spatstat v1.42-0

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by Adrian Baddeley

Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests

Comprehensive toolbox 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, space-time point patterns in any number of dimensions, and point patterns on a linear network. Contains about 2000 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, tessellations, and linear networks. 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
Extract.fv Extract or Replace Subset of Function Values
Extract.listof Extract or Replace Subset of a List of Things
Concom The Connected Component Process Model
Extract.owin Extract Subset of Window
F3est Empty Space Function of a Three-Dimensional Point Pattern
Hardcore The Hard Core Point Process Model
Extract.psp Extract Subset of Line Segment Pattern
G3est Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
Extract.msr Extract Subset of Signed or Vector Measure
Smooth.fv Apply Smoothing to Function Values
DiggleGatesStibbard Diggle-Gates-Stibbard Point Process Model
Extract.quad Subset of Quadrature Scheme
Extract.layered Extract or Replace Subset of a Layered Object
Extract.anylist Extract or Replace Subset of a List of Things
Gcom Model Compensator of Nearest Neighbour Function
Linhom L-function
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
Jdot Multitype J Function (i-to-any)
Extract.solist Extract or Replace Subset of a List of Spatial Objest
Gfox Foxall's Distance Functions
Extract.leverage.ppm Extract Subset of Leverage Object
Kcross Multitype K Function (Cross-type)
LambertW Lambert's W Function
Extract.hyperframe Extract or Replace Subset of Hyperframe
Triplets The Triplet Point Process Model
Extract.ppp Extract or Replace Subset of Point Pattern
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
as.layered Convert Data To Layered Object
Gest Nearest Neighbour Distance Function G
K3est K-function of a Three-Dimensional Point Pattern
Kmeasure Reduced Second Moment Measure
Gres Residual G Function
Jmulti Marked J Function
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Strauss The Strauss Point Process Model
as.mask.psp Convert Line Segment Pattern to Binary Pixel Mask
AreaInter The Area Interaction Point Process Model
Kcross.inhom Inhomogeneous Cross K Function
Kmark Mark-Weighted K Function
Geyer Geyer's Saturation Point Process Model
Kovesi Colour Sequences with Uniform Perceptual Contrast
affine.ppp Apply Affine Transformation To Point Pattern
Kdot.inhom Inhomogeneous Multitype K Dot Function
coef.mppm Coefficients of Point Process Model Fitted to Multiple Point Patterns
HierStraussHard The Hierarchical Strauss Hard Core Point Process Model
Emark Diagnostics for random marking
Extract.influence.ppm Extract Subset of Influence Object
as.linnet.linim Extract Linear Network from Data on a Linear Network
Pairwise Generic Pairwise Interaction model
as.data.frame.ppp Coerce Point Pattern to a Data Frame
beginner Print Introduction For Beginners
Hest Spherical Contact Distribution Function
Fiksel The Fiksel Interaction
Softcore The Soft Core Point Process Model
Extract.im Extract Subset of Image
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
Extract.linnet Extract Subset of Linear Network
OrdThresh Ord's Interaction model
Tstat Third order summary statistic
Kmulti.inhom Inhomogeneous Marked K-Function
Frame Extract or Change the Containing Rectangle of a Spatial Object
Extract.splitppp Extract or Replace Sub-Patterns
clarkevans.test Clark and Evans Test
anova.mppm ANOVA for Fitted Multiple Point Process Models
Fest Estimate the Empty Space Function or its Hazard Rate
Lcross Multitype L-function (cross-type)
Hybrid Hybrid Interaction Point Process Model
Kest.fft K-function using FFT
affine.linnet Apply Geometrical Transformations to a Linear Network
Kinhom Inhomogeneous K-function
DiggleGratton Diggle-Gratton model
HierHard The Hierarchical Hard Core Point Process Model
