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spatstat (version 1.15-1)

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. 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

16,590

Version

1.15-1

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

April 1st, 2009

Functions in spatstat (1.15-1)

The Piecewise Constant Pairwise Interaction Point Process Model

Morphological Closing of a Window

Classify Points in a Point Pattern

Expand Window By Factor

Fitted Conditional Intensity for Point Process Model

spatstat-internal

Internal spatstat functions

Lurking variable plot

Convex Hull of Points

Evaluate Expression Involving Functions

Plot a Pixel Image

Estimate the empty space function F

K-function using FFT

Tropical rain forest trees

Multitype L-function (i-to-any)

Distance for a Point Pattern Matching

New Zealand Trees Point Pattern

Convert Pixel Image from Numeric to Factor

Hybrid Geyer Point Process Model

Plot a List of Things

Class of Point Patterns

Multitype J Function (i-to-j)

Test Whether Points Are Inside A Window

Estimate the J-function

Inhomogeneous Multitype K Dot Function

Pair Correlation Function

Multitype pair correlation function

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Quadrature Scheme Based on Pixel Grid

Random Perturbation of a Point Pattern

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

Create a Window

Orientation Angles of Line Segments

Reduced Sample Estimator using Histogram Data

Calculate four standard summary functions of a point pattern.

Multitype K Function (i-to-any)

The Area Interaction Point Process Model

Summary of a Line Segment Pattern Dataset

pppmatching.object

Class of Point Matchings

project2segment

Move Point To Nearest Line

Inhomogeneous Cross K Function

Apply Function to Every Neighbourhood in a Point Pattern

Create a Point Matching

Estimate the I-function

Fry Plot of Point Pattern

Generic Ord Interaction model

Hutchings' Bramble Canes data

Areas of Morphological Erosions

Contour plot of pixel image

Harkness-Isham ants' nests data

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

Test Whether Two Function Objects Are Compatible

Area of a Window

Convert Data To Class psp

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Endpoints of Line Segment Pattern

Interactively Define a Polygon

Distance Map of Line Segment Pattern

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Diameter of a Window

Biological Cells Point Pattern

The Spatstat Package

Evaluate Expression Involving Function Arrays

Poisson Point Process Model

Multitype K Function (Cross-type)

Marked J Function

Convert Data To Class owin

Test Whether An Object Is A Pixel Image

Beadlet Anemones Data

pairdist.default

Pairwise distances

Pixel Image Approximation of a Window

complement.owin

Take Complement of a Window

Dirichlet Tessellation of Point Pattern

Apply Affine Transformation

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Test Whether An Object Is A Point Pattern

plot a Fitted Point Process Model

The Strauss Point Process Model

Crossing Points of Two Line Segment Patterns

Find Largest Circle Inside Window

Convert Window to Another Unit of Length

Test Whether An Object Is A Fitted Point Process Model

Diggle's Heather Data

Berman-Huntington points and lines data

Generate Poisson Point Pattern

Geyer's Saturation Point Process Model

Concatenate x,y Coordinate Vectors

Union of Data and Dummy Points

Nearest neighbour distances between line segments

model.matrix.ppm

Extract Design Matrix from Point Process Model

Kaplan-Meier Estimator using Histogram Data

Interpolate a Pixel Image

Mark Correlation Function

Delaunay Triangulation of Point Pattern

Summarizing a Pixel Image

Intersection or Union of Two Windows

Kernel Smoothing of Line Segment Pattern

Difference of Disc Areas

Coefficients of Fitted Point Process Model

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Nearest-Neighbour Correlation of Marked Point Pattern

Compute Quadrature Weights Based on Grid Counts

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

Apply Affine Transformation To Line Segment Pattern

Pair Correlation Function obtained from array of K functions

Test Whether A Point Process Model is Marked

Subset of Quadrature Scheme

Apply Affine Transformation To Window

Pairwise distances

Aherne's hamster tumour data

Corners of a rectangle

Pairwise distances between two different line segment patterns

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

Test Whether A Point Pattern is Marked

Generate a Default Pattern of Dummy Points

rescue.rectangle

Convert Window Back To Rectangle

Chorley-Ribble Cancer Data

Diggle-Gratton model

Distance Map of Point Pattern

Beta Ganglion Cells in Cat Retina

Basis for Harmonic Functions

Extract Original Data from a Fitted Point Process Model

Summarise Marks in Every Neighbourhood in a Point Pattern

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Function Arrays for Spatial Patterns

