spatstat v1.35-0

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by Adrian Baddeley

Spatial Point Pattern analysis, model-fitting, simulation, tests

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 1500 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 quadrat counts, K-functions and their simulation envelopes, 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, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported. Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.

Functions in spatstat

Name Description
affine.im Apply Affine Transformation To Pixel Image
Fest Estimate the empty space function F
Kmodel K function of a model
as.hyperframe Convert Data to Hyperframe
as.psp Convert Data To Class psp
Kmeasure Reduced Second Moment Measure
Jmulti Marked J Function
Gres Residual G Function
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
Hardcore The Hard Core Point Process Model
ants Harkness-Isham ants' nests data
bind.fv Combine Function Value Tables
as.linim Convert to Pixel Image on Linear Network
append.psp Combine Two Line Segment Patterns
complement.owin Take Complement of a Window
Pairwise Generic Pairwise Interaction model
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
bei Tropical rain forest trees
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
Kcross.inhom Inhomogeneous Cross K Function
delaunay Delaunay Triangulation of Point Pattern
bounding.box.xy Convex Hull of Points
Extract.splitppp Extract or Replace Sub-Patterns
affine.ppp Apply Affine Transformation To Point Pattern
bw.frac Bandwidth Selection Based on Window Geometry
Extract.owin Extract Subset of Window
Extract.fasp Extract Subset of Function Array
Finhom Inhomogeneous Empty Space Function
Tstat Third order summary statistic
Extract.psp Extract Subset of Line Segment Pattern
Extract.layered Extract Subset of a Layered Object
Ginhom Inhomogeneous Nearest Neighbour Function
cbind.hyperframe Combine Hyperframes by Rows or by Columns
area.owin Area of a Window
Concom The Connected Component Process Model
Extract.ppx Extract Subset of Multidimensional Point Pattern
discpartarea Area of Part of Disc
angles.psp Orientation Angles of Line Segments
Extract.im Extract Subset of Image
Kres Residual K Function
as.matrix.owin Convert Pixel Image to Matrix
affine.linnet Apply Geometrical Transformations to a Linear Network
MultiHard The Multitype Hard Core Point Process Model
Extract.fv Extract Subset of Function Values
as.polygonal Convert a Window to a Polygonal Window
blur Apply Gaussian Blur to a Pixel Image
coef.mppm Coefficients of Point Process Model Fitted to Multiple Point Patterns
crossdist.default Pairwise distances between two different sets of points
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
deltametric Delta Metric
Kdot Multitype K Function (i-to-any)
areaGain Difference of Disc Areas
eem Exponential Energy Marks
gridweights Compute Quadrature Weights Based on Grid Counts
dfbetas.ppm Parameter influence measure
as.box3 Convert Data to Three-Dimensional Box
anova.lppm ANOVA for Fitted Point Process Models on Linear Network
edge.Ripley Ripley's Isotropic Edge Correction
allstats Calculate four standard summary functions of a point pattern.
data.ppm Extract Original Data from a Fitted Point Process Model
cut.im Convert Pixel Image from Numeric to Factor
G3est Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
envelope Simulation Envelopes of Summary Function
closing Morphological Closing
Kinhom Inhomogeneous K-function
linearpcfcross Multitype Pair Correlation Function (Cross-type) for Linear Point Pattern
hyytiala Scots pines and other trees at Hyytiala
Extract.listof Extract or Replace Subset of a List of Things
corners Corners of a rectangle
Extract.quad Subset of Quadrature Scheme
as.lpp Convert Data to a Point Pattern on a Linear Network
commonGrid Determine A Common Spatial Domain And Pixel Resolution
Fiksel The Fiksel Interaction
Jinhom Inhomogeneous J-function
Geyer Geyer's Saturation Point Process Model
Poisson Poisson Point Process Model
Lcross.inhom Inhomogeneous Cross Type L Function
bronzefilter Bronze gradient filter data
Extract.linnet Extract Subset of Linear Network
formula.ppm Model Formulae for Gibbs Point Process Models
ewcdf Weighted Empirical Cumulative Distribution Function
K3est K-function of a Three-Dimensional Point Pattern
OrdThresh Ord's Interaction model
intensity Intensity of a Dataset or a Model