affine.psp Apply Affine Transformation To Line Segment Pattern
Extract.lpp Extract Subset of Point Pattern on Linear Network
Gmulti Marked Nearest Neighbour Distance Function
as.mask Pixel Image Approximation of a Window
anylist List of Objects
Math.im S3 Group Generic methods for images
append.psp Combine Two Line Segment Patterns
Saturated Saturated Pairwise Interaction model
add.texture Fill Plot With Texture
areaLoss Difference of Disc Areas
BadGey Hybrid Geyer Point Process Model
Jest Estimate the J-function
Jcross Multitype J Function (i-to-j)
bw.stoyan Stoyan's Rule of Thumb for Bandwidth Selection
bdist.pixels Distance to Boundary of Window
area.owin Area of a Window
as.rectangle Window Frame
box3 Three-Dimensional Box
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
as.im Convert to Pixel Image
delaunayDistance Distance on Delaunay Triangulation
affine.owin Apply Affine Transformation To Window
Smooth Spatial smoothing of data
Kmodel.kppm K Function or Pair Correlation Function of Cluster Model or Cox model
Ldot.inhom Inhomogeneous Multitype L Dot Function
anova.slrm Analysis of Deviance for Spatial Logistic Regression Models
cauchy.estpcf Fit the Neyman-Scott cluster process with Cauchy kernel
MultiStrauss The Multitype Strauss Point Process Model
affine Apply Affine Transformation
Kscaled Locally Scaled K-function
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
Kdot Multitype K Function (i-to-any)
Extract.tess Extract or Replace Subset of Tessellation
HierStrauss The Hierarchical Strauss Point Process Model
anova.lppm ANOVA for Fitted Point Process Models on Linear Network
bei Tropical rain forest trees
as.hyperframe Convert Data to Hyperframe
anemones Beadlet Anemones Data
applynbd Apply Function to Every Neighbourhood in a Point Pattern
Iest Estimate the I-function
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
Kmulti Marked K-Function
as.ppp Convert Data To Class ppp
clickdist Interactively Measure Distance
betacells Beta Ganglion Cells in Cat Retina
boundingbox Bounding Box of a Window, Image, or Point Pattern
border Border Region of a Window
commonGrid Determine A Common Spatial Domain And Pixel Resolution
bw.relrisk Cross Validated Bandwidth Selection for Relative Risk Estimation
branchlabelfun Tree Branch Membership Labelling Function
deriv.fv Calculate Derivative of Function Values
Lest L-function
bw.frac Bandwidth Selection Based on Window Geometry
Kcom Model Compensator of K Function
cbind.hyperframe Combine Hyperframes by Rows or by Columns
centroid.owin Centroid of a window
dendrite Dendritic Spines Data
connected Connected components
convexhull.xy Convex Hull of Points
Ginhom Inhomogeneous Nearest Neighbour Function
Jinhom Inhomogeneous J-function
clickbox Interactively Define a Rectangle
clusterradius Compute or Extract Effective Range of Cluster Kernel
Lcross.inhom Inhomogeneous Cross Type L Function
Finhom Inhomogeneous Empty Space Function
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
corners Corners of a rectangle
chorley Chorley-Ribble Cancer Data
addvar Added Variable Plot for Point Process Model
as.linim Convert to Pixel Image on Linear Network
Ksector Sector K-function
amacrine Hughes' Amacrine Cell Data
Math.linim S3 Group Generic Methods for Images on a Linear Network
affine.lpp Apply Geometrical Transformations to Point Pattern on a Linear Network
clusterfield Field of clusters
as.matrix.owin Convert Pixel Image to Matrix
as.box3 Convert Data to Three-Dimensional Box
coef.slrm Coefficients of Fitted Spatial Logistic Regression Model
colourmap Colour Lookup Tables
Smooth.ppp Spatial smoothing of observations at irregular points
concatxy Concatenate x,y Coordinate Vectors
connected.ppp Connected components of a point pattern
bramblecanes Hutchings' Bramble Canes data
bw.smoothppp Cross Validated Bandwidth Selection for Spatial Smoothing
contour.imlist Array of Contour Plots
allstats Calculate four standard summary functions of a point pattern.
