Learn R Programming

⚠️There's a newer version (3.2-1) of this package.Take me there.

spatstat (version 1.15-3)

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. 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).

Copy Link

Version

Install

install.packages('spatstat')

Monthly Downloads

19,373

Version

1.15-3

License

GPL (>= 2)

Maintainer

Adrian Baddeley

Last Published

May 14th, 2009

Functions in spatstat (1.15-3)

Beta Ganglion Cells in Cat Retina

Crossing Points of Two Line Segment Patterns

Pairwise distances between two different point patterns

The Strauss / Hard Core Point Process Model

The Strauss Point Process Model

dirichlet.weights

Compute Quadrature Weights Based on Dirichlet Tessellation

as.data.frame.psp

Coerce Line Segment Pattern to a Data Frame

Colour Lookup Tables

The Soft Core Point Process Model

Centroid of a window

Artificial Data Point Pattern

Weighted Empirical Cumulative Distribution Function

Convert Data To Class ppp

Delaunay Triangulation of Point Pattern

Distance Map of Window

Hyper Data Frame

Pixel Image Approximation of a Window

complement.owin

Take Complement of a Window

compatible.fasp

Test Whether Two Function Arrays Are Compatible

Interactively Add Points

Convert Data To Tessellation

Convert Polygonal Region into Different Format

Distance Map of Point Pattern

Clark and Evans Aggregation Index

Evaluate Expression Involving Functions

Calculate Summary Statistic for All Types in a Multitype Point Pattern

Determine Whether One Window is Contained In Another

Function Arrays for Spatial Patterns

Data Frames of Function Values

ANOVA for Fitted Point Process Models

Morphological Closing of a Window

Midpoints of Line Segment Pattern

Calculate four standard summary functions of a point pattern.

