Learn R Programming

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

spatstat (version 1.21-3)

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. Also supports three-dimensional point patterns, and space-time point patterns in any number of dimensions. Contains over 1000 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. Exploratory methods include K-functions, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics etc. Point process models can be fitted to point pattern data using functions ppm, kppm, slrm similar to glm. Models may include dependence on covariates, interpoint interaction, cluster formation 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

16,015

Version

1.21-3

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

January 17th, 2011

Functions in spatstat (1.21-3)

Hybrid Geyer Point Process Model

Estimate the I-function

Poisson Point Process Model

Multitype L-function (i-to-any)

Estimate the J-function

Diggle-Gratton model

Marked J Function

Subset of Quadrature Scheme

Saturated Pairwise Interaction model

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

The Lennard-Jones Potential

Multi-Dimensional Box

The Soft Core Point Process Model

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

The Strauss / Hard Core Point Process Model

Extract or Replace Subset of Point Pattern

Multitype K Function (i-to-any)

Combine Function Value Tables

Corners of a rectangle

Diagnostic Plots for Fitted Point Process Model

Convert Pixel Image from Numeric to Factor

Extract Subset of Signed or Vector Measure

Extract Subset of Function Values

Extract or Replace Subset of a List of Things

Artificial Data Point Pattern

Estimate the empty space function F

Reset Values in Subset of Image

Compute Expansion Window for Simulation

Fitted Probabilities for Spatial Logistic Regression

Evaluate Expression Involving Pixel Images

Determine Whether One Window is Contained In Another

Biological Cells Point Pattern

Kaplan-Meier Estimator using Histogram Data

Contour plot of pixel image

Interactively Add Points

Extract Subset of Line Segment Pattern

Extract or Replace Subset of Tessellation

Lansing Woods Point Pattern

Test Whether a Window is Convex

Intersect Infinite Straight Lines with a Window

Print News About Latest Version of Package

The Fiksel Interaction

model.frame.ppm

Extract the Environment of a Point Process Model

Weighted Histogram

Multitype K Function (Cross-type)

Pairwise distances between two different line segment patterns

The Hard Core Point Process Model

Exponential Energy Marks

The Strauss Point Process Model

The Multitype Hard Core Point Process Model

DiggleGatesStibbard

Diggle-Gates-Stibbard Point Process Model

Methods for Multidimensional Space-Time Point Patterns

Determine Duplicated Points in a Spatial Point Pattern

Fit the Thomas Point Process by Minimum Contrast

Ord's Interaction model

K-function using FFT

Diggle's Heather Data

Identify Pixelwise Maximum of Several Pixel Images

Inhomogeneous Cross Type L Function

The Multitype Strauss Point Process Model

Pairwise distances in Three Dimensions

Pairwise distances

Morphological Erosion

Marked Nearest Neighbour Distance Function

Plot a Simulation Envelope

Plot a Fitted Spatial Logistic Regression

Compute Quadrature Weights Based on Grid Counts

Multitype L-function (cross-type)

Create a Pixel Image Object

Multitype J Function (i-to-j)

Pixel Image Approximation of a Window

Distance for a Point Pattern Matching

Class of Quadrature Schemes

Generic Pairwise Interaction model

Difference of Disc Areas

Extract.splitppp

Extract or Replace Sub-Patterns

Log Likelihood for Poisson Point Process Model

Convert Data To Class owin

K-function of a Three-Dimensional Point Pattern

Analysis of Deviance for Spatial Logistic Regression Models

Convert Pixel Image to Matrix or Array

Spherical Contact Distribution Function

multiplicity.ppp

Count Multiplicity of Duplicate Points

Signed or Vector-Valued Measure

Multitype J Function (i-to-any)

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Simulate Matern Cluster Process

Calculate four standard summary functions of a point pattern.

