spatstat v1.36-0

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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
Gcom Model Compensator of Nearest Neighbour Function
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Extract.quad Subset of Quadrature Scheme
Extract.msr Extract Subset of Signed or Vector Measure
G3est Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
Lcross.inhom Inhomogeneous Cross Type L Function
Gfox Foxall's Distance Functions
Geyer Geyer's Saturation Point Process Model
affine.psp Apply Affine Transformation To Line Segment Pattern
LennardJones The Lennard-Jones Potential
Emark Diagnostics for random marking
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
as.rectangle Window Frame
DiggleGratton Diggle-Gratton model
MultiStrauss The Multitype Strauss Point Process Model
Hardcore The Hard Core Point Process Model
Extract.listof Extract or Replace Subset of a List of Things
Iest Estimate the I-function
Jcross Multitype J Function (i-to-j)
Gmulti Marked Nearest Neighbour Distance Function
BadGey Hybrid Geyer Point Process Model
Smooth.ppp Spatial smoothing of observations at irregular points
affine.lpp Apply Geometrical Transformations to Point Pattern on a Linear Network
Ord Generic Ord Interaction model
Extract.ppp Extract or Replace Subset of Point Pattern
Ldot Multitype L-function (i-to-any)
Jest Estimate the J-function
Smooth Spatial smoothing of data
Linhom L-function
Kest K-function
Extract.fasp Extract Subset of Function Array
coef.mppm Coefficients of Point Process Model Fitted to Multiple Point Patterns
bounding.box.xy Convex Hull of Points
MultiHard The Multitype Hard Core Point Process Model
AreaInter The Area Interaction Point Process Model
as.data.frame.hyperframe Coerce Hyperframe to Data Frame
Kdot.inhom Inhomogeneous Multitype K Dot Function
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
Jdot Multitype J Function (i-to-any)
F3est Empty Space Function of a Three-Dimensional Point Pattern
amacrine Hughes' Amacrine Cell Data
Kmodel K Function or Pair Correlation Function of a Point Process Model
anova.ppm ANOVA for Fitted Point Process Models
Extract.layered Extract Subset of a Layered Object
Saturated Saturated Pairwise Interaction model
Kmodel.ppm K Function or Pair Correlation Function of Gibbs Point Process model
contour.listof Plot a List of Things
Kmulti.inhom Inhomogeneous Marked K-Function
as.owin Convert Data To Class owin
Jinhom Inhomogeneous J-function
as.function.fv Convert Function Value Table to Function
OrdThresh Ord's Interaction model
Concom The Connected Component Process Model
LambertW Lambert's W Function
crossdist.lpp Pairwise distances between two point patterns on a linear network
Kcross Multitype K Function (Cross-type)
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
Ginhom Inhomogeneous Nearest Neighbour Function
as.interact Extract Interaction Structure
as.lpp Convert Data to a Point Pattern on a Linear Network
as.polygonal Convert a Window to a Polygonal Window
Kmodel.kppm K Function or Pair Correlation Function of Cluster Model or Cox model
Strauss The Strauss Point Process Model
Fiksel The Fiksel Interaction
bei Tropical rain forest trees
distcdf Distribution Function of Interpoint Distance
Extract.im Extract Subset of Image
bw.relrisk Cross Validated Bandwidth Selection for Relative Risk Estimation
clickpoly Interactively Define a Polygon
Pairwise Generic Pairwise Interaction model
Kinhom Inhomogeneous K-function
Extract.splitppp Extract or Replace Sub-Patterns
corners Corners of a rectangle
bw.ppl Likelihood Cross Validation Bandwidth Selection for Kernel Density
Kmeasure Reduced Second Moment Measure
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
Kest.fft K-function using FFT
density.psp Kernel Smoothing of Line Segment Pattern
diameter.owin Diameter of a Window
Extract.owin Extract Subset of Window
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
Poisson Poisson Point Process Model
Extract.lpp Extract Subset of Point Pattern on Linear Network
colourtools Convert and Compare Colours in Different Formats
clmfires Castilla-La Mancha Forest Fires
distfun.lpp Distance Map on Linear Network
allstats Calculate four standard summary functions of a point pattern.