Convert Pixel Image to Matrix

Subdivide a Window or Tessellation using a Set of Lines

Evaluate Expression Involving Pixel Images

Coefficients of Fitted Point Process Model

as.data.frame.ppp

Coerce Point Pattern to a Data Frame

crossdist.default

Pairwise distances between two different sets of points

Berman-Huntington points and lines data

Fitted Conditional Intensity for Point Process Model

Concatenate x,y Coordinate Vectors

bounding.box.xy

Convex Hull of Points

inforder.family

Infinite Order Interaction Family

Bounding Box of a Window or Point Pattern

Pairwise distances

Interactively Define a Polygon

adaptive.density

Intensity Estimate of Point Pattern Using Tessellation

Apply Affine Transformation To Line Segment Pattern

Orientation Angles of Line Segments

Apply Function to Image Broken Down by Factor

Diagnostic Plots for Fitted Point Process Model

Distance to Boundary of Window

pairdist.default

Pairwise distances

Fit a Log-Gaussian Cox Point Process by Minimum Contrast

Hutchings' Bramble Canes data

Create a Point Matching

Chorley-Ribble Cancer Data

Apply Gaussian Blur to a Pixel Image

Saturated Pairwise Interaction Point Process Family

Apply Affine Transformation

Extract Original Data from a Fitted Point Process Model

Convert Data To Class psp

Test Whether Two Pixel Images Are Compatible

Connected components of an image or window

Dirichlet Tessellation of Point Pattern

Determine Duplicated Points in a Spatial Point Pattern

Distance Map of Line Segment Pattern

Kernel Smoothed Intensity of Point Pattern

Aherne's hamster tumour data

Prediction from a Fitted Cluster Point Process Model

Extract the Interaction from a Fitted Point Process Model

is.multitype.ppp

Test Whether A Point Pattern is Multitype

Areas of Morphological Erosions

Generate N Uniform Random Points in a Disc

Apply Function to Every Neighbourhood in a Point Pattern

Create a Window

Exponential Energy Marks

Kaplan-Meier and Reduced Sample Estimator using Histograms

Distance to Boundary of Window

Distance Between Two Point Patterns

Convert Pixel Image from Numeric to Factor

Kernel Smoothing of Line Segment Pattern

Test Whether Marks Are Present

Intersect Infinite Straight Lines with a Window

Area of a Window

Mark Correlation Function

Apply a Function to a Point Pattern Broken Down by Factor

Class of Line Segment Patterns

Endpoints of Line Segment Pattern

Fit the Matern Cluster Point Process by Minimum Contrast

Biological Cells Point Pattern

pairwise.family

Pairwise Interaction Process Family

Rectangular grid of points

Beadlet Anemones Data

Difference of Disc Areas

Pair Correlation Function obtained from K Function

Evaluate Expression Involving Function Arrays

Apply Affine Transformation To Point Pattern

Interpolate a Pixel Image

Convert Data To Class owin

Fry Plot of Point Pattern

Harkness-Isham ants' nests data

Pairwise distances between two different line segment patterns

Spruces Point Pattern

Simulation envelopes of summary function

Hughes' Amacrine Cell Data

Extract Dummy Points Used to Fit a Point Process Model

Test Whether A Point Process Model is Marked

Convert Point Pattern to Another Unit of Length

Tropical rain forest trees

Divide Region into Quadrats

Reduced Sample Estimator using Histogram Data

Convert Point Pattern to Pixel Image

multiplicity.ppp

Count Multiplicity of Duplicate Points

Mean, Median and Range of Pixel Values in an Image

Simulate Baddeley-Silverman Cell Process

Intersection or Union of Two Windows

Test Whether Points Are Inside A Window

Convert Line Segment Pattern to Another Unit of Length

spatstat-deprecated

Deprecated spatstat functions

Histogram of Pixel Values in an Image

New Zealand Trees Point Pattern

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

Test Whether An Object Is A Fitted Point Process Model

Interpret Fitted Model for Metropolis-Hastings Simulation.

Find Line Segment Nearest to Each Point

Beta Ganglion Cells in Cat Retina, Old Version

Apply Vector Translation To Window

Pair Correlation Function

Dilate a Window

Tabulate Marks in Neighbourhood of Every Point in a Point Pattern

Log Likelihood for Poisson Point Process Model

Summarizing a Pixel Image

Murchison gold deposits

Plot a tessellation

Infinite Straight Lines

Plot a plotppm Object Created by plot.ppm

Plot a fitted cluster point process

Simulate Matern Model II

Test whether Object is Multitype

Test Whether Two Function Objects Are Compatible

density.splitppp

Kernel Smoothed Intensity of Split Point Pattern

Compute Quadrature Weights Based on Grid Counts

Classify Points in a Point Pattern

Identify Points in a Point Pattern

summary.splitppp

Summary of a Split Point Pattern

Safely Convert Point Pattern Window to Binary Mask

Point Patterns of New Brunswick Forest Fires

Nearest neighbour

Simulate Simple Sequential Inhibition

Generate N Random Points

Class of Fitted Point Process Models

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

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

Expand Window By Factor

Generate a Quadrature Scheme from a Point Pattern

Evaluate an Expression in Each Row of a Hyperframe

Rotate a Line Segment Pattern

Generate a Default Pattern of Dummy Points

Pine saplings in Finland.

Method of Minimum Contrast

Extract Quadrature Scheme Used to Fit a Point Process Model

Kolmogorov-Smirnov Test for Point Process Model

Sample Quantiles of Pixel Image

Simulate from a Fitted Point Process Model

Distance for a Point Pattern Matching

California Redwoods Point Pattern (Entire Dataset)

Nearest neighbour distances

rshift.splitppp

Randomly Shift a List of Point Patterns

Place Points Evenly Along Specified Lines

Divide Point Pattern into Sub-patterns

Simulate Gauss-Poisson Process

Perfect Simulation of the Strauss Process

Extract List of Tiles in a Tessellation

Determine Initial State for Metropolis-Hastings Simulation.

Pair Correlation Function of Point Pattern

Circular Window

Apply Vector Translation To Pixel Image

Test Whether An Object Is A Pixel Image

Define Point Process Model for Metropolis-Hastings Simulation.