bdist.tiles Distance to Boundary of Window
betacells Beta Ganglion Cells in Cat Retina
LambertW Lambert's W Function
edge.Trans Translation Edge Correction
Smooth Spatial smoothing of data
bw.diggle Cross Validated Bandwidth Selection for Kernel Density
diameter Diameter of an Object
anemones Beadlet Anemones Data
LennardJones The Lennard-Jones Potential
Lcross Multitype L-function (cross-type)
lurking Lurking variable plot
affine.psp Apply Affine Transformation To Line Segment Pattern
fv.object Function Value Table
dilation Morphological Dilation
bdist.points Distance to Boundary of Window
as.interact Extract Interaction Structure
bounding.box Bounding Box of a Window or Point Pattern
envelope.envelope Recompute Envelopes
AreaInter The Area Interaction Point Process Model
bw.scott Scott's Rule for Bandwidth Selection for Kernel Density
by.im Apply Function to Image Broken Down by Factor
deriv.fv Calculate Derivative of Function Values
Gcom Model Compensator of Nearest Neighbour Function
affine.owin Apply Affine Transformation To Window
Gfox Foxall's Distance Functions
Extract.tess Extract or Replace Subset of Tessellation
as.data.frame.hyperframe Coerce Hyperframe to Data Frame
Kest K-function
amacrine Hughes' Amacrine Cell Data
convexhull.xy Convex Hull of Points
bw.smoothppp Cross Validated Bandwidth Selection for Spatial Smoothing
Gest Nearest Neighbour Distance Function G
affine.lpp Apply Geometrical Transformations to Point Pattern on a Linear Network
ganglia Beta Ganglion Cells in Cat Retina, Old Version
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
beginner Print Introduction For Beginners
convolve.im Convolution of Pixel Images
disc Circular Window
Kest.fft K-function using FFT
anova.ppm ANOVA for Fitted Point Process Models
edges2vees List Dihedral Triples in a Graph
distmap.owin Distance Map of Window
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
Hybrid Hybrid Interaction Point Process Model
Iest Estimate the I-function
beachcolours Create Colour Scheme for a Range of Numbers
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
crossdist.ppp Pairwise distances between two different point patterns
default.dummy Generate a Default Pattern of Dummy Points
Ldot Multitype L-function (i-to-any)
is.owin Test Whether An Object Is A Window
Kmulti.inhom Inhomogeneous Marked K-Function
copper Berman-Huntington points and lines data
boxx Multi-Dimensional Box
Strauss The Strauss Point Process Model
as.mask.psp Convert Line Segment Pattern to Binary Pixel Mask
markconnect Mark Connection Function
as.data.frame.ppp Coerce Point Pattern to a Data Frame
gorillas Gorilla Nesting Sites
inforder.family Infinite Order Interaction Family
density.ppp Kernel Smoothed Intensity of Point Pattern
methods.linnet Methods for Linear Networks
as.mask Pixel Image Approximation of a Window
diameter.boxx Geometrical Calculations for Multi-Dimensional Box
Kcross Multitype K Function (Cross-type)
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
convexhull Convex Hull
dummify Convert Data to Numeric Values by Constructing Dummy Variables
Jdot Multitype J Function (i-to-any)
delaunay.distance Distance on Delaunay Triangulation
harmonic Basis for Harmonic Functions
DiggleGatesStibbard Diggle-Gates-Stibbard Point Process Model
hybrid.family Hybrid Interaction Family
interp.colourmap Interpolate smoothly between specified colours
Gmulti Marked Nearest Neighbour Distance Function
box3 Three-Dimensional Box
eval.fasp Evaluate Expression Involving Function Arrays
as.ppm Extract Fitted Point Process Model
methods.fii Methods for Fitted Interactions
F3est Empty Space Function of a Three-Dimensional Point Pattern
nndist Nearest neighbour distances
clmfires Castilla-La Mancha Forest Fires
linearKcross.inhom Inhomogeneous multitype K Function (Cross-type) for Linear Point Pattern
methods.rhohat Methods for Intensity Functions of Spatial Covariate
compareFit Residual Diagnostics for Multiple Fitted Models
is.multitype Test whether Object is Multitype
intensity.ppp Empirical Intensity of Point Pattern
localKinhom Inhomogeneous Neighbourhood Density Function
crossdist.psp Pairwise distances between two different line segment patterns
diameter.box3 Geometrical Calculations for Three-Dimensional Box
circumradius Circumradius and Diameter of a Linear Network
inside.owin Test Whether Points Are Inside A Window
crossdist Pairwise distances
rStrauss Perfect Simulation of the Strauss Process