anova.mppm ANOVA for Fitted Multiple Point Process Models
append.psp Combine Two Line Segment Patterns
Lcross Multitype L-function (cross-type)
data.ppm Extract Original Data from a Fitted Point Process Model
dfbetas.ppm Parameter influence measure
centroid.owin Centroid of a window
Hybrid Hybrid Interaction Point Process Model
as.mask Pixel Image Approximation of a Window
Smooth.msr Smooth a Signed or Vector-Valued Measure
Hest Spherical Contact Distribution Function
as.hyperframe.ppx Extract coordinates and marks of multidimensional point pattern
ants Harkness-Isham ants' nests data
addvar Added Variable Plot for Point Process Model
cbind.hyperframe Combine Hyperframes by Rows or by Columns
clickjoin Interactively join vertices on a plot
bronzefilter Bronze gradient filter data
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
compatible Test Whether Objects Are Compatible
clarkevans Clark and Evans Aggregation Index
Kscaled Locally Scaled K-function
bw.smoothppp Cross Validated Bandwidth Selection for Spatial Smoothing
affine.ppp Apply Affine Transformation To Point Pattern
convolve.im Convolution of Pixel Images
as.psp Convert Data To Class psp
as.tess Convert Data To Tessellation
chorley Chorley-Ribble Cancer Data
as.matrix.owin Convert Pixel Image to Matrix
by.im Apply Function to Image Broken Down by Factor
areaGain Difference of Disc Areas
affine.im Apply Affine Transformation To Pixel Image
bw.frac Bandwidth Selection Based on Window Geometry
integral.msr Integral of a Measure
Softcore The Soft Core Point Process Model
dirichlet Dirichlet Tessellation of Point Pattern
delaunay Delaunay Triangulation of Point Pattern
envelope.lpp Envelope for Point Patterns on Linear Network
Triplets The Triplet Point Process Model
dclf.test Diggle-Cressie-Loosmore-Ford and Maximum Absolute Deviation Tests
identify.ppp Identify Points in a Point Pattern
distmap Distance Map
formula.fv Extract or Change the Plot Formula for a Function Value Table
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
fryplot Fry Plot of Point Pattern
chop.tess Subdivide a Window or Tessellation using a Set of Lines
is.lpp Test Whether An Object Is A Point Pattern on a Linear Network
demohyper Demonstration Example of Hyperframe of Spatial Data
is.marked.ppm Test Whether A Point Process Model is Marked
blur Apply Gaussian Blur to a Pixel Image
flipxy Exchange X and Y Coordinates
markcorr Mark Correlation Function
envelope.envelope Recompute Envelopes
bermantest Berman's Tests for Point Process Model
crossdist.default Pairwise distances between two different sets of points
bdist.pixels Distance to Boundary of Window
layered Create List of Plotting Layers
bdist.points Distance to Boundary of Window
eval.im Evaluate Expression Involving Pixel Images
envelope.pp3 Simulation Envelopes of Summary Function for 3D Point Pattern
diameter Diameter of an Object
heather Diggle's Heather Data
bounding.box Bounding Box of a Window or Point Pattern
default.expand Default Expansion Rule for Simulation of Model
crossdist.ppx Pairwise Distances Between Two Different Multi-Dimensional Point Patterns
as.mask.psp Convert Line Segment Pattern to Binary Pixel Mask
area.owin Area of a Window
default.rmhcontrol Set Default Control Parameters for Metropolis-Hastings Algorithm.
fasp.object Function Arrays for Spatial Patterns
is.convex Test Whether a Window is Convex
coords Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern
anova.lppm ANOVA for Fitted Point Process Models on Linear Network
is.ppp Test Whether An Object Is A Point Pattern
discretise Safely Convert Point Pattern Window to Binary Mask
anemones Beadlet Anemones Data
fitin.ppm Extract the Interaction from a Fitted Point Process Model
pixellate Convert Spatial Object to Pixel Image
complement.owin Take Complement of a Window
inforder.family Infinite Order Interaction Family
disc Circular Window
is.hybrid Test Whether Object is a Hybrid
predict.lppm Predict Point Process Model on Linear Network
anova.slrm Analysis of Deviance for Spatial Logistic Regression Models
border Border Region of a Window
as.ppp Convert Data To Class ppp
betacells Beta Ganglion Cells in Cat Retina
expand.owin Apply Expansion Rule
bw.scott Scott's Rule for Bandwidth Selection for Kernel Density
bramblecanes Hutchings' Bramble Canes data
harmonic Basis for Harmonic Functions
hamster Aherne's hamster tumour data
bw.diggle Cross Validated Bandwidth Selection for Kernel Density
distmap.psp Distance Map of Line Segment Pattern
connected Connected components
clickppp Interactively Add Points
inside.owin Test Whether Points Are Inside A Window
is.rectangle Determine Type of Window
japanesepines Japanese Pines Point Pattern
lgcp.estpcf Fit a Log-Gaussian Cox Point Process by Minimum Contrast
distmap.owin Distance Map of Window
dilation Morphological Dilation
exactMPLEstrauss Exact Maximum Pseudolikelihood Estimate for Stationary Strauss Process
is.ppm Test Whether An Object Is A Fitted Point Process Model
erosion Morphological Erosion
linim Create Pixel Image on Linear Network
eval.fv Evaluate Expression Involving Functions
is.multitype Test whether Object is Multitype
closepairs Close Pairs of Points
crossdist Pairwise distances
kaplan.meier Kaplan-Meier Estimator using Histogram Data
clusterset Allard-Fraley Estimator of Cluster Feature
as.matrix.im Convert Pixel Image to Matrix or Array
is.multitype.ppm Test Whether A Point Process Model is Multitype
Kcom Model Compensator of K Function
applynbd Apply Function to Every Neighbourhood in a Point Pattern
finpines Pine saplings in Finland.