Simulate Thomas Process

Class of Images

Profile Maximum Pseudolikelihood

Interaction Distance of a Point Process

Plot a Function Array

spatstat-internal

Internal spatstat functions

Lansing Woods Point Pattern

Morishita Index Plot

quadratresample

Resample a Point Pattern by Resampling Quadrats

Humberside Data on Childhood Leukaemia and Lymphoma

Extract Subset of Function Array

Intersection of Two Tessellations

Spatial smoothing of observations at irregular points

Longleaf Pines Point Pattern

Lurking variable plot

Diggle's Heather Data

Randomly Shift a Line Segment Pattern

Galaxies in the Shapley Supercluster

Level Set of a Pixel Image

Plot a Spatial Window

plot a Fitted Point Process Model

Extract or Replace Subset of a List of Things

Neighbourhood density function

is.multitype.ppm

Test Whether A Point Process Model is Multitype

quadrat.test.splitppp

Chi-Squared Test of CSR for Split Point Pattern

Data and Code From JRSS Discussion Paper on Residuals

Simulate Matern Cluster Process

Morphological Opening of a Window

Mosaic Random Set

plot a Spatial Line Segment Pattern

Nearest-Neighbour Correlation Indices of Marked Point Pattern

Basis for Harmonic Functions

Simulate a fitted cluster point process model.

rmhmodel.default

Build Point Process Model for Metropolis-Hastings Simulation.

Subset of Quadrature Scheme

Quadrat counting for a point pattern

Rotate a Window

Evaluate an Expression in a Function Table

Fit the Thomas Point Process by Minimum Contrast

Cartesian Coordinates for a Pixel Raster

Mark Connection Function

Sufficient Statistic of Point Process Model

Variance-Covariance Matrix for a Fitted Point Process Model

plot.hyperframe

Plot Entries in a Hyperframe

Summarise Marks in Every Neighbourhood in a Point Pattern

Random Thinning

Compute Integral of Function Against Cumulative Distribution

Fit cluster point process model

Fit Point Process Model to Data

Mark Correlation Integral

Summary of a Spatial Window

Ord Interaction Process Family

model.matrix.ppm

Extract Design Matrix from Point Process Model

Plot a Pixel Image

Plot Function Valuesn

Apply Affine Transformation To Window

Quadrature Scheme Based on Pixel Grid

Lengths of Line Segments

Vertices of a Window

project2segment

Move Point To Nearest Line

Compute Images of Constructed Covariates

nearest.raster.point

Find Pixel Nearest to a Given Point

Random Re-Labelling of Point Pattern

selfcrossing.psp

Crossing Points in a Line Segment Pattern

Summary of a Point Pattern Dataset

Simulate systematic random point pattern

Convert dataset to another unit of length

Contour plot of pixel image

Generate Poisson Random Line Process

Summarizing a Fitted Point Process Model

Perspective Plot of Pixel Image

Convert to Pixel Image

Diameter of a Window

Rotate a Point Pattern

Nearest neighbour distances between line segments

Generate Multitype Poisson Point Pattern

Union of Data and Dummy Points

Poisson Line Tessellation

Simulate Matern Model I

Plot a List of Things

plot a Spatial Point Pattern

Class of Quadrature Schemes

Print Progress Reports

Pair Correlation Function obtained from array of K functions

Pairwise distances between line segments

Print Brief Details of a Line Segment Pattern Dataset

Create a Point Pattern

Convert Pixel Image to Another Unit of Length

Convert Window to Another Unit of Length

Extract Subset of Line Segment Pattern

Multitype pair correlation function

Estimate window from points alone

Plot a Colour Map

Japanese Pines Point Pattern

Simulate Point Process Models using the Metropolis-Hastings Algorithm.

California Redwoods Point Pattern (Ripley's Subset)

Ponderosa Pine Tree Point Pattern

Print Brief Details of a Point Pattern Dataset

Simulate point patterns using the Metropolis-Hastings algorithm.