ants Harkness-Isham ants' nests data
clip.infline Intersect Infinite Straight Lines with a Window
Smoothfun.ppp Smooth Interpolation of Marks as a Spatial Function
crossdist.psp Pairwise distances between two different line segment patterns
dilation Morphological Dilation
funxy Spatial Function Class
affine.tess Apply Geometrical Transformation To Tessellation
as.hyperframe.ppx Extract coordinates and marks of multidimensional point pattern
berman.test Berman's Tests for Point Process Model
as.ppm Extract Fitted Point Process Model
affine.im Apply Affine Transformation To Pixel Image
as.owin Convert Data To Class owin
auc Area Under ROC Curve
circumradius Circumradius of a Window
collapse.fv Collapse Several Function Tables into One
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
as.interact Extract Interaction Structure
density.lpp Kernel Estimate of Intensity on a Linear Network
bdist.tiles Distance to Boundary of Window
crossdist.pp3 Pairwise distances between two different three-dimensional point patterns
diameter.boxx Geometrical Calculations for Multi-Dimensional Box
copyExampleFiles Copy Data Files for Example
eval.im Evaluate Expression Involving Pixel Images
MultiHard The Multitype Hard Core Point Process Model
blur Apply Gaussian Blur to a Pixel Image
bdist.points Distance to Boundary of Window
demohyper Demonstration Example of Hyperframe of Spatial Data
as.polygonal Convert a Window to a Polygonal Window
anova.ppm ANOVA for Fitted Point Process Models
data.ppm Extract Original Data from a Fitted Point Process Model
fasp.object Function Arrays for Spatial Patterns
flipxy Exchange X and Y Coordinates
bounding.box.xy Convex Hull of Points
distcdf Distribution Function of Interpoint Distance
bdspots Breakdown Spots in Microelectronic Materials
edit.ppp Invoke Text Editor on Spatial Data
default.expand Default Expansion Rule for Simulation of Model
clickjoin Interactively join vertices on a plot
clarkevans Clark and Evans Aggregation Index
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
idw Inverse-distance weighted smoothing of observations at irregular points
clickppp Interactively Add Points
dummify Convert Data to Numeric Values by Constructing Dummy Variables
fvnames Abbreviations for Groups of Columns in Function Value Table
Window Extract or Change the Window of a Spatial Object
Poisson Poisson Point Process Model
dclf.test Diggle-Cressie-Loosmore-Ford and Maximum Absolute Deviation Tests
density.psp Kernel Smoothing of Line Segment Pattern
coef.ppm Coefficients of Fitted Point Process Model
bw.ppl Likelihood Cross Validation Bandwidth Selection for Kernel Density
beachcolours Create Colour Scheme for a Range of Numbers
cauchy.estK Fit the Neyman-Scott cluster process with Cauchy kernel
demopat Artificial Data Point Pattern
as.matrix.im Convert Pixel Image to Matrix or Array
LennardJones The Lennard-Jones Potential
closepairs.pp3 Close Pairs of Points in 3 Dimensions
as.lpp Convert Data to a Point Pattern on a Linear Network
bw.scott Scott's Rule for Bandwidth Selection for Kernel Density
chicago Chicago Street Crime Data
crossing.psp Crossing Points of Two Line Segment Patterns
dmixpois Mixed Poisson Distribution
clusterset Allard-Fraley Estimator of Cluster Feature
boxx Multi-Dimensional Box
discretise Safely Convert Point Pattern Window to Binary Mask
areaGain Difference of Disc Areas
diameter.owin Diameter of a Window
compatible.im Test Whether Pixel Images Are Compatible
im.object Class of Images
intersect.owin Intersection, Union or Set Subtraction of Windows
Smooth.msr Smooth a Signed or Vector-Valued Measure
diameter Diameter of an Object
contour.im Contour plot of pixel image
WindowOnly Extract Window of Spatial Object
cells Biological Cells Point Pattern
default.dummy Generate a Default Pattern of Dummy Points
envelope Simulation Envelopes of Summary Function
density.ppp Kernel Smoothed Intensity of Point Pattern
angles.psp Orientation Angles of Line Segments
Kest K-function
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
cdf.test.mppm Spatial Distribution Test for Multiple Point Process Model
diameter.linnet Circumradius and Diameter of a Linear Network
lansing Lansing Woods Point Pattern
circdensity Density Estimation for Circular Data
deltametric Delta Metric
intensity.ppp Empirical Intensity of Point Pattern
expand.owin Apply Expansion Rule
clmfires Castilla-La Mancha Forest Fires
convolve.im Convolution of Pixel Images
complement.owin Take Complement of a Window
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
compareFit Residual Diagnostics for Multiple Fitted Models
logLik.kppm Log Likelihood and AIC for Fitted Cox or Cluster Point Process Model
cdf.test Spatial Distribution Test for Point Pattern or Point Process Model
copper Berman-Huntington points and lines data
Extract.ppx Extract Subset of Multidimensional Point Pattern
Extract.fasp Extract Subset of Function Array
Ord Generic Ord Interaction model
Kres Residual K Function
Kmodel K Function or Pair Correlation Function of a Point Process Model
Replace.im Reset Values in Subset of Image
Kmodel.ppm K Function or Pair Correlation Function of Gibbs Point Process model
begins Check Start of Character String
as.data.frame.hyperframe Coerce Hyperframe to Data Frame
coords Extract or Change Coordinates of a Spatial or Spatiotemporal Point Pattern