crossdist.ppp Pairwise distances between two different point patterns
integral.im Integral of a Pixel Image
density.ppp Kernel Smoothed Intensity of Point Pattern
cut.im Convert Pixel Image from Numeric to Factor
StraussHard The Strauss / Hard Core Point Process Model
funxy Spatial Function Class
im.object Class of Images
compatible.fasp Test Whether Function Arrays Are Compatible
chicago Chicago Street Crime Data
delaunay.distance Distance on Delaunay Triangulation
model.matrix.slrm Extract Design Matrix from Spatial Logistic Regression Model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
linearKdot.inhom Inhomogeneous multitype K Function (Dot-type) for Linear Point Pattern
as.data.frame.im Convert Pixel Image to Data Frame
methods.fii Methods for Fitted Interactions
hextess Hexagonal Grid or Tessellation
is.multitype.ppp Test Whether A Point Pattern is Multitype
gorillas Gorilla Nesting Sites
methods.kppm Methods for Cluster Point Process Models
Kres Residual K Function
ord.family Ord Interaction Process Family
ppx Multidimensional Space-Time Point Pattern
lineardisc Compute Disc of Given Radius in Linear Network
is.empty Test Whether An Object Is Empty
model.frame.ppm Extract the Variables in a Point Process Model
methods.funxy Methods for Spatial Functions
infline Infinite Straight Lines
lohboot Bootstrap Confidence Bands for Summary Function
dilated.areas Areas of Morphological Dilations
endpoints.psp Endpoints of Line Segment Pattern
pairsat.family Saturated Pairwise Interaction Point Process Family
cauchy.estpcf Fit the Neyman-Scott cluster process with Cauchy kernel
ganglia Beta Ganglion Cells in Cat Retina, Old Version
fitted.ppm Fitted Conditional Intensity for Point Process Model
coef.slrm Coefficients of Fitted Spatial Logistic Regression Model
distmap.ppp Distance Map of Point Pattern
fv Create a Function Value Table
as.hyperframe Convert Data to Hyperframe
levelset Level Set of a Pixel Image
edge.Trans Translation Edge Correction
box3 Three-Dimensional Box
plot.envelope Plot a Simulation Envelope
logLik.ppm Log Likelihood and AIC for Point Process Model
methods.pp3 Methods for three-dimensional point patterns
methods.linfun Methods for Functions on Linear Network
nnwhich.ppx Nearest Neighbours in Any Dimensions
nsegments Number of Line Segments in a Line Segment Pattern
affine Apply Affine Transformation
pixellate.ppp Convert Point Pattern to Pixel Image
methods.rhohat Methods for Intensity Functions of Spatial Covariate
Extract.tess Extract or Replace Subset of Tessellation
kppm Fit Cluster or Cox Point Process Model
intensity.ppm Intensity of Fitted Point Process Model
edges2triangles List Triangles in a Graph
circumradius Circumradius and Diameter of a Linear Network
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
nztrees New Zealand Trees Point Pattern
logLik.mppm Log Likelihood for Poisson Point Process Model
flu Influenza Virus Proteins
is.im Test Whether An Object Is A Pixel Image
linearpcfinhom Inhomogeneous Linear Pair Correlation Function
linearmarkequal Mark Connection Function for Multitype Point Pattern on Linear Network
pcf.fasp Pair Correlation Function obtained from array of K functions
im.apply Apply Function Pixelwise to List of Images
Extract.linnet Extract Subset of Linear Network
as.box3 Convert Data to Three-Dimensional Box
crossing.psp Crossing Points of Two Line Segment Patterns
compatible.im Test Whether Pixel Images Are Compatible
gridweights Compute Quadrature Weights Based on Grid Counts
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
idw Inverse-distance weighted smoothing of observations at irregular points
interp.colourmap Interpolate smoothly between specified colours
pcf.ppp Pair Correlation Function of Point Pattern
is.marked Test Whether Marks Are Present
linearKcross Multitype K Function (Cross-type) for Linear Point Pattern
linearpcf Linear Pair Correlation Function
colourmap Colour Lookup Tables
fv.object Function Value Table
plot.listof Plot a List of Things
concatxy Concatenate x,y Coordinate Vectors
objsurf Objective Function Surface