Swedish Pines Point Pattern

Plot a List of Point Patterns

pppmatching.object

Class of Point Matchings

rescue.rectangle

Convert Window Back To Rectangle

Kaplan-Meier Estimator using Histogram Data

Set Control Parameters for Metropolis-Hastings Algorithm.

Prediction from a Fitted Point Process Model

Generate Poisson Point Pattern

Extract or Replace Subset of Point Pattern

Set Covariance of a Window

Apply Vector Translation To Point Pattern

Randomly Shift a Point Pattern

Random Perturbation of a Point Pattern

subset.splitppp

Extract or Replace Sub-Patterns

Read Point Pattern From Data File

Reset Values in Subset of Image

Class of Point Patterns

spatstat.options

Internal Options in Spatstat Package

Generate grid of parallel lines with random displacement

Print a Fitted Point Process Model

Marked Nearest Neighbour Distance Function

Extract or Replace Subset of Tessellation

Simulate Stratified Random Point Pattern

Define Point Process Model for Metropolis-Hastings Simulation.

Extract Subset of Function Values

Set or Reset the Marks in a Point Pattern

Create a Line Segment Pattern

plot a Spatial Quadrature Scheme

Q-Q Plot of Residuals from Fitted Point Process Model

Print Brief Details of an Image

Create a Tessellation

Mosaic Random Field

Update a Fitted Cluster Point Process Model

Test Whether An Object Is A Point Pattern

Summary of a List of Things

Poisson Point Process Model

Extract Unique Points from a Spatial Point Pattern

Simulate Neyman-Scott Process

The Lennard-Jones Potential

Generate Poisson Point Pattern on Line Segments

Urkiola Woods Point Pattern

Reduced Second Moment Measure

runifpointOnLines

Generate N Uniform Random Points On Line Segments

Name for Unit of Length

Pairwise distances

Diagnostics for random marking

Multitype J Function (i-to-j)

Geyer's Saturation Point Process Model

Spokes pattern of dummy points

Window in Shape of Letter R

K-function using FFT

Generate N Uniform Random Points

Summarizing a Quadrature Scheme

The Piecewise Constant Pairwise Interaction Point Process Model

Simulated Point Pattern

Generate N Random Multitype Points

Superimpose Several Line Segment Patterns

Cut margins from rectangle

Saturated Pairwise Interaction model

Multitype K Function (Cross-type)

Marked J Function

Multitype J Function (i-to-any)

Superimpose Several Point Patterns

Print Brief Details of a Spatial Window

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

Ord's Interaction model

Nearest Neighbours Between Two Patterns

MultiStraussHard

The Multitype/Hard Core Strauss Point Process Model

Pairwise distances

Nearest Neighbour Distance Function G

Corners of a rectangle

Extract Subset of Image

Residuals for Fitted Point Process Model

Apply Vector Translation

The Area Interaction Point Process Model

Inhomogeneous K-function

Convex Hull of Points

Print a Quadrature Scheme

Test Whether A Point Pattern is Marked

The Spatstat Package

Update a Fitted Point Process Model

Estimate the empty space function F

Spherical Contact Distribution Function

Hybrid Geyer Point Process Model

Generic Pairwise Interaction model

Estimate the I-function

Multitype K Function (i-to-any)

Inhomogeneous Multitype K Dot Function

Multitype L-function (cross-type)

Generic Ord Interaction model

Estimate the J-function

The Multitype Strauss Point Process Model

Marked K-Function

Inhomogeneous Cross K Function

Multitype L-function (i-to-any)

Combine Two Line Segment Patterns

Diggle-Gratton model

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

Divide Image Into Sub-images

Apply Vector Translation To Line Segment Pattern

Test Whether An Object Is A Window

Piecewise Constant Saturated Pairwise Interaction Point Process Model

Summary of a Line Segment Pattern Dataset

Find Largest Circle Inside Window

Create a Pixel Image Object