as.ppp Convert Data To Class ppp
BadGey Hybrid Geyer Point Process Model
eroded.areas Areas of Morphological Erosions
bermantest Berman's Tests for Point Process Model
as.fv Convert Data To Class fv
methods.lppm Methods for Fitted Point Process Models on a Linear Network
compatible Test Whether Objects Are Compatible
as.owin Convert Data To Class owin
addvar Added Variable Plot for Point Process Model
clickppp Interactively Add Points
Hest Spherical Contact Distribution Function
linearmarkconnect Mark Connection Function for Multitype Point Pattern on Linear Network
rHardcore Perfect Simulation of the Hardcore Process
Extract.lpp Extract Subset of Point Pattern on Linear Network
as.tess Convert Data To Tessellation
colourmap Colour Lookup Tables
chicago Chicago Street Crime Data
demohyper Demonstration Example of Hyperframe of Spatial Data
border Border Region of a Window
Saturated Saturated Pairwise Interaction model
clickpoly Interactively Define a Polygon
layered Create List of Plotting Layers
connected Connected components
Jcross Multitype J Function (i-to-j)
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
fasp.object Function Arrays for Spatial Patterns
model.matrix.ppm Extract Design Matrix from Point Process Model
clickjoin Interactively join vertices on a plot
Replace.im Reset Values in Subset of Image
linearKdot.inhom Inhomogeneous multitype K Function (Dot-type) for Linear Point Pattern
is.lpp Test Whether An Object Is A Point Pattern on a Linear Network
linfun Function on a Linear Network
distmap Distance Map
distmap.psp Distance Map of Line Segment Pattern
coef.ppm Coefficients of Fitted Point Process Model
envelope.lpp Envelope for Point Patterns on Linear Network
methods.ppx Methods for Multidimensional Space-Time Point Patterns
plot.listof Plot a List of Things
anova.mppm ANOVA for Fitted Multiple Point Process Models
as.matrix.im Convert Pixel Image to Matrix or Array
kaplan.meier Kaplan-Meier Estimator using Histogram Data
as.data.frame.im Convert Pixel Image to Data Frame
endpoints.psp Endpoints of Line Segment Pattern
idw Inverse-distance weighted smoothing of observations at irregular points
rcell Simulate Baddeley-Silverman Cell Process
eval.im Evaluate Expression Involving Pixel Images
centroid.owin Centroid of a window
as.im Convert to Pixel Image
is.ppm Test Whether An Object Is A Fitted Point Process Model
MultiStrauss The Multitype Strauss Point Process Model
bramblecanes Hutchings' Bramble Canes data
compatible.im Test Whether Pixel Images Are Compatible
distfun.lpp Distance Map on Linear Network
chorley Chorley-Ribble Cancer Data
bw.ppl Likelihood Cross Validation Bandwidth Selection for Kernel Density
fryplot Fry Plot of Point Pattern
flipxy Exchange X and Y Coordinates
crossing.psp Crossing Points of Two Line Segment Patterns
funxy Spatial Function Class
matchingdist Distance for a Point Pattern Matching
distcdf Distribution Function of Interpoint Distance
Ord Generic Ord Interaction model
layerplotargs Extract or Replace the Plot Arguments of a Layered Object
plot.linnet Plot a linear network
linearKdot Multitype K Function (Dot-type) for Linear Point Pattern
hamster Aherne's hamster tumour data
concatxy Concatenate x,y Coordinate Vectors
opening Morphological Opening
plot.influence.ppm Plot Influence Measure
linearKcross Multitype K Function (Cross-type) for Linear Point Pattern
linearmarkequal Mark Connection Function for Multitype Point Pattern on Linear Network
letterR Window in Shape of Letter R
fitted.slrm Fitted Probabilities for Spatial Logistic Regression
matclust.estpcf Fit the Matern Cluster Point Process by Minimum Contrast Using Pair Correlation
dclf.progress Progress Plot of Test of Spatial Pattern
Ldot.inhom Inhomogeneous Multitype L Dot Function
plot.psp plot a Spatial Line Segment Pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
lpp Create Point Pattern on Linear Network
localpcf Local pair correlation function
fitin.ppm Extract the Interaction from a Fitted Point Process Model
latest.news Print News About Latest Version of Package
linearpcf Linear Pair Correlation Function
dclf.test Diggle-Cressie-Loosmore-Ford and Maximum Absolute Deviation Tests
midpoints.psp Midpoints of Line Segment Pattern
chop.tess Subdivide a Window or Tessellation using a Set of Lines
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
lgcp.estpcf Fit a Log-Gaussian Cox Point Process by Minimum Contrast
finpines Pine saplings in Finland.