The Area Interaction Point Process Model

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Simulate Thomas Process

Distance to Boundary of Window

Area of a Window

Foxall's Distance Functions

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Apply Affine Transformation To Window

Inhomogeneous Cross K Function

Mark Correlation Function

Cross Validated Bandwidth Selection for Relative Risk Estimation

California Redwoods Point Pattern (Entire Dataset)

Diagnostics for random marking

Inhomogeneous Multitype L Dot Function

Pair Correlation Function of Point Pattern

The Piecewise Constant Pairwise Interaction Point Process Model

Bounding Box of a Window or Point Pattern

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Generic Ord Interaction model

Extract Subset of Function Array

Convert a Window to a Polygonal Window

Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern

Bronze gradient filter data

Test Whether Two Pixel Images Are Compatible

Convert Point Pattern to Pixel Image

Interpret Fitted Model for Metropolis-Hastings Simulation.

Multitype pair correlation function (i-to-any)

Coefficients of Fitted Spatial Logistic Regression Model

Stoyan's Rule of Thumb for Bandwidth Selection

Plot a Signed or Vector-Valued Measure

Locally Scaled K-function

Beta Ganglion Cells in Cat Retina, Old Version

Generate Poisson Point Pattern on Line Segments

Summarizing a Fitted Point Process Model

Reduced Second Moment Measure

Marked K-Function

Inhomogeneous Multitype K Dot Function

Diameter of an Object

Spokes pattern of dummy points

crossdist.default

Pairwise distances between two different sets of points

Class of Line Segment Patterns

Kernel Smoothing of Line Segment Pattern

spatstat-deprecated

Deprecated spatstat functions

with.hyperframe

Evaluate an Expression in Each Row of a Hyperframe

Plot a plotppm Object Created by plot.ppm

Morphological Dilation

Find Largest Circle Inside Window

Distance to Boundary of Window

Simulation Envelopes of Summary Function for 3D Point Pattern

Extract Original Data from a Fitted Point Process Model

Distance Map of Window

Dirichlet Tessellation of Point Pattern

plot a Spatial Line Segment Pattern

Test Whether An Object Is A Fitted Point Process Model

inforder.family

Infinite Order Interaction Family

Geyer's Saturation Point Process Model

Print Progress Reports

Areas of Morphological Erosions

Geometrical Calculations for Three-Dimensional Box

project2segment

Move Point To Nearest Line

Harkness-Isham ants' nests data

as.hyperframe.ppx

Extract coordinates and marks of multidimensional point pattern

Identify Points in a Point Pattern

Rectangular grid of points

Sample Quantiles of Pixel Image

Plot a Pixel Image

Convert Data to Three-Dimensional Box

Safely Convert Point Pattern Window to Binary Mask

Test Whether An Object Is Empty

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

Variance-Covariance Matrix for a Fitted Point Process Model

Colour Lookup Tables

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Evaluate an Expression in a Function Table

Classify Points in a Point Pattern

Combine Two Line Segment Patterns

Estimate window from points alone

Apply Function to Image Broken Down by Factor

Diameter of a Window

Test Whether Marks Are Present

Pine saplings in Finland.

