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spatstat (version 1.15-2)

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. 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

40,191

Version

1.15-2

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

April 16th, 2009

Functions in spatstat (1.15-2)

Rotate a Window

Simulate systematic random point pattern

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Extract Subset of Function Array

Update a Fitted Cluster Point Process Model

Summary of a Point Pattern Dataset

Interpret Fitted Model for Metropolis-Hastings Simulation.

Extract Subset of Function Values

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Inhomogeneous Cross K Function

Random Thinning

Extract Unique Points from a Spatial Point Pattern

Superimpose Several Point Patterns

Summary of a Spatial Window

Simulate a fitted cluster point process model.

Extract List of Tiles in a Tessellation

Simulation envelopes of summary function

subset.splitppp

Extract or Replace Sub-Patterns

Generate Poisson Random Line Process

Create a Point Pattern

Determine Initial State for Metropolis-Hastings Simulation.

Data Frames of Function Values

Read Point Pattern From Data File

Compute Integral of Function Against Cumulative Distribution

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

Fitted Conditional Intensity for Point Process Model

Spokes pattern of dummy points

Subset of Quadrature Scheme

Extract Subset of Image

Divide Image Into Sub-images

Simulate Stratified Random Point Pattern

Simulate point patterns using the Metropolis-Hastings algorithm.

Cut margins from rectangle

Variance-Covariance Matrix for a Fitted Point Process Model

Generate Multitype Poisson Point Pattern

Extract or Replace Subset of a List of Things

Superimpose Several Line Segment Patterns

Update a Fitted Point Process Model

Rotate a Line Segment Pattern

Summary of a List of Things

Extract Subset of Line Segment Pattern

summary.splitppp

Summary of a Split Point Pattern

Apply Vector Translation To Line Segment Pattern

Apply Vector Translation To Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Swedish Pines Point Pattern

Fit the Thomas Point Process by Minimum Contrast

Generate N Uniform Random Points in a Disc

Create a Tessellation

Set Covariance of a Window

Extract or Replace Subset of Point Pattern

Randomly Shift a Point Pattern

Reset Values in Subset of Image

Set or Reset the Marks in a Point Pattern

Divide Point Pattern into Sub-patterns

bounding.box.xy

Convex Hull of Points

Extract or Replace Subset of Tessellation

Name for Unit of Length

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Apply Affine Transformation To Point Pattern

Spruces Point Pattern

Generate Poisson Point Pattern on Line Segments

Orientation Angles of Line Segments

Randomly Shift a Line Segment Pattern

Apply Vector Translation To Pixel Image

Generate N Random Multitype Points

Apply Vector Translation To Window

Apply Vector Translation

Multitype K Function (i-to-any)

Poisson Line Tessellation

Geyer's Saturation Point Process Model

Generate N Uniform Random Points

The Piecewise Constant Pairwise Interaction Point Process Model

Convert Data To Class owin

Convert Data To Class psp

Intersect Infinite Straight Lines with a Window

Summarizing a Fitted Point Process Model

Rotate a Point Pattern

Intersection of Two Tessellations

Convert Data To Class ppp

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

Generate Poisson Point Pattern

Humberside Data on Childhood Leukaemia and Lymphoma

Generate N Random Points

Multitype L-function (cross-type)

Apply Affine Transformation To Window

Simulated Point Pattern

Kernel Smoothing of Line Segment Pattern

Dirichlet Tessellation of Point Pattern

Summarizing a Pixel Image

Fry Plot of Point Pattern

Spatial smoothing of observations at irregular points

Combine Two Line Segment Patterns

Generic Pairwise Interaction model

Distance to Boundary of Window

Convert Pixel Image to Matrix

Multitype L-function (i-to-any)

Test whether Object is Multitype

Endpoints of Line Segment Pattern

Estimate the empty space function F

Crossing Points of Two Line Segment Patterns

Sufficient Statistic of Point Process Model

Harkness-Isham ants' nests data

Summary of a Line Segment Pattern Dataset

Urkiola Woods Point Pattern

Pairwise distances between two different point patterns

Clark and Evans Aggregation Index

rshift.splitppp

Randomly Shift a List of Point Patterns

Class of Images

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

Safely Convert Point Pattern Window to Binary Mask

Classify Points in a Point Pattern

Print a Quadrature Scheme

pairwise.family

Pairwise Interaction Process Family

Pair Correlation Function

Colour Lookup Tables

Difference of Disc Areas

Prediction from a Fitted Point Process Model

Hughes' Amacrine Cell Data

Find Line Segment Nearest to Each Point

Kernel Smoothed Intensity of Point Pattern

Hybrid Geyer Point Process Model

Simulate Neyman-Scott Process

Coefficients of Fitted Point Process Model

Apply a Function to a Point Pattern Broken Down by Factor

Ord's Interaction model

Diagnostics for random marking

complement.owin

Take Complement of a Window

Evaluate an Expression in Each Row of a Hyperframe

The Strauss Point Process Model

Pairwise distances

Test Whether An Object Is A Point Pattern

Random Perturbation of a Point Pattern

inforder.family

Infinite Order Interaction Family

Convert Polygonal Region into Different Format

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Plot a List of Point Patterns