methods.layered Methods for Layered Objects
pcf.fasp Pair Correlation Function obtained from array of K functions
im Create a Pixel Image Object
perimeter Perimeter Length of Window
model.frame.ppm Extract the Variables in a Point Process Model
clip.infline Intersect Infinite Straight Lines with a Window
plot.owin Plot a Spatial Window
is.stationary Recognise Stationary and Poisson Point Process Models
logLik.slrm Loglikelihood of Spatial Logistic Regression
edges2triangles List Triangles in a Graph
kppm Fit Cluster or Cox Point Process Model
marks.psp Marks of a Line Segment Pattern
areaLoss Difference of Disc Areas
is.rectangle Determine Type of Window
pppmatching Create a Point Matching
summary.owin Summary of a Spatial Window
cauchy.estpcf Fit the Neyman-Scott cluster process with Cauchy kernel
is.marked.ppp Test Whether A Point Pattern is Marked
lppm Fit Point Process Model to Point Pattern on Linear Network
coef.slrm Coefficients of Fitted Spatial Logistic Regression Model
linearKinhom Inhomogeneous Linear K Function
Emark Diagnostics for random marking
fv Create a Function Value Table
is.im Test Whether An Object Is A Pixel Image
nnwhich Nearest neighbour
bdist.pixels Distance to Boundary of Window
infline Infinite Straight Lines
pairwise.family Pairwise Interaction Process Family
methods.boxx Methods for Multi-Dimensional Box
dilated.areas Areas of Morphological Dilations
split.ppp Divide Point Pattern into Sub-patterns
fvnames Abbreviations for Groups of Columns in Function Value Table
collapse.fv Collapse Several Function Tables into One
nnwhich.ppx Nearest Neighbours in Any Dimensions
closepairs Close Pairs of Points
rpoisppx Generate Poisson Point Pattern in Any Dimensions
methods.lpp Methods for Point Patterns on a Linear Network
diameter.owin Diameter of a Window
plot.colourmap Plot a Colour Map
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
mppm Fit Point Process Model to Several Point Patterns
expand.owin Apply Expansion Rule
Lest L-function
is.multitype.ppm Test Whether A Point Process Model is Multitype
incircle Find Largest Circle Inside Window
markcorrint Mark Correlation Integral
as.rectangle Window Frame
cauchy.estK Fit the Neyman-Scott cluster process with Cauchy kernel
iplot Point and Click Interface for Displaying Spatial Data
density.psp Kernel Smoothing of Line Segment Pattern
Triplets The Triplet Point Process Model
methods.linfun Methods for Functions on Linear Network
linearpcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-type) for Linear Point Pattern
imcov Spatial Covariance of a Pixel Image
nztrees New Zealand Trees Point Pattern
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
model.matrix.slrm Extract Design Matrix from Spatial Logistic Regression Model
cut.ppp Classify Points in a Point Pattern
humberside Humberside Data on Childhood Leukaemia and Lymphoma
mean.im Maximum, Minimum, Mean, Median, Range or Sum of Pixel Values in an Image
as.hyperframe.ppx Extract coordinates and marks of multidimensional point pattern
mincontrast Method of Minimum Contrast
ppm.object Class of Fitted Point Process Models
stieltjes Compute Integral of Function Against Cumulative Distribution
objsurf Objective Function Surface
nnfun Nearest Neighbour Index Map as a Function
heather Diggle's Heather Data
pairdist Pairwise distances
linearpcfdot Multitype Pair Correlation Function (Dot-type) for Linear Point Pattern
demopat Artificial Data Point Pattern
default.rmhcontrol Set Default Control Parameters for Metropolis-Hastings Algorithm.
owin Create a Window
plot.lppm Plot a Fitted Point Process Model on a Linear Network
linearpcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Dot-type) for Linear Point Pattern
psp.object Class of Line Segment Patterns
rhohat Smoothing Estimate of Covariate Transformation
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
fitted.ppm Fitted Conditional Intensity for Point Process Model
Kdot.inhom Inhomogeneous Multitype K Dot Function
crossdist.lpp Pairwise distances between two point patterns on a linear network
model.images Compute Images of Constructed Covariates
coords Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern
gordon People in Gordon Square
Kmulti Marked K-Function
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
ippm Optimise Irregular Trend Parameters in Point Process Model
rcellnumber Generate Random Numbers of Points for Cell Process
is.marked.ppm Test Whether A Point Process Model is Marked
markvario Mark Variogram
npfun Dummy Function Returns Number of Points
lut Lookup Tables
pairsat.family Saturated Pairwise Interaction Point Process Family
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
erosion Morphological Erosion
envelope.pp3 Simulation Envelopes of Summary Function for 3D Point Pattern
model.depends Identify Covariates Involved in each Model Term
eval.linim Evaluate Expression Involving Pixel Images on Linear Network
dirichlet Dirichlet Tessellation of Point Pattern
quantile.im Sample Quantiles of Pixel Image
project2segment Move Point To Nearest Line
hist.im Histogram of Pixel Values in an Image
marks Marks of a Point Pattern
plot.hyperframe Plot Entries in a Hyperframe
distmap.ppp Distance Map of Point Pattern
is.empty Test Whether An Object Is Empty
rMatClust Simulate Matern Cluster Process
plot.im Plot a Pixel Image
ppx Multidimensional Space-Time Point Pattern
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
methods.funxy Methods for Spatial Functions
ord.family Ord Interaction Process Family
clusterset Allard-Fraley Estimator of Cluster Feature
pcf.ppp Pair Correlation Function of Point Pattern
plot.ppp plot a Spatial Point Pattern
nndist.lpp Nearest neighbour distances on a linear network
spruces Spruces Point Pattern