istat Point and Click Interface for Exploratory Analysis of Point Pattern
methods.rho2hat Methods for Intensity Functions of Two Spatial Covariates
gridcentres Rectangular grid of points
linearpcfdot Multitype Pair Correlation Function (Dot-type) for Linear Point Pattern
hybrid.family Hybrid Interaction Family
nearestsegment Find Line Segment Nearest to Each Point
pcfinhom Inhomogeneous Pair Correlation Function
paracou Kimboto trees at Paracou, French Guiana
letterR Window in Shape of Letter R
distfun Distance Map as a Function
linearpcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-type) for Linear Point Pattern
hyytiala Scots pines and other trees at Hyytiala
is.stationary Recognise Stationary and Poisson Point Process Models
nbfires Point Patterns of New Brunswick Forest Fires
linfun Function on a Linear Network
intersect.owin Intersection, Union or Set Subtraction of Two Windows
Extract.psp Extract Subset of Line Segment Pattern
latest.news Print News About Latest Version of Package
dclf.progress Progress Plot of Test of Spatial Pattern
fitted.mppm Fitted Conditional Intensity for Multiple Point Process Model
Tstat Third order summary statistic
eroded.areas Areas of Morphological Erosions
fvnames Abbreviations for Groups of Columns in Function Value Table
crossdist.pp3 Pairwise distances between two different three-dimensional point patterns
linearKdot Multitype K Function (Dot-type) for Linear Point Pattern
predict.kppm Prediction from a Fitted Cluster Point Process Model
methods.lpp Methods for Point Patterns on a Linear Network
incircle Find Largest Circle Inside Window
im Create a Pixel Image Object
lurking Lurking variable plot
pairdist.psp Pairwise distances between line segments
identify.psp Identify Segments in a Line Segment Pattern
nncross Nearest Neighbours Between Two Patterns
predict.mppm Prediction for Fitted Multiple Point Process Model
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
nndist.lpp Nearest neighbour distances on a linear network
npoints Number of Points in a Point Pattern
intensity.quadratcount Intensity Estimates Using Quadrat Counts
quadrat.test Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rGaussPoisson Simulate Gauss-Poisson Process
linearpcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Dot-type) for Linear Point Pattern
parres Partial Residuals for Point Process Model
npfun Dummy Function Returns Number of Points
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
reach Interaction Distance of a Point Process
localpcf Local pair correlation function
boxx Multi-Dimensional Box
gordon People in Gordon Square
rHardcore Perfect Simulation of the Hardcore Process
print.ppm Print a Fitted Point Process Model
clip.infline Intersect Infinite Straight Lines with a Window
plot.pp3 Plot a three-dimensional point pattern
pixelquad Quadrature Scheme Based on Pixel Grid
midpoints.psp Midpoints of Line Segment Pattern
areaLoss Difference of Disc Areas
plot.scan.test Plot Result of Scan Test
pool.envelope Pool Data from Several Envelopes
closing Morphological Closing
compareFit Residual Diagnostics for Multiple Fitted Models
lpp Create Point Pattern on Linear Network
methods.objsurf Methods for Objective Function Surfaces
leverage.ppm Leverage Measure for Spatial Point Process Model
pcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)
rescale Convert dataset to another unit of length
methods.layered Methods for Layered Objects
eem Exponential Energy Marks
plot.bermantest Plot Result of Berman Test
pixellate.owin Convert Window to Pixel Image
as.im Convert to Pixel Image
pairs.im Scatterplot Matrix for Pixel Images
model.depends Identify Covariates Involved in each Model Term
methods.units Methods for Units
markconnect Mark Connection Function
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
pcfmulti Marked pair correlation function
plot.leverage.ppm Plot Leverage Function
formula.ppm Model Formulae for Gibbs Point Process Models
nnmark Mark of Nearest Neighbour
plot.quadrattest Display the result of a quadrat counting test.
layout.boxes Generate a Row or Column Arrangement of Rectangles.