Cut margins from rectangle

Apply Affine Transformation

Evaluate Expression Involving Functions

Generate a Default Pattern of Dummy Points

Tropical rain forest trees

Pairwise distances between two different point patterns

Identify Segments in a Line Segment Pattern

Generate Poisson Point Pattern

model.matrix.ppm

Extract Design Matrix from Point Process Model

Quadrat counting for a point pattern

Histogram of Pixel Values in an Image

Generate Poisson Random Line Process

Convert Data to Hyperframe

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Class of Images

Generate Poisson Point Pattern in Any Dimensions

bounding.box.xy

Convex Hull of Points

Kernel Smoothed Intensity of Point Pattern

Nearest neighbour distances

Simulated Point Pattern

Simulate from a Fitted Point Process Model

Distance to Boundary of Window

Hyper Data Frame

Vertices of a Window

Basis for Harmonic Functions

Saturated Pairwise Interaction Point Process Family

Plot a Spatial Window

Simulate Neyman-Scott Process

Intersection of Two Tessellations

Superimpose Several Point Patterns

as.data.frame.hyperframe

Coerce Hyperframe to Data Frame

Convert to Pixel Image

Print a Quadrature Scheme

Test Whether A Point Process Model is Marked

Three-Dimensional Box

Longleaf Pines Point Pattern

Apply Affine Transformation To Line Segment Pattern

Interactively Define a Polygon

Apply Function to Every Neighbourhood in a Point Pattern

Create a Window

Cartesian Coordinates for a Pixel Raster

Spatial smoothing of observations at irregular points

Interpolate a Pixel Image

Local pair correlation function

Convert Data To Class ppp

Test Whether Two Function Objects Are Compatible

Pairwise distances

Intersection, Union or Set Subtraction of Two Windows

Data Frames of Function Values

Point and Click Interface for Exploratory Analysis of Point Pattern

Spatial Logistic Regression

Marks of a Point Pattern

Orientation Angles of Line Segments

Convert Window to Pixel Image

Ord Interaction Process Family

Generate a Quadrature Scheme from a Point Pattern

Beadlet Anemones Data

Convert Window to Another Unit of Length

Divide Point Pattern into Sub-patterns

Apply Vector Translation To Pixel Image

Extract Unique Points from a Spatial Point Pattern

Convert Data To Tessellation

Hutchings' Bramble Canes data

Fitted Conditional Intensity for Point Process Model

Plot a Spatial Kolmogorov-Smirnov Test

Beta Ganglion Cells in Cat Retina

Test Whether An Object Is A Window

Perimeter Length of Window

Difference of Disc Areas

Apply Gaussian Blur to a Pixel Image

Convert dataset to another unit of length

Expand Window By Factor

Subdivide a Window or Tessellation using a Set of Lines

Update a Fitted Cluster Point Process Model

Pairwise distances between two different three-dimensional point patterns

Lurking variable plot

Apply Smoothing to Function Values

Simulate systematic random point pattern

cbind.hyperframe

Combine Hyperframes by Rows or by Columns

Pairwise Distances Between Two Different Multi-Dimensional Point Patterns

Scatterplot Matrix for Pixel Images

Convert Line Segment Pattern to Binary Pixel Mask

Name for Unit of Length

plot.hyperframe

Plot Entries in a Hyperframe

Evaluate Expression Involving Function Arrays

Volume of an Object

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Collapse Several Function Tables into One

Berman's Tests for Point Process Model

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Concatenate x,y Coordinate Vectors

Print Brief Details of an Image

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Areas of Morphological Dilations

Infinite Straight Lines

Urkiola Woods Point Pattern

Apply Affine Transformation To Point Pattern

Humberside Data on Childhood Leukaemia and Lymphoma

Pairwise Distances in Any Dimensions

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Apply a Function to a Point Pattern Broken Down by Factor

Japanese Pines Point Pattern

plot.bermantest

Plot Result of Berman Test

Superimpose Several Line Segment Patterns

Plot a Function Array

spatstat-internal

Internal spatstat functions

Kolmogorov-Smirnov Test for Point Process Model

Hughes' Amacrine Cell Data

Loglikelihood of Spatial Logistic Regression

Function Arrays for Spatial Patterns

pppmatching.object

Class of Point Matchings

Perspective Plot of Pixel Image

Distance Map of Point Pattern

ANOVA for Fitted Point Process Models

Apply Vector Translation To Line Segment Pattern

Extract Dummy Points Used to Fit a Point Process Model

Pair Correlation Function of a Three-Dimensional Point Pattern

Coefficients of Fitted Point Process Model

Plot a List of Point Patterns

Methods for Multi-Dimensional Box

Extract the Interaction from a Fitted Point Process Model

Morphological Closing

Plot a fitted cluster point process

Connected components of an image or window

Methods for Three-Dimensional Box

Print a Fitted Point Process Model

Three Dimensional Point Pattern

Distance Map of Line Segment Pattern

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Lengths of Line Segments

Find Line Segment Nearest to Each Point

Divide Region into Quadrats

default.rmhcontrol

Set Default Control Parameters for Metropolis-Hastings Algorithm.