Jest Estimate the J-function
plot.layered Layered Plot
kstest.mppm Kolmogorov-Smirnov Test for Multiple Point Process Model
is.marked Test Whether Marks Are Present
npoints Number of Points in a Point Pattern
Linhom L-function
runifpoint3 Generate N Uniform Random Points in Three Dimensions
cells Biological Cells Point Pattern
rshift.splitppp Randomly Shift a List of Point Patterns
rStraussHard Perfect Simulation of the Strauss-Hardcore Process
summary.quad Summarizing a Quadrature Scheme
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
intensity.ppm Intensity of Fitted Point Process Model
clarkevans.test Clark and Evans Test
swedishpines Swedish Pines Point Pattern
hyperframe Hyper Data Frame
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
colourtools Convert and Compare Colours in Different Formats
crossdist.ppx Pairwise Distances Between Two Different Multi-Dimensional Point Patterns
pixellate Convert Spatial Object to Pixel Image
discretise Safely Convert Point Pattern Window to Binary Mask
pixellate.ppp Convert Point Pattern to Pixel Image
periodify Make Periodic Copies of a Spatial Pattern
formula.fv Extract or Change the Plot Formula for a Function Value Table
nndist.ppx Nearest Neighbour Distances in Any Dimensions
contour.im Contour plot of pixel image
crossdist.pp3 Pairwise distances between two different three-dimensional point patterns
bw.relrisk Cross Validated Bandwidth Selection for Relative Risk Estimation
rmhexpand Specify Simulation Window or Expansion Rule
split.ppx Divide Multidimensional Point Pattern into Sub-patterns
distfun Distance Map as a Function
compatible.fv Test Whether Function Objects Are Compatible
plot.pp3 Plot a three-dimensional point pattern
harmonise.im Make Pixel Images Compatible
linearpcfinhom Inhomogeneous Linear Pair Correlation Function
pp3 Three Dimensional Point Pattern
identify.psp Identify Segments in a Line Segment Pattern
pairdist.ppx Pairwise Distances in Any Dimensions
Kcom Model Compensator of K Function
gridcentres Rectangular grid of points
integral.im Integral of a Pixel Image
quadrat.test.mppm Chi-Squared Test for Multiple Point Process Model Based on Quadrat Counts
exactMPLEstrauss Exact Maximum Pseudolikelihood Estimate for Stationary Strauss Process
plot.kppm Plot a fitted cluster point process
intensity.lpp Empirical Intensity of Point Pattern on Linear Network
connected.ppp Connected components of a point pattern
subfits Extract List of Individual Point Process Models
thomas.estpcf Fit the Thomas Point Process by Minimum Contrast
pcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)
plot.bermantest Plot Result of Berman Test
split.im Divide Image Into Sub-images
Kscaled Locally Scaled K-function
is.multitype.ppp Test Whether A Point Pattern is Multitype
nnfun.lpp Nearest Neighbour Map on Linear Network
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
kstest.ppm Kolmogorov-Smirnov Test for Point Pattern or Point Process Model
mucosa Cells in Gastric Mucosa
rotate.owin Rotate a Window
japanesepines Japanese Pines Point Pattern
psstG Pseudoscore Diagnostic For Fitted Model against Saturation Alternative
quadrat.test.splitppp Dispersion Test of CSR for Split Point Pattern Based on Quadrat Counts
pcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-Type)
simplenet Simple Example of Linear Network
murchison Murchison gold deposits
integral.msr Integral of a Measure
sidelengths.owin Side Lengths of Enclosing Rectangle of a Window
lohboot Bootstrap Confidence Bands for Summary Function
rGaussPoisson Simulate Gauss-Poisson Process
predict.slrm Predicted or Fitted Values from Spatial Logistic Regression
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
owin.object Class owin
plot.tess Plot a tessellation
nnclean Nearest Neighbour Clutter Removal
identify.ppp Identify Points in a Point Pattern
bw.stoyan Stoyan's Rule of Thumb for Bandwidth Selection
unique.ppp Extract Unique Points from a Spatial Point Pattern
nndist.pp3 Nearest neighbour distances in three dimensions
localK Neighbourhood density function
paracou Kimboto trees at Paracou, French Guiana
pool.rat Pool Data from Several Ratio Objects
Softcore The Soft Core Point Process Model
rMosaicField Mosaic Random Field
logLik.mppm Log Likelihood for Poisson Point Process Model
update.rmhcontrol Update Control Parameters of Metropolis-Hastings Algorithm
lineardisc Compute Disc of Given Radius in Linear Network
rthin Random Thinning
reduced.sample Reduced Sample Estimator using Histogram Data
plot.splitppp Plot a List of Point Patterns
is.ppp Test Whether An Object Is A Point Pattern
rescale.ppp Convert Point Pattern to Another Unit of Length
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
reflect Reflect In Origin
raster.x Cartesian Coordinates for a Pixel Raster
pcfcross Multitype pair correlation function (cross-type)
pyramidal Pyramidal Neurons in Cingulate Cortex
print.ppp Print Brief Details of a Point Pattern Dataset
markcorr Mark Correlation Function
eval.fv Evaluate Expression Involving Functions
rLGCP Simulate Log-Gaussian Cox Process
nsegments Number of Line Segments in a Line Segment Pattern
will.expand Test Expansion Rule
urkiola Urkiola Woods Point Pattern
shift.psp Apply Vector Translation To Line Segment Pattern
rknn Theoretical Distribution of Nearest Neighbour Distance
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
print.ppm Print a Fitted Point Process Model
pppmatching.object Class of Point Matchings
simplify.owin Approximate a Polygon by a Simpler Polygon
nncross Nearest Neighbours Between Two Patterns
miplot Morishita Index Plot
flu Influenza Virus Proteins
intersect.tess Intersection of Two Tessellations
waterstriders Waterstriders data. Three independent replications of a point pattern formed by insects.