bw.stoyan Stoyan's Rule of Thumb for Bandwidth Selection
edges2vees List Dihedral Triples in a Graph
imcov Spatial Covariance of a Pixel Image
intensity Intensity of a Dataset or a Model
ppp Create a Point Pattern
kstest.ppm Kolmogorov-Smirnov Test for Point Pattern or Point Process Model
plot.im Plot a Pixel Image
murchison Murchison gold deposits
lansing Lansing Woods Point Pattern
is.owin Test Whether An Object Is A Window
predict.ppm Prediction from a Fitted Point Process Model
owin Create a Window
project.ppm Force Point Process Model to be Valid
nncross.pp3 Nearest Neighbours Between Two Patterns in 3D
persp.im Perspective Plot of Pixel Image
miplot Morishita Index Plot
pairdist.default Pairwise distances
nndist.ppx Nearest Neighbour Distances in Any Dimensions
quadrats Divide Region into Quadrats
edge.Ripley Ripley's Isotropic Edge Correction
pppdist Distance Between Two Point Patterns
markvario Mark Variogram
discpartarea Area of Part of Disc
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
pcfdot Multitype pair correlation function (i-to-any)
localK Neighbourhood density function
rpoisppx Generate Poisson Point Pattern in Any Dimensions
osteo Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns
quadscheme Generate a Quadrature Scheme from a Point Pattern
influence.ppm Influence Measure for Spatial Point Process Model
residualspaper Data and Code From JRSS Discussion Paper on Residuals
demopat Artificial Data Point Pattern
spokes Spokes pattern of dummy points
plot.plotppm Plot a plotppm Object Created by plot.ppm
mincontrast Method of Minimum Contrast
linearK Linear K Function
shift.ppp Apply Vector Translation To Point Pattern
stieltjes Compute Integral of Function Against Cumulative Distribution
marks.psp Marks of a Line Segment Pattern
print.psp Print Brief Details of a Line Segment Pattern Dataset
rotate.owin Rotate a Window
intersect.tess Intersection of Two Tessellations
quad.object Class of Quadrature Schemes
ppm.object Class of Fitted Point Process Models
matchingdist Distance for a Point Pattern Matching
fitted.slrm Fitted Probabilities for Spatial Logistic Regression
rshift.splitppp Randomly Shift a List of Point Patterns
redwoodfull California Redwoods Point Pattern (Entire Dataset)
rpoislpp Poisson Point Process on a Linear Network
longleaf Longleaf Pines Point Pattern
kstest.mppm Kolmogorov-Smirnov Test for Multiple Point Process Model
plot.colourmap Plot a Colour Map
rVarGamma Simulate Neyman-Scott Point Process with Variance Gamma cluster kernel
pairdist Pairwise distances
sharpen Data Sharpening of Point Pattern
spatstat-internal Internal spatstat functions
methods.ppx Methods for Multidimensional Space-Time Point Patterns
trim.rectangle Cut margins from rectangle
tiles Extract List of Tiles in a Tessellation
copper Berman-Huntington points and lines data
localKinhom Inhomogeneous Neighbourhood Density Function
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
summary.quad Summarizing a Quadrature Scheme
linnet Create a Linear Network
bdist.tiles Distance to Boundary of Window
pairwise.family Pairwise Interaction Process Family
methods.box3 Methods for Three-Dimensional Box
rescale.ppp Convert Point Pattern to Another Unit of Length
rshift.ppp Randomly Shift a Point Pattern
linearKcross.inhom Inhomogeneous multitype K Function (Cross-type) for Linear Point Pattern
methods.slrm Methods for Spatial Logistic Regression Models
deriv.fv Calculate Derivative of Function Values
affine.owin Apply Affine Transformation To Window
rlinegrid Generate grid of parallel lines with random displacement
reload.or.compute Compute Unless Previously Saved
quadrat.test.mppm Chi-Squared Test for Multiple Point Process Model Based on Quadrat Counts
nndensity.ppp Estimate Intensity of Point Pattern Using Nearest Neighbour Distances
sidelengths.owin Side Lengths of Enclosing Rectangle of a Window
multiplicity.ppp Count Multiplicity of Duplicate Points
simulate.kppm Simulate a Fitted Cluster Point Process Model
nndist.psp Nearest neighbour distances between line segments
overlap.owin Compute Area of Overlap
pppmatching Create a Point Matching
nndist.pp3 Nearest neighbour distances in three dimensions
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
rcell Simulate Baddeley-Silverman Cell Process
pool Pool Data
opening Morphological Opening
quantile.ewcdf Quantiles of Weighted Empirical Cumulative Distribution Function
rescale.psp Convert Line Segment Pattern to Another Unit of Length
stratrand Stratified random point pattern
nnmap K-th Nearest Point Map
rpoisline Generate Poisson Random Line Process
pcf3est Pair Correlation Function of a Three-Dimensional Point Pattern
rescale.owin Convert Window to Another Unit of Length
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
tweak.colourmap Change Colour Values in a Colour Map
nnfun Nearest Neighbour Index Map as a Function
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