bw.diggle Cross Validated Bandwidth Selection for Kernel Density
Ldot Multitype L-function (i-to-any)
dirichletWeights Compute Quadrature Weights Based on Dirichlet Tessellation
crossdist.ppp Pairwise distances between two different point patterns
harmonise Make Objects Compatible
harmonise.owin Make Windows Compatible
chop.tess Subdivide a Window or Tessellation using a Set of Lines
intensity.quadratcount Intensity Estimates Using Quadrat Counts
is.empty Test Whether An Object Is Empty
flu Influenza Virus Proteins
heather Diggle's Heather Data
edge.Ripley Ripley's Isotropic Edge Correction
layered Create List of Plotting Layers
linearKinhom Inhomogeneous Linear K Function
clusterfit Fit Cluster or Cox Point Process Model via Minimum Contrast
eval.fasp Evaluate Expression Involving Function Arrays
bind.fv Combine Function Value Tables
localKinhom Inhomogeneous Neighbourhood Density Function
eval.linim Evaluate Expression Involving Pixel Images on Linear Network
convexhull Convex Hull
linearmarkequal Mark Connection Function for Multitype Point Pattern on Linear Network
integral.msr Integral of a Measure
dclf.progress Progress Plot of Test of Spatial Pattern
pairdist.default Pairwise distances
compatible Test Whether Objects Are Compatible
clusterkernel Extract Cluster Offspring Kernel
fardist Farthest Distance to Boundary of Window
japanesepines Japanese Pines Point Pattern
foo Foo is Not a Real Name
lurking Lurking variable plot
deletebranch Delete or Extract a Branch of a Tree
letterR Window in Shape of Letter R
dirichletAreas Compute Areas of Tiles in Dirichlet Tessellation
clickpoly Interactively Define a Polygon
erosion Morphological Erosion
delaunayNetwork Linear Network of Delaunay Triangulation or Dirichlet Tessellation
as.data.frame.im Convert Pixel Image to Data Frame
eval.fv Evaluate Expression Involving Functions
methods.slrm Methods for Spatial Logistic Regression Models
is.convex Test Whether a Window is Convex
nbfires Point Patterns of New Brunswick Forest Fires
hyytiala Scots pines and other trees at Hyytiala
lpp Create Point Pattern on Linear Network
default.rmhcontrol Set Default Control Parameters for Metropolis-Hastings Algorithm.
edges2triangles List Triangles in a Graph
gauss.hermite Gauss-Hermite Quadrature Approximation to Expectation for Normal Distribution
distfun.lpp Distance Map on Linear Network
hamster Aherne's hamster tumour data
pairs.im Scatterplot Matrix for Pixel Images
paracou Kimboto trees at Paracou, French Guiana
dirichlet Dirichlet Tessellation of Point Pattern
exactMPLEstrauss Exact Maximum Pseudolikelihood Estimate for Stationary Strauss Process
is.multitype.ppp Test Whether A Point Pattern is Multitype
methods.kppm Methods for Cluster Point Process Models
gorillas Gorilla Nesting Sites
methods.objsurf Methods for Objective Function Surfaces
levelset Level Set of a Pixel Image
harmonise.fv Make Function Tables Compatible
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
edges2vees List Dihedral Triples in a Graph
is.dppm Recognise Fitted Determinantal Point Process Models
nncross.pp3 Nearest Neighbours Between Two Patterns in 3D
crossdist.default Pairwise distances between two different sets of points
distfun Distance Map as a Function
discpartarea Area of Part of Disc
closing Morphological Closing
formula.fv Extract or Change the Plot Formula for a Function Value Table
crossdist Pairwise distances
envelope.envelope Recompute Envelopes
bronzefilter Bronze gradient filter data
distmap Distance Map
as.tess Convert Data To Tessellation
lppm Fit Point Process Model to Point Pattern on Linear Network
harmonise.im Make Pixel Images Compatible
is.im Test Whether An Object Is A Pixel Image
crossdist.lpp Pairwise distances between two point patterns on a linear network
print.owin Print Brief Details of a Spatial Window
lineardisc Compute Disc of Given Radius in Linear Network
as.data.frame.owin Convert Window to Data Frame
rStraussHard Perfect Simulation of the Strauss-Hardcore Process
fryplot Fry Plot of Point Pattern
cut.ppp Classify Points in a Point Pattern
edit.hyperframe Invoke Text Editor on Hyperframe
is.ppm Test Whether An Object Is A Fitted Point Process Model
discs Union of Discs
harmonic Basis for Harmonic Functions
compatible.fasp Test Whether Function Arrays Are Compatible
endpoints.psp Endpoints of Line Segment Pattern
as.fv Convert Data To Class fv
domain Extract the Domain of any Spatial Object
as.function.fv Convert Function Value Table to Function
fitted.mppm Fitted Conditional Intensity for Multiple Point Process Model
envelope.pp3 Simulation Envelopes of Summary Function for 3D Point Pattern
as.linnet.psp Convert Line Segment Pattern to Linear Network
linearpcfinhom Inhomogeneous Linear Pair Correlation Function
delaunay Delaunay Triangulation of Point Pattern
formula.ppm Model Formulae for Gibbs Point Process Models
eroded.areas Areas of Morphological Erosions
methods.lppm Methods for Fitted Point Process Models on a Linear Network
dilated.areas Areas of Morphological Dilations
ewcdf Weighted Empirical Cumulative Distribution Function
is.hybrid Test Whether Object is a Hybrid
StraussHard The Strauss / Hard Core Point Process Model
invoke.symbolmap Plot Data Using Graphics Symbol Map
parres Partial Residuals for Point Process Model
ellipse Elliptical Window.