nndensity.ppp Estimate Intensity of Point Pattern Using Nearest Neighbour Distances
parres Partial Residuals for Point Process Model
pixelquad Quadrature Scheme Based on Pixel Grid
pcfdot Multitype pair correlation function (i-to-any)
linearK Linear K Function
quadrat.test Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
round.ppp Apply Numerical Rounding to Spatial Coordinates
predict.mppm Prediction for Fitted Multiple Point Process Model
shift.owin Apply Vector Translation To Window
methods.kppm Methods for Cluster Point Process Models
plot.ppm plot a Fitted Point Process Model
overlap.owin Compute Area of Overlap
rescale Convert dataset to another unit of length
pairdist.ppp Pairwise distances
nbfires Point Patterns of New Brunswick Forest Fires
pairdist.psp Pairwise distances between line segments
plot.plotppm Plot a plotppm Object Created by plot.ppm
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
interp.im Interpolate a Pixel Image
istat Point and Click Interface for Exploratory Analysis of Point Pattern
lengths.psp Lengths of Line Segments
linnet Create a Linear Network
is.subset.owin Determine Whether One Window is Contained In Another
scanpp Read Point Pattern From Data File
predict.lppm Predict Point Process Model on Linear Network
longleaf Longleaf Pines Point Pattern
pool.quadrattest Pool Several Quadrat Tests
contour.listof Plot a List of Things
methods.slrm Methods for Spatial Logistic Regression Models
nnwhich.pp3 Nearest neighbours in three dimensions
rDGS Perfect Simulation of the Diggle-Gates-Stibbard Process
Extract.ppp Extract or Replace Subset of Point Pattern
spatstat-package The Spatstat Package
is.convex Test Whether a Window is Convex
methods.pp3 Methods for three-dimensional point patterns
summary.splitppp Summary of a Split Point Pattern
pcfinhom Inhomogeneous Pair Correlation Function
summary.ppp Summary of a Point Pattern Dataset
rescale.psp Convert Line Segment Pattern to Another Unit of Length
rotate.psp Rotate a Line Segment Pattern
spatstat-internal Internal spatstat functions
pairdist.default Pairwise distances
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
ponderosa Ponderosa Pine Tree Point Pattern
msr Signed or Vector-Valued Measure
nncross.lpp Nearest Neighbours on a Linear Network
pairdist.lpp Pairwise shortest-path distances between points on a linear network
reach Interaction Distance of a Point Process
rsyst Simulate systematic random point pattern
project.ppm Force Point Process Model to be Valid
rgbim Create Colour-Valued Pixel Image
plot.linim Plot Pixel Image on Linear Network
DiggleGratton Diggle-Gratton model
shift Apply Vector Translation
rpoint Generate N Random Points
unitname Name for Unit of Length
print.owin Print Brief Details of a Spatial Window
slrm Spatial Logistic Regression
im.object Class of Images
scan.test Spatial Scan Test
pcf.fv Pair Correlation Function obtained from K Function
shapley Galaxies in the Shapley Supercluster
layout.boxes Generate a Row or Column Arrangement of Rectangles.
