarizing a Quadrature Scheme

Plot a List of Things

Rectangular grid of points

Evaluate an Expression in a Function Table

Print Progress Reports

Morishita Index Plot

Convert dataset to another unit of length

Generate Poisson Point Pattern

Plot a Function Array

Name for Unit of Length

Apply Vector Translation To Point Pattern

Quadrature Scheme Based on Pixel Grid

Mosaic Random Set

Update a Fitted Point Process Model

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Pair Correlation Function obtained from array of K functions

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Variance-Covariance Matrix for a Fitted Point Process Model

Divide Region into Quadrats

Random Thinning

Simulate Neyman-Scott Process

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Circular Window

Diameter of a Window

Create a Point Pattern

K-function of a Three-Dimensional Point Pattern

Maximum, Minimum, Mean, Median, Range or Sum of Pixel Values in an Image