fitted.slrm Fitted Probabilities for Spatial Logistic Regression
pcf.fasp Pair Correlation Function obtained from array of K functions
dfbetas.ppm Parameter influence measure
as.function.im Convert Pixel Image to Function of Coordinates
distmap.owin Distance Map of Window
as.psp Convert Data To Class psp
distmap.ppp Distance Map of Point Pattern
envelope.lpp Envelope for Point Patterns on Linear Network
markcorr Mark Correlation Function
pixellate.owin Convert Window to Pixel Image
linearpcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-type) for Linear Point Pattern
by.im Apply Function to Image Broken Down by Factor
imcov Spatial Covariance of a Pixel Image
markvario Mark Variogram
hyperframe Hyper Data Frame
logLik.mppm Log Likelihood for Poisson Point Process Model
marks.psp Marks of a Line Segment Pattern
overlap.owin Compute Area of Overlap
nndensity.ppp Estimate Intensity of Point Pattern Using Nearest Neighbour Distances
is.subset.owin Determine Whether One Window is Contained In Another
hopskel Hopkins-Skellam Test
is.rectangle Determine Type of Window
relrisk.ppm Parametric Estimate of Spatially-Varying Relative Risk
fv.object Function Value Table
edge.Trans Translation Edge Correction
objsurf Objective Function Surface
identify.ppp Identify Points in a Point Pattern
edges Extract Boundary Edges of a Window.
methods.ppx Methods for Multidimensional Space-Time Point Patterns
kppm Fit Cluster or Cox Point Process Model
marks.tess Marks of a Tessellation
pairdist.psp Pairwise distances between line segments
closepairs Close Pairs of Points
humberside Humberside Data on Childhood Leukaemia and Lymphoma
inside.owin Test Whether Points Are Inside A Window
fitin.ppm Extract the Interaction from a Fitted Point Process Model
ord.family Ord Interaction Process Family
incircle Find Largest Circle Inside Window
linearKcross Multitype K Function (Cross-type) for Linear Point Pattern
model.depends Identify Covariates Involved in each Model Term
methods.linfun Methods for Functions on Linear Network
pairwise.family Pairwise Interaction Process Family
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
intersect.tess Intersection of Two Tessellations
hist.im Histogram of Pixel Values in an Image
shift.ppp Apply Vector Translation To Point Pattern
methods.box3 Methods for Three-Dimensional Box
distmap.psp Distance Map of Line Segment Pattern
ganglia Beta Ganglion Cells in Cat Retina, Old Version
plot.msr Plot a Signed or Vector-Valued Measure
pixellate.ppp Convert Point Pattern to Pixel Image
localpcf Local pair correlation function
matchingdist Distance for a Point Pattern Matching
hextess Hexagonal Grid or Tessellation
localK Neighbourhood density function
pixelcentres Extract Pixel Centres as Point Pattern
improve.kppm Improve Intensity Estimate of Fitted Cluster Point Process Model
linearKdot Multitype K Function (Dot-type) for Linear Point Pattern
increment.fv Increments of a Function
pairdist.pp3 Pairwise distances in Three Dimensions
im.apply Apply Function Pixelwise to List of Images
linearKdot.inhom Inhomogeneous multitype K Function (Dot-type) for Linear Point Pattern
plot.ppm plot a Fitted Point Process Model
colourtools Convert and Compare Colours in Different Formats
unitname Name for Unit of Length
is.marked Test Whether Marks Are Present
markconnect Mark Connection Function
methods.funxy Methods for Spatial Functions
mincontrast Method of Minimum Contrast
methods.lpp Methods for Point Patterns on a Linear Network
intensity.lpp Empirical Intensity of Point Pattern on Linear Network
fitted.ppm Fitted Conditional Intensity for Point Process Model
plot.solist Plot a List of Spatial Objects
quadrat.test Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
union.quad Union of Data and Dummy Points
methods.rho2hat Methods for Intensity Functions of Two Spatial Covariates
linearmarkconnect Mark Connection Function for Multitype Point Pattern