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
rNeymanScott Simulate Neyman-Scott Process
plot.msr Plot a Signed or Vector-Valued Measure
rThomas Simulate Thomas Process
quadrats Divide Region into Quadrats
residuals.mppm Residuals for Point Process Model Fitted to Multiple Point Patterns
union.quad Union of Data and Dummy Points
nnmark Mark of Nearest Neighbour
is.hybrid Test Whether Object is a Hybrid
selfcrossing.psp Crossing Points in a Line Segment Pattern
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
tilenames Names of Tiles in a Tessellation
quadscheme.logi Generate a Logistic Regression Quadrature Scheme from a Point Pattern
unnormdensity Weighted kernel smoother
methods.rho2hat Methods for Intensity Functions of Two Spatial Covariates
trim.rectangle Cut margins from rectangle
rpoispp3 Generate Poisson Point Pattern in Three Dimensions
unmark Remove Marks
pixellate.owin Convert Window to Pixel Image
rounding Detect Numerical Rounding
spatstat.options Internal Options in Spatstat Package
nearestsegment Find Line Segment Nearest to Each Point
leverage.ppm Leverage Measure for Spatial Point Process Model
runifpoint Generate N Uniform Random Points
scaletointerval Rescale Data to Lie Between Specified Limits
linim Create Pixel Image on Linear Network
print.quad Print a Quadrature Scheme
rshift.psp Randomly Shift a Line Segment Pattern
superimpose Superimpose Several Geometric Patterns
rDiggleGratton Perfect Simulation of the Diggle-Gratton Process
rMaternII Simulate Matern Model II
quadratresample Resample a Point Pattern by Resampling Quadrats
tweak.colourmap Change Colour Values in a Colour Map
rotate.im Rotate a Pixel Image
pppdist Distance Between Two Point Patterns
tile.areas Compute Areas of Tiles in a Tessellation
profilepl Profile Maximum Pseudolikelihood
ppp.object Class of Point Patterns
logLik.ppm Log Likelihood and AIC for Point Process Model
simulate.kppm Simulate a Fitted Cluster Point Process Model
methods.box3 Methods for Three-Dimensional Box
vcov.kppm Variance-Covariance Matrix for a Fitted Cluster Point Process Model
setcov Set Covariance of a Window
rstrat Simulate Stratified Random Point Pattern
progressreport Print Progress Reports
default.expand Default Expansion Rule for Simulation of Model
nncross.pp3 Nearest Neighbours Between Two Patterns in 3D
persp.im Perspective Plot of Pixel Image
shift.im Apply Vector Translation To Pixel Image
pixellate.psp Convert Line Segment Pattern to Pixel Image
pcf3est Pair Correlation Function of a Three-Dimensional Point Pattern
plot.mppm plot a Fitted Multiple Point Process Model
rotate.ppp Rotate a Point Pattern
lansing Lansing Woods Point Pattern
pairdist.pp3 Pairwise distances in Three Dimensions
rmpoint Generate N Random Multitype Points
quad.object Class of Quadrature Schemes
plot.fv Plot Function Values
rescale.owin Convert Window to Another Unit of Length
which.max.im Identify Pixelwise Maximum of Several Pixel Images
methods.objsurf Methods for Objective Function Surfaces
pairs.im Scatterplot Matrix for Pixel Images
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
simulate.ppm Simulate a Fitted Gibbs Point Process Model
plot.leverage.ppm Plot Leverage Function
relrisk Nonparametric Estimate of Spatially-Varying Relative Risk
thomas.estK Fit the Thomas Point Process by Minimum Contrast
summary.psp Summary of a Line Segment Pattern Dataset
pool.envelope Pool Data from Several Envelopes
update.ppm Update a Fitted Point Process Model
residualspaper Data and Code From JRSS Discussion Paper on Residuals
residuals.ppm Residuals for Fitted Point Process Model
pointsOnLines Place Points Evenly Along Specified Lines
rSSI Simulate Simple Sequential Inhibition
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
run.simplepanel Run Point-and-Click Interface
pcf Pair Correlation Function
clarkevans Clark and Evans Aggregation Index
predict.ppm Prediction from a Fitted Point Process Model
psst Pseudoscore Diagnostic For Fitted Model against General Alternative
rpoislinetess Poisson Line Tessellation
transect.im Pixel Values Along a Transect
psstA Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative
nnwhich.lpp Identify Nearest Neighbours on a Linear Network
nearest.raster.point Find Pixel Nearest to a Given Point
tess Create a Tessellation
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
spatstat-deprecated Deprecated spatstat functions
zapsmall.im Rounding of Pixel Values
rpoisline Generate Poisson Random Line Process
rMaternI Simulate Matern Model I
volume Volume of an Object
fitted.mppm Fitted Conditional Intensity for Multiple Point Process Model
redwoodfull California Redwoods Point Pattern (Entire Dataset)
rmpoispp Generate Multitype Poisson Point Pattern
with.fv Evaluate an Expression in a Function Table
levelset Level Set of a Pixel Image
predict.kppm Prediction from a Fitted Cluster Point Process Model
stratrand Stratified random point pattern