simplify.owin Approximate a Polygon by a Simpler Polygon
mean.im Maximum, Minimum, Mean, Median, Range or Sum of Pixel Values in an Image
quadrat.test.splitppp Dispersion Test of CSR for Split Point Pattern Based on Quadrat Counts
plot.ppm plot a Fitted Point Process Model
tile.areas Compute Areas of Tiles in a Tessellation
connected.ppp Connected components of a point pattern
plot.psp plot a Spatial Line Segment Pattern
rCauchy Simulate Neyman-Scott Point Process with Cauchy cluster kernel
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
summary.listof Summary of a List of Things
matclust.estpcf Fit the Matern Cluster Point Process by Minimum Contrast Using Pair Correlation
psstA Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative
square Square Window
progressreport Print Progress Reports
superimpose Superimpose Several Geometric Patterns
summary.im Summarizing a Pixel Image
shift.owin Apply Vector Translation To Window
convexhull Convex Hull
residuals.mppm Residuals for Point Process Model Fitted to Multiple Point Patterns
simulate.slrm Simulate a Fitted Spatial Logistic Regression Model
summary.splitppp Summary of a Split Point Pattern
rotate.im Rotate a Pixel Image
summary.owin Summary of a Spatial Window
rlabel Random Re-Labelling of Point Pattern
rshift.psp Randomly Shift a Line Segment Pattern
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
vcov.kppm Variance-Covariance Matrix for a Fitted Cluster Point Process Model
redwood California Redwoods Point Pattern (Ripley's Subset)
as.linim Convert to Pixel Image on Linear Network
nncross.lpp Nearest Neighbours on a Linear Network
rMosaicField Mosaic Random Field
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
varblock Estimate Variance of Summary Statistic by Subdivision
pairdist.pp3 Pairwise distances in Three Dimensions
pppmatching.object Class of Point Matchings
plot.influence.ppm Plot Influence Measure
rshift Random Shift
rMatClust Simulate Matern Cluster Process
rmhexpand Specify Simulation Window or Expansion Rule
scanLRTS Likelihood Ratio Test Statistic for Scan Test
plot.linnet Plot a linear network
rMosaicSet Mosaic Random Set
pairdist.ppx Pairwise Distances in Any Dimensions
rMaternII Simulate Matern Model II
update.ppm Update a Fitted Point Process Model
shift.im Apply Vector Translation To Pixel Image
predict.slrm Predicted or Fitted Values from Spatial Logistic Regression
waka Trees in Waka national park
ponderosa Ponderosa Pine Tree Point Pattern
rThomas Simulate Thomas Process
commonGrid Determine A Common Spatial Domain And Pixel Resolution
profilepl Profile Maximum Pseudolikelihood
round.ppp Apply Numerical Rounding to Spatial Coordinates
rotate Rotate
lut Lookup Tables
runifdisc Generate N Uniform Random Points in a Disc
union.quad Union of Data and Dummy Points
plot.quad Plot a Spatial Quadrature Scheme
simdat Simulated Point Pattern
rStrauss Perfect Simulation of the Strauss Process
pool.rat Pool Data from Several Ratio Objects
rat Ratio object
scanpp Read Point Pattern From Data File
sessionLibs Print Names and Version Numbers of Libraries Loaded
pixellate.psp Convert Line Segment Pattern to Pixel Image
summary.ppm Summarizing a Fitted Point Process Model
unmark Remove Marks
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
quadratresample Resample a Point Pattern by Resampling Quadrats
pool.fasp Pool Data from Several Function Arrays
psst Pseudoscore Diagnostic For Fitted Model against General Alternative
print.quad Print a Quadrature Scheme
rhohat Smoothing Estimate of Covariate Transformation
psp Create a Line Segment Pattern
rgbim Create Colour-Valued Pixel Image
update.rmhcontrol Update Control Parameters of Metropolis-Hastings Algorithm
rounding Detect Numerical Rounding
simplenet Simple Example of Linear Network
quadratcount Quadrat counting for a point pattern
urkiola Urkiola Woods Point Pattern
plot.fasp Plot a Function Array
simplepanel Simple Point-and-Click Interface Panels
mppm Fit Point Process Model to Several Point Patterns
msr Signed or Vector-Valued Measure
will.expand Test Expansion Rule
plot.ppp plot a Spatial Point Pattern
slrm Spatial Logistic Regression
timed Record the Computation Time
runiflpp Uniform Random Points on a Linear Network
rknn Theoretical Distribution of Nearest Neighbour Distance
sumouter Compute Quadratic Forms
cells Biological Cells Point Pattern
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
pcf Pair Correlation Function
nearest.raster.point Find Pixel Nearest to a Given Point
is.marked.ppp Test Whether A Point Pattern is Marked
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
unitname Name for Unit of Length
print.ppp Print Brief Details of a Point Pattern Dataset
runifpointx Generate N Uniform Random Points in Any Dimensions
quantile.im Sample Quantiles of Pixel Image
ppp.object Class of Point Patterns
rDiggleGratton Perfect Simulation of the Diggle-Gratton Process