Safely Convert Point Pattern Window to Binary Mask

Artificial Data Point Pattern

Perspective Plot of Pixel Image

Dilate a Window

Morphological Opening of a Window

Level Set of a Pixel Image

Diagnostic Plots for Fitted Point Process Model

Japanese Pines Point Pattern

Plot Function Valuesn

Read Point Pattern From Data File

Random Re-Labelling of Point Pattern

Create a Pixel Image Object

Multitype L-function (cross-type)

Point Patterns of New Brunswick Forest Fires

The Multitype Strauss Point Process Model

Pairwise distances

Profile Maximum Pseudolikelihood

Rotate a Line Segment Pattern

plot a Spatial Point Pattern

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Interaction Distance of a Point Process

Evaluate an Expression in Each Row of a Hyperframe

Convert Point Pattern to Pixel Image

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

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Intersection of Two Tessellations

Kaplan-Meier and Reduced Sample Estimator using Histograms

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

plot a Spatial Quadrature Scheme

Fit the Thomas Point Process by Minimum Contrast

Inhomogeneous K-function

Divide Point Pattern into Sub-patterns

Generate Poisson Random Line Process

Ord Interaction Process Family

Ponderosa Pine Tree Point Pattern

multiplicity.ppp

Count Multiplicity of Duplicate Points

Class of Fitted Point Process Models

Print Brief Details of a Line Segment Pattern Dataset

Fit cluster point process model

Prediction from a Fitted Cluster Point Process Model

Plot a plotppm Object Created by plot.ppm

Q-Q Plot of Residuals from Fitted Point Process Model

bounding.box.xy

Convex Hull of Points

Nearest Neighbour in Another Point Pattern

Colour Lookup Tables

Simulate systematic random point pattern

Convert Line Segment Pattern to Another Unit of Length

Set Control Parameters for Metropolis-Hastings Algorithm.

inforder.family

Infinite Order Interaction Family

Randomly Shift a Point Pattern

Swedish Pines Point Pattern

Class of Images

Saturated Pairwise Interaction model

Convert Pixel Image to Matrix

Apply Function to Image Broken Down by Factor

Multitype J Function (i-to-any)

Lengths of Line Segments

Pairwise distances between line segments

Morishita Index Plot

Clark and Evans Aggregation Index

Simulate Matern Cluster Process

Plot a Function Array

Generate Multitype Poisson Point Pattern

Simulate Gauss-Poisson Process

Spherical Contact Distribution Function

The Lennard-Jones Potential

Interactively Add Points

plot a Spatial Line Segment Pattern

Hughes' Amacrine Cell Data

Distance Map of Window

Apply a Function to a Point Pattern Broken Down by Factor

ANOVA for Fitted Point Process Models

Distance to Boundary of Window

Marked Nearest Neighbour Distance Function

Convert Pixel Image to Another Unit of Length

Evaluate Expression Involving Pixel Images

Create a Tessellation

Pair Correlation Function of Point Pattern

Extract the Interaction from a Fitted Point Process Model

Vertices of a Window

Kernel Smoothed Intensity of Point Pattern

plot.hyperframe

Plot Entries in a Hyperframe

Test Whether An Object Is A Window

Rectangular grid of points

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

is.multitype.ppm

Test Whether A Point Process Model is Multitype

Weighted Empirical Cumulative Distribution Function

Pairwise distances

Midpoints of Line Segment Pattern

Spruces Point Pattern

Data Frames of Function Values

Determine Initial State for Metropolis-Hastings Simulation.

Compute Integral of Function Against Cumulative Distribution

Convert Point Pattern to Another Unit of Length

Simulation envelopes of summary function

Identify Points in a Point Pattern

spatstat-deprecated

Deprecated spatstat functions

Longleaf Pines Point Pattern

Log Likelihood for Poisson Point Process Model

Reset Values in Subset of Image

Class of Line Segment Patterns

Random Thinning

Rotate a Window

Method of Minimum Contrast

Plot a fitted cluster point process

Compute Images of Constructed Covariates

Kolmogorov-Smirnov Test for Point Process Model

Generate Poisson Point Pattern on Line Segments

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Set Covariance of a Window

Extract Subset of Function Values

Distance Between Two Point Patterns

Summarizing a Fitted Point Process Model

Apply Vector Translation

Fit Point Process Model to Data

Nearest Neighbour Distance Function G

Neighbourhood density function

Rotate a Point Pattern

Interpret Fitted Model for Metropolis-Hastings Simulation.