compatible.fasp Test Whether Function Arrays Are Compatible
quadratcount Quadrat counting for a point pattern
sessionLibs Print Names and Version Numbers of Libraries Loaded
rMosaicSet Mosaic Random Set
plot.envelope Plot a Simulation Envelope
rshift.ppp Randomly Shift a Point Pattern
rat Ratio object
simdat Simulated Point Pattern
scalardilate Apply Scalar Dilation
osteo Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns
shift.ppp Apply Vector Translation To Point Pattern
sharpen Data Sharpening of Point Pattern
methods.units Methods for Units
waka Trees in Waka national park
applynbd Apply Function to Every Neighbourhood in a Point Pattern
simulate.slrm Simulate a Fitted Spatial Logistic Regression Model
plot.fasp Plot a Function Array
summary.im Summarizing a Pixel Image
print.psp Print Brief Details of a Line Segment Pattern Dataset
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
pool Pool Data
pool.fasp Pool Data from Several Function Arrays
ppm Fit Point Process Model to Data
vcov.mppm Calculate Variance-Covariance Matrix for Fitted Multiple Point Process Model
rescue.rectangle Convert Window Back To Rectangle
rjitter Random Perturbation of a Point Pattern
rho2hat Smoothed Relative Density of Pairs of Covariate Values
rshift Random Shift
vertices Vertices of a Window
print.im Print Brief Details of an Image
plot.quad plot a Spatial Quadrature Scheme
rCauchy Simulate Neyman-Scott Point Process with Cauchy cluster kernel
spokes Spokes pattern of dummy points
redwood California Redwoods Point Pattern (Ripley's Subset)
timed Record the Computation Time
multiplicity.ppp Count Multiplicity of Duplicate Points
tiles Extract List of Tiles in a Tessellation
simba Simulated data from a two-group experiment with replication within each group.
plot.slrm Plot a Fitted Spatial Logistic Regression
intersect.owin Intersection, Union or Set Subtraction of Two Windows
rpoislpp Poisson Point Process on a Linear Network
nnmap K-th Nearest Point Map
smooth.msr Smooth a Signed or Vector-Valued Measure
with.hyperframe Evaluate an Expression in Each Row of a Hyperframe
rpoispp Generate Poisson Point Pattern
nndist.psp Nearest neighbour distances between line segments
suffstat Sufficient Statistic of Point Process Model
vargamma.estpcf Fit the Neyman-Scott Cluster Point Process with Variance Gamma kernel
vargamma.estK Fit the Neyman-Scott Cluster Point Process with Variance Gamma kernel
psp Create a Line Segment Pattern
runifdisc Generate N Uniform Random Points in a Disc
sumouter Compute Quadratic Forms
rPoissonCluster Simulate Poisson Cluster Process
ripras Estimate window from points alone
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
rlabel Random Re-Labelling of Point Pattern
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
runifpointx Generate N Uniform Random Points in Any Dimensions
summary.listof Summary of a List of Things
whist Weighted Histogram
summary.ppm Summarizing a Fitted Point Process Model
ppp Create a Point Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
varblock Estimate Variance of Summary Statistic by Subdivision
Extract.msr Extract Subset of Signed or Vector Measure
rlinegrid Generate grid of parallel lines with random displacement
as.function.fv Convert Function Value Table to Function
valid.ppm Check Whether Point Process Model is Valid
runiflpp Uniform Random Points on a Linear Network
update.kppm Update a Fitted Cluster Point Process Model
rVarGamma Simulate Neyman-Scott Point Process with Variance Gamma cluster kernel
rotate Rotate
triplet.family Triplet Interaction Family
vcov.slrm Variance-Covariance Matrix for a Fitted Spatial Logistic Regression
runifpointOnLines Generate N Uniform Random Points On Line Segments
quadscheme Generate a Quadrature Scheme from a Point Pattern
square Square Window
smooth.ppp Spatial smoothing of observations at irregular points
simplepanel Simple Point-and-Click Interface Panels
rmh.ppm Simulate from a Fitted Point Process Model
rescale.im Convert Pixel Image to Another Unit of Length
smooth.fv Apply Smoothing to Function Values
affine Apply Affine Transformation
StraussHard The Strauss / Hard Core Point Process Model
anova.slrm Analysis of Deviance for Spatial Logistic Regression Models
influence.ppm Influence Measure for Spatial Point Process Model
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Nickname Multiple Personality
Date 2013-12-12
License GPL (>= 2)
URL http://www.spatstat.org
LazyData true
NeedsCompilation yes
ByteCompile true
Packaged 2013-12-12 12:12:12 UTC; adrian
Repository CRAN
Date/Publication 2013-12-12 17:47:25
depends abind , base (>= 3.0.2) , deldir (>= 0.0-21) , graphics , grDevices , mgcv , polyclip (>= 1.2-0) , R (>= 3.0.2) , stats , tensor , utils
suggests gsl , locfit , maptools , RandomFields (>= 3.0.0) , rpanel , scatterplot3d , sm , spatial , tkrplot
Contributors Rolf Turner, Adrian Baddeley

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