Simulate Thomas Process

Pairwise distances between line segments

Evaluate Expression Involving Functions

Convert Data To Tessellation

Kaplan-Meier and Reduced Sample Estimator using Histograms

Aherne's hamster tumour data

Estimate the J-function

Exponential Energy Marks

Plot a Colour Map

rescue.rectangle

Convert Window Back To Rectangle

Nearest-Neighbour Correlation of Marked Point Pattern

Inhomogeneous K-function

Apply Affine Transformation

Interactively Add Points

Class of Line Segment Patterns

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Kaplan-Meier Estimator using Histogram Data

Perfect Simulation of the Strauss Process

Concatenate x,y Coordinate Vectors

spatstat-internal

Internal spatstat functions

Inhomogeneous Multitype K Dot Function

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

California Redwoods Point Pattern (Ripley's Subset)

Murchison gold deposits

Test Whether A Point Pattern is Marked

Nearest Neighbours Between Two Patterns

Multitype K Function (Cross-type)

Distance Map of Line Segment Pattern

compatible.fasp

Test Whether Two Function Arrays Are Compatible

plot a Spatial Line Segment Pattern

model.matrix.ppm

Extract Design Matrix from Point Process Model

Plot a plotppm Object Created by plot.ppm

Class of Point Patterns

Apply Function to Every Neighbourhood in a Point Pattern

nearest.raster.point

Find Pixel Nearest to a Given Point

The Lennard-Jones Potential

Multitype J Function (i-to-j)

Distance Between Two Point Patterns

Quadrat counting for a point pattern

Pixel Image Approximation of a Window

Perspective Plot of Pixel Image

Calculate four standard summary functions of a point pattern.

Marked K-Function

Apply Gaussian Blur to a Pixel Image

Longleaf Pines Point Pattern

Pair Correlation Function of Point Pattern

Artificial Data Point Pattern

spatstat-deprecated

Deprecated spatstat functions

Plot a tessellation

Nearest Neighbour Distance Function G

Pairwise distances

Convert to Pixel Image

Random Re-Labelling of Point Pattern

Data and Code From JRSS Discussion Paper on Residuals

Prediction from a Fitted Cluster Point Process Model

Distance to Boundary of Window

Mosaic Random Set

Spherical Contact Distribution Function

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Estimate the I-function

Generate grid of parallel lines with random displacement

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

Define Point Process Model for Metropolis-Hastings Simulation.

Compute Images of Constructed Covariates

Subdivide a Window or Tessellation using a Set of Lines

Circular Window

Determine Duplicated Points in a Spatial Point Pattern

Extract the Interaction from a Fitted Point Process Model

Interaction Distance of a Point Process

Extract Original Data from a Fitted Point Process Model

Calculate Summary Statistic for All Types in a Multitype Point Pattern

The Area Interaction Point Process Model

Quadrature Scheme Based on Pixel Grid

Convert Pixel Image to Another Unit of Length

Class of Fitted Point Process Models

Mean, Median and Range of Pixel Values in an Image

Test Whether An Object Is A Pixel Image

Diggle's Heather Data

Centroid of a window

Hyper Data Frame

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

K-function using FFT

Residuals for Fitted Point Process Model

Simulate Matern Model II

Convex Hull of Points

ANOVA for Fitted Point Process Models

Diggle-Gratton model

Tropical rain forest trees

Multitype J Function (i-to-any)

project2segment

Move Point To Nearest Line

Chorley-Ribble Cancer Data

Nearest neighbour distances between line segments

Generate a Default Pattern of Dummy Points

Pair Correlation Function obtained from K Function

Create a Pixel Image Object

Find Largest Circle Inside Window

Create a Line Segment Pattern

Test Whether Marks Are Present

Histogram of Pixel Values in an Image

Simulate from a Fitted Point Process Model

Nearest neighbour distances

Lansing Woods Point Pattern

Kolmogorov-Smirnov Test for Point Process Model

Convert Point Pattern to Another Unit of Length

Marked J Function

Corners of a rectangle

Plot a Spatial Window

multiplicity.ppp

Count Multiplicity of Duplicate Points

Fit the Matern Cluster Point Process by Minimum Contrast

Morishita Index Plot

Extract Dummy Points Used to Fit a Point Process Model

Dilate a Window

Lengths of Line Segments

Create a Window

Neighbourhood density function

Plot a List of Things

Ord Interaction Process Family

Area of a Window

Convert Point Pattern to Pixel Image

Test Whether Two Function Objects Are Compatible

Weighted Empirical Cumulative Distribution Function

Japanese Pines Point Pattern

Fit cluster point process model

Infinite Straight Lines

Apply Affine Transformation To Line Segment Pattern

California Redwoods Point Pattern (Entire Dataset)

The Multitype Strauss Point Process Model

plot a Fitted Point Process Model

Test Whether An Object Is A Fitted Point Process Model

Beta Ganglion Cells in Cat Retina

Morphological Closing of a Window

Pine saplings in Finland.