Test whether Object is Multitype

Methods for three-dimensional point patterns

Fry Plot of Point Pattern

Midpoints of Line Segment Pattern

Mark Connection Function

Integral of a Pixel Image

Crossing Points of Two Line Segment Patterns

Define Point Process Model for Metropolis-Hastings Simulation.

Convert Polygonal Region into Different Format

Plot a List of Things

Ponderosa Pine Tree Point Pattern

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Border Region of a Window

California Redwoods Point Pattern (Ripley's Subset)

Fit Point Process Model to Data

Endpoints of Line Segment Pattern

Mark Correlation Integral

Nearest Neighbour Clutter Removal

Nearest neighbour distances between line segments

Create a Point Pattern

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Extract Quadrature Scheme Used to Fit a Point Process Model

Generate N Random Multitype Points

Fit the Matern Cluster Point Process by Minimum Contrast

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Fit cluster point process model

Nearest Neighbours Between Two Patterns

Rotate a Line Segment Pattern

Distance Between Two Point Patterns

Centroid of a window

Pair Correlation Function obtained from array of K functions

Simulate Gauss-Poisson Process

Morishita Index Plot

Test Whether Points Are Inside A Window

Murchison gold deposits

Convert and Compare Colours in Different Formats

clarkevans.test

Clark and Evans Test

Interaction Distance of a Point Process

Point and Click Interface for Displaying a Point Pattern

Data and Code From JRSS Discussion Paper on Residuals

Print Brief Details of a Spatial Window

Weighted Empirical Cumulative Distribution Function

Random Thinning

Generate N Uniform Random Points in Any Dimensions

Q-Q Plot of Residuals from Fitted Point Process Model

Morphological Opening

pairdist.default

Pairwise distances

Theoretical Distribution of Nearest Neighbour Distance

Test Whether An Object Is A Point Pattern

Make Periodic Copies of a Spatial Pattern

Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns

Create a Tessellation

Nearest neighbour

Class of Fitted Point Process Models

Number of Points in a Point Pattern

Predicted or Fitted Values from Spatial Logistic Regression

nearest.raster.point

Find Pixel Nearest to a Given Point

Nearest neighbours in three dimensions

Smoothing Estimate of Covariate Transformation

Randomly Shift a Point Pattern

Nearest Neighbours in Any Dimensions

Generate N Random Points

Plot a Colour Map

Pairwise distances

pairwise.family

Pairwise Interaction Process Family

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

Summary of a Point Pattern Dataset

complement.owin

Take Complement of a Window

Plot Function Values

Point Patterns of New Brunswick Forest Fires

rshift.splitppp

Randomly Shift a List of Point Patterns

Generate grid of parallel lines with random displacement

Nearest Neighbour Distances in Any Dimensions

Simulate a Fitted Gibbs Point Process Model

Generate Poisson Point Pattern in Three Dimensions

Pairwise distances between line segments

plot a Fitted Point Process Model

plot a Spatial Quadrature Scheme

Convex Hull of Points

Berman-Huntington points and lines data

Multitype pair correlation function (cross-type)

Convert Line Segment Pattern to Pixel Image

Inhomogeneous Multitype Pair Correlation Function (Cross-Type)

Plot a three-dimensional point pattern

Area of Part of Disc

Random Perturbation of a Point Pattern

Summary of a Line Segment Pattern Dataset

Simulate a Fitted Cluster Point Process Model

Place Points Evenly Along Specified Lines

Delaunay Triangulation of Point Pattern

Print Brief Details of a Line Segment Pattern Dataset

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

Create a Line Segment Pattern

Reduced Sample Estimator using Histogram Data

Generate N Uniform Random Points in a Disc

quadratresample

Resample a Point Pattern by Resampling Quadrats

Mosaic Random Set

Mosaic Random Field

Compute Integral of Function Against Cumulative Distribution

Profile Maximum Pseudolikelihood

Update a Fitted Point Process Model

Class of Point Patterns

Determine Initial State for Metropolis-Hastings Simulation.