Determine Duplicated Points in a Spatial Point Pattern

Estimate window from points alone

Pairwise distances between two different point patterns

The Soft Core Point Process Model

Summary of a Point Pattern Dataset

subset.splitppp

Extract or Replace Sub-Patterns

Sufficient Statistic of Point Process Model

Apply Affine Transformation To Point Pattern

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Evaluate an Expression in a Function Table

Extract Subset of Image

Simulate Stratified Random Point Pattern

Generic Pairwise Interaction model

Fit the Matern Cluster Point Process by Minimum Contrast

Generate N Uniform Random Points

Simulated Point Pattern

Create a Point Pattern

rshift.splitppp

Randomly Shift a List of Point Patterns

Marked K-Function

Apply Vector Translation To Line Segment Pattern

Extract or Replace Subset of Point Pattern

Urkiola Woods Point Pattern

Cartesian Coordinates for a Pixel Raster

Generate a Quadrature Scheme from a Point Pattern

Apply Vector Translation To Pixel Image

Convert dataset to another unit of length

Generate N Uniform Random Points in a Disc

Perfect Simulation of the Strauss Process

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

Superimpose Several Point Patterns

nearest.raster.point

Find Pixel Nearest to a Given Point

Print Brief Details of a Spatial Window

Simulate Baddeley-Silverman Cell Process

Generate N Random Multitype Points

Extract Subset of Function Array

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Extract or Replace Subset of a List of Things

Murchison gold deposits

Simulate Neyman-Scott Process

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Plot a List of Point Patterns

Generate N Random Points

Convert Data To Class ppp

Simulate Matern Model II

Print a Fitted Point Process Model

Humberside Data on Childhood Leukaemia and Lymphoma

Convert to Pixel Image

Simulate from a Fitted Point Process Model

Place Points Evenly Along Specified Lines

Prediction from a Fitted Point Process Model

Extract or Replace Subset of Tessellation

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Update a Fitted Cluster Point Process Model

Apply Vector Translation To Window

Print Progress Reports

Extract List of Tiles in a Tessellation

Centroid of a window

Extract Quadrature Scheme Used to Fit a Point Process Model

pairwise.family

Pairwise Interaction Process Family

Test whether Object is Multitype

Plot a Spatial Window

Spatial smoothing of observations at irregular points

Data and Code From JRSS Discussion Paper on Residuals

Lansing Woods Point Pattern

Simulate Simple Sequential Inhibition

Name for Unit of Length

Apply Vector Translation To Point Pattern

Divide Image Into Sub-images

Define Point Process Model for Metropolis-Hastings Simulation.

Simulate point patterns using the Metropolis-Hastings algorithm.

Find Line Segment Nearest to Each Point

Generate grid of parallel lines with random displacement

California Redwoods Point Pattern (Ripley's Subset)

Apply Gaussian Blur to a Pixel Image

Extract Dummy Points Used to Fit a Point Process Model

Nearest neighbour distances

Residuals for Fitted Point Process Model

Spokes pattern of dummy points

Saturated Pairwise Interaction Point Process Family

Summary of a Spatial Window

Print Brief Details of an Image

Randomly Shift a Line Segment Pattern

Print a Quadrature Scheme

Exponential Energy Marks

Divide Region into Quadrats

Sample Quantiles of Pixel Image

Plot a tessellation

Hyper Data Frame

Plot a Colour Map

Extract Unique Points from a Spatial Point Pattern

Set or Reset the Marks in a Point Pattern

Extract Subset of Line Segment Pattern

Test Whether Marks Are Present

Superimpose Several Line Segment Patterns

Summary of a List of Things

Convert Polygonal Region into Different Format

Variance-Covariance Matrix for a Fitted Point Process Model

Create a Line Segment Pattern

Convert Data To Tessellation

Simulate a fitted cluster point process model.

spatstat.options

Internal Options in Spatstat Package

Cut margins from rectangle

Print Brief Details of a Point Pattern Dataset

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

Class of Quadrature Schemes

Define Point Process Model for Metropolis-Hastings Simulation.

Pine saplings in Finland.

Histogram of Pixel Values in an Image

The Strauss / Hard Core Point Process Model

Nearest neighbour

California Redwoods Point Pattern (Entire Dataset)

Test Whether Two Pixel Images Are Compatible

Window in Shape of Letter R

Quadrat counting for a point pattern

Ord's Interaction model

Determine Whether One Window is Contained In Another

Pair Correlation Function obtained from K Function

Simulate Thomas Process

Combine Two Line Segment Patterns

crossdist.default

Pairwise distances between two different sets of points

Reduced Second Moment Measure

quadratresample

Resample a Point Pattern by Resampling Quadrats

Summarizing a Quadrature Scheme

Update a Fitted Point Process Model

Bounding Box of a Window or Point Pattern

summary.splitppp

Summary of a Split Point Pattern

Circular Window

Beta Ganglion Cells in Cat Retina, Old Version

Simulate Matern Model I

Distance to Boundary of Window

Mean, Median and Range of Pixel Values in an Image