Interactively Define a Polygon

Expand Window By Factor

Multitype pair correlation function

Set Control Parameters for Metropolis-Hastings Algorithm.

Plot a Pixel Image

Distance Map of Window

Evaluate Expression Involving Pixel Images

Distance for a Point Pattern Matching

Print a Fitted Point Process Model

Q-Q Plot of Residuals from Fitted Point Process Model

Convert Line Segment Pattern to Another Unit of Length

The Soft Core Point Process Model

Intersection or Union of Two Windows

Contour plot of pixel image

Convert Window to Another Unit of Length

pppmatching.object

Class of Point Matchings

Convert Pixel Image from Numeric to Factor

Simulate Matern Model I

Simulate Simple Sequential Inhibition

Print Brief Details of a Spatial Window

Areas of Morphological Erosions

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Method of Minimum Contrast

spatstat.options

Internal Options in Spatstat Package

Function Arrays for Spatial Patterns

Plot a Function Array

Delaunay Triangulation of Point Pattern

Hutchings' Bramble Canes data

Biological Cells Point Pattern

New Zealand Trees Point Pattern

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Determine Whether One Window is Contained In Another

Rectangular grid of points

Summarise Marks in Every Neighbourhood in a Point Pattern

The Spatstat Package

Apply Function to Image Broken Down by Factor

Mark Correlation Function

Poisson Point Process Model

Create a Point Matching

Window in Shape of Letter R

Simulate Gauss-Poisson Process

Evaluate Expression Involving Function Arrays

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Print Progress Reports

Distance Map of Point Pattern

Level Set of a Pixel Image

Pair Correlation Function obtained from array of K functions

Estimate window from points alone

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Saturated Pairwise Interaction Point Process Family

Ponderosa Pine Tree Point Pattern

Mosaic Random Field

Reduced Second Moment Measure

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Generic Ord Interaction model

Berman-Huntington points and lines data

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Log Likelihood for Poisson Point Process Model

Fit Point Process Model to Data

Point Patterns of New Brunswick Forest Fires

Simulate Matern Cluster Process

Place Points Evenly Along Specified Lines

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Cartesian Coordinates for a Pixel Raster

Compute Quadrature Weights Based on Grid Counts

Mark Correlation Integral

plot a Spatial Point Pattern

Diameter of a Window

Profile Maximum Pseudolikelihood

Extract Quadrature Scheme Used to Fit a Point Process Model

pairdist.default

Pairwise distances

Lurking variable plot

Simulate Baddeley-Silverman Cell Process

Union of Data and Dummy Points

Mark Connection Function

Sample Quantiles of Pixel Image

Basis for Harmonic Functions

Print Brief Details of an Image

Saturated Pairwise Interaction model

Print Brief Details of a Point Pattern Dataset

The Strauss / Hard Core Point Process Model

Class of Quadrature Schemes

Beta Ganglion Cells in Cat Retina, Old Version

Midpoints of Line Segment Pattern

Divide Region into Quadrats

crossdist.default

Pairwise distances between two different sets of points

Test Whether A Point Process Model is Marked

Bounding Box of a Window or Point Pattern

Nearest neighbour

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

Interpolate a Pixel Image

Identify Points in a Point Pattern

Plot Function Valuesn

Test Whether An Object Is A Window

Marked Nearest Neighbour Distance Function

Pairwise distances

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Morphological Opening of a Window

plot a Spatial Quadrature Scheme

Test Whether Two Pixel Images Are Compatible

Test Whether Points Are Inside A Window

Vertices of a Window

Generate a Quadrature Scheme from a Point Pattern

Pairwise distances between two different line segment patterns

Evaluate an Expression in a Function Table

Print Brief Details of a Line Segment Pattern Dataset

plot.hyperframe

Plot Entries in a Hyperframe

quadratresample

Resample a Point Pattern by Resampling Quadrats

Diagnostic Plots for Fitted Point Process Model

Plot a fitted cluster point process

Reduced Sample Estimator using Histogram Data

Summarizing a Quadrature Scheme

Beadlet Anemones Data

Convert dataset to another unit of length