runifpoint3 Generate N Uniform Random Points in Three Dimensions
nnwhich.pp3 Nearest neighbours in three dimensions
rescale.im Convert Pixel Image to Another Unit of Length
reduced.sample Reduced Sample Estimator using Histogram Data
pairdist.lpp Pairwise shortest-path distances between points on a linear network
vargamma.estpcf Fit the Neyman-Scott Cluster Point Process with Variance Gamma kernel
thomas.estpcf Fit the Thomas Point Process by Minimum Contrast
whist Weighted Histogram
linearpcfcross Multitype Pair Correlation Function (Cross-type) for Linear Point Pattern
rho2hat Smoothed Relative Density of Pairs of Covariate Values
print.owin Print Brief Details of a Spatial Window
with.hyperframe Evaluate an Expression in Each Row of a Hyperframe
spatstat-package The Spatstat Package
plot.msr Plot a Signed or Vector-Valued Measure
diameter.box3 Geometrical Calculations for Three-Dimensional Box
ppm Fit Point Process Model to Data
setcov Set Covariance of a Window
rstrat Simulate Stratified Random Point Pattern
rmpoint Generate N Random Multitype Points
plot.quadratcount Plot Quadrat Counts
beginner Print Introduction For Beginners
scalardilate Apply Scalar Dilation
rSSI Simulate Simple Sequential Inhibition
rLGCP Simulate Log-Gaussian Cox Process
rpoispp Generate Poisson Point Pattern
rPoissonCluster Simulate Poisson Cluster Process
plot.lppm Plot a Fitted Point Process Model on a Linear Network
psp.object Class of Line Segment Patterns
run.simplepanel Run Point-and-Click Interface
update.kppm Update a Fitted Cluster Point Process Model
model.images Compute Images of Constructed Covariates
simulate.ppm Simulate a Fitted Gibbs Point Process Model
rotate.psp Rotate a Line Segment Pattern
summary.psp Summary of a Line Segment Pattern Dataset
relrisk Nonparametric Estimate of Spatially-Varying Relative Risk
rStraussHard Perfect Simulation of the Strauss-Hardcore Process
volume Volume of an Object
print.im Print Brief Details of an Image
methods.boxx Methods for Multi-Dimensional Box
shift Apply Vector Translation
rNeymanScott Simulate Neyman-Scott Process
rpoispp3 Generate Poisson Point Pattern in Three Dimensions
K3est K-function of a Three-Dimensional Point Pattern
subfits Extract List of Individual Point Process Models
pointsOnLines Place Points Evenly Along Specified Lines
plot.splitppp Plot a List of Point Patterns
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
Jmulti Marked J Function
unnormdensity Weighted kernel smoother
rcellnumber Generate Random Numbers of Points for Cell Process
vertices Vertices of a Window
waterstriders Waterstriders data. Three independent replications of a point pattern formed by insects.
runifpoint Generate N Uniform Random Points
plot.slrm Plot a Fitted Spatial Logistic Regression
swedishpines Swedish Pines Point Pattern
triplet.family Triplet Interaction Family
thomas.estK Fit the Thomas Point Process by Minimum Contrast
rpoislinetess Poisson Line Tessellation
valid.ppm Check Whether Point Process Model is Valid
vcov.mppm Calculate Variance-Covariance Matrix for Fitted Multiple Point Process Model
pairdist.ppp Pairwise distances
unique.ppp Extract Unique Points from a Spatial Point Pattern
plot.owin Plot a Spatial Window
plot.tess Plot a tessellation
rMaternI Simulate Matern Model I
pcf.fv Pair Correlation Function obtained from K Function
project2segment Move Point To Nearest Line
raster.x Cartesian Coordinates for a Pixel Raster
plot.mppm plot a Fitted Multiple Point Process Model
psstG Pseudoscore Diagnostic For Fitted Model against Saturation Alternative
rjitter Random Perturbation of a Point Pattern
tess Create a Tessellation
tilenames Names of Tiles in a Tessellation
plot.hyperframe Plot Entries in a Hyperframe
rmh.ppm Simulate from a Fitted Point Process Model
quadscheme.logi Generate a Logistic Regression Quadrature Scheme from a Point Pattern
rmpoispp Generate Multitype Poisson Point Pattern
plot.kppm Plot a fitted cluster point process
shapley Galaxies in the Shapley Supercluster
spatstat-deprecated Deprecated spatstat functions
pcfcross Multitype pair correlation function (cross-type)
spatstat.options Internal Options in Spatstat Package
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
zapsmall.im Rounding of Pixel Values
rsyst Simulate systematic random point pattern
scaletointerval Rescale Data to Lie Between Specified Limits
periodify Make Periodic Copies of a Spatial Pattern
Extract.fv Extract Subset of Function Values
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
DiggleGatesStibbard Diggle-Gates-Stibbard Point Process Model
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
Lest L-function
as.fv Convert Data To Class fv
Kdot Multitype K Function (i-to-any)
bind.fv Combine Function Value Tables
compatible.fv Test Whether Function Objects Are Compatible
interp.im Interpolate a Pixel Image
deltametric Delta Metric
default.dummy Generate a Default Pattern of Dummy Points