Convert Line Segment Pattern to Another Unit of Length

Quadrature Scheme Based on Pixel Grid

Prediction from a Fitted Point Process Model

summary.splitppp

Summary of a Split Point Pattern

Prediction from a Fitted Cluster Point Process Model

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Simulation Envelopes of Summary Function

Nonparametric Estimate of Spatially-Varying Relative Risk

Simulate Matern Model I

Swedish Pines Point Pattern

Randomly Shift a Line Segment Pattern

Create a Point Matching

Set Control Parameters for Metropolis-Hastings Algorithm.

Simulate Simple Sequential Inhibition

Simulate Baddeley-Silverman Cell Process

Create a Function Value Table

Simulate Matern Model II

Test Whether A Point Pattern is Marked

Perfect Simulation of the Strauss Process

Test Whether An Object Is A Pixel Image

Approximate a Polygon by a Simpler Polygon

Rotate a Window

spatstat.options

Internal Options in Spatstat Package

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Residuals for Fitted Point Process Model

Summarizing a Pixel Image

is.multitype.ppp

Test Whether A Point Pattern is Multitype

spatstat-package

The Spatstat Package

Poisson Line Tessellation

Estimate Variance of Summary Statistic by Subdivision

Summarizing a Quadrature Scheme

Rotate a Point Pattern

Summary of a Spatial Window

Apply Vector Translation To Window

Set Covariance of a Window

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

Simulate Stratified Random Point Pattern

Galaxies in the Shapley Supercluster

Spruces Point Pattern

Union of Data and Dummy Points

Sufficient Statistic of Point Process Model

Apply Vector Translation To Point Pattern

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Smooth a Signed or Vector-Valued Measure

Level Set of a Pixel Image

Neighbourhood density function

Method of Minimum Contrast

Fit the Thomas Point Process by Minimum Contrast

Window in Shape of Letter R

Divide Image Into Sub-images

Summary of a List of Things

Convert Spatial Object to Pixel Image

Pair Correlation Function obtained from K Function

Nearest neighbour distances in three dimensions

Pair Correlation Function

Plot a tessellation

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

rescue.rectangle

Convert Window Back To Rectangle

Convert Pixel Image to Another Unit of Length

Read Point Pattern From Data File

Simulate point patterns using the Metropolis-Hastings algorithm.

Extract List of Tiles in a Tessellation

Extract Subset of Image

Nearest Neighbour Distance Function G

Empty Space Function of a Three-Dimensional Point Pattern

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

Inhomogeneous K-function

as.data.frame.im

Convert Pixel Image to Data Frame

Chorley-Ribble Cancer Data

Convert Data To Class psp

Clark and Evans Aggregation Index

Distance Map as a Function

Geometrical Calculations for Multi-Dimensional Box

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

Aherne's hamster tumour data

Kaplan-Meier and Reduced Sample Estimator using Histograms

methods.distfun

Methods for Distance Functions

Summarise Marks in Every Neighbourhood in a Point Pattern

matclust.estpcf

Fit the Matern Cluster Point Process by Minimum Contrast Using Pair Correlation

Compute Images of Constructed Covariates

New Zealand Trees Point Pattern

Inhomogeneous Pair Correlation Function

Circular Window

plot a Spatial Point Pattern

Print Brief Details of a Point Pattern Dataset

Multidimensional Space-Time Point Pattern

Convert Point Pattern to Another Unit of Length

Random Re-Labelling of Point Pattern

Generate N Uniform Random Points in Three Dimensions

Generate N Uniform Random Points

Define Point Process Model for Metropolis-Hastings Simulation.

Generate Multitype Poisson Point Pattern

Data Sharpening of Point Pattern

Compute Areas of Tiles in a Tessellation

Apply Vector Translation