envelope Simulation Envelopes of Summary Function
ippm Optimise Irregular Trend Parameters in Point Process Model
iplot Point and Click Interface for Displaying Spatial Data
lppm Fit Point Process Model to Point Pattern on Linear Network
model.matrix.ppm Extract Design Matrix from Point Process Model
markcorrint Mark Correlation Integral
owin.object Class owin
humberside Humberside Data on Childhood Leukaemia and Lymphoma
spruces Spruces Point Pattern
split.im Divide Image Into Sub-images
shift.psp Apply Vector Translation To Line Segment Pattern
transect.im Pixel Values Along a Transect
residuals.ppm Residuals for Fitted Point Process Model
with.fv Evaluate an Expression in a Function Table
pcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-Type)
pyramidal Pyramidal Neurons in Cingulate Cortex
pp3 Three Dimensional Point Pattern
Gest Nearest Neighbour Distance Function G
Kmulti Marked K-Function
beachcolours Create Colour Scheme for a Range of Numbers
as.data.frame.ppp Coerce Point Pattern to a Data Frame
cut.ppp Classify Points in a Point Pattern
clarkevans.test Clark and Evans Test
diameter.boxx Geometrical Calculations for Multi-Dimensional Box
hist.im Histogram of Pixel Values in an Image
Extract.ppx Extract Subset of Multidimensional Point Pattern
methods.linnet Methods for Linear Networks
marks Marks of a Point Pattern
logLik.slrm Loglikelihood of Spatial Logistic Regression
nnwhich.lpp Identify Nearest Neighbours on a Linear Network
nndist Nearest neighbour distances
plot.linim Plot Pixel Image on Linear Network
plot.fv Plot Function Values
rotate.ppp Rotate a Point Pattern
plot.layered Layered Plot
rthin Random Thinning
summary.ppp Summary of a Point Pattern Dataset
split.ppx Divide Multidimensional Point Pattern into Sub-patterns
rDGS Perfect Simulation of the Diggle-Gates-Stibbard Process
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
Replace.im Reset Values in Subset of Image
Ldot.inhom Inhomogeneous Multitype L Dot Function
Kcross.inhom Inhomogeneous Cross K Function
Smooth.fv Apply Smoothing to Function Values
cauchy.estK Fit the Neyman-Scott cluster process with Cauchy kernel
coef.ppm Coefficients of Fitted Point Process Model
convexhull.xy Convex Hull of Points
hyperframe Hyper Data Frame
intensity.lpp Empirical Intensity of Point Pattern on Linear Network
eval.linim Evaluate Expression Involving Pixel Images on Linear Network
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
ewcdf Weighted Empirical Cumulative Distribution Function
nnwhich Nearest neighbour
lengths.psp Lengths of Line Segments
perimeter Perimeter Length of Window
nnclean Nearest Neighbour Clutter Removal
methods.lppm Methods for Fitted Point Process Models on a Linear Network
mucosa Cells in Gastric Mucosa
linearmarkconnect Mark Connection Function for Multitype Point Pattern on Linear Network
pool.quadrattest Pool Several Quadrat Tests
simba Simulated data from a two-group experiment with replication within each group.
vcov.slrm Variance-Covariance Matrix for a Fitted Spatial Logistic Regression
suffstat Sufficient Statistic of Point Process Model
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
Finhom Inhomogeneous Empty Space Function
angles.psp Orientation Angles of Line Segments
as.ppm Extract Fitted Point Process Model
affine.tess Apply Geometrical Transformation To Tessellation
crossdist.psp Pairwise distances between two different line segment patterns
Fest Estimate the empty space function F
collapse.fv Collapse Several Function Tables into One
dummify Convert Data to Numeric Values by Constructing Dummy Variables
contour.im Contour plot of pixel image
intensity.ppp Empirical Intensity of Point Pattern
eval.fasp Evaluate Expression Involving Function Arrays
harmonise.im Make Pixel Images Compatible
layerplotargs Extract or Replace the Plot Arguments of a Layered Object
is.subset.owin Determine Whether One Window is Contained In Another
nnfun.lpp Nearest Neighbour Map on Linear Network
linearKinhom Inhomogeneous Linear K Function
reflect Reflect In Origin
selfcrossing.psp Crossing Points in a Line Segment Pattern
ripras Estimate window from points alone
Gres Residual G Function
rpoint Generate N Random Points
scan.test Spatial Scan Test
affine.linnet Apply Geometrical Transformations to a Linear Network
rescue.rectangle Convert Window Back To Rectangle
split.ppp Divide Point Pattern into Sub-patterns
vargamma.estK Fit the Neyman-Scott Cluster Point Process with Variance Gamma kernel
runifpointOnLines Generate N Uniform Random Points On Line Segments
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Nickname Intense Scrutiny
Date 2014-02-18
License GPL (>= 2)
URL http://www.spatstat.org
LazyData true
NeedsCompilation yes
ByteCompile true
Packaged 2014-02-18 05:14:55 UTC; adrian
Repository CRAN
Date/Publication 2014-02-18 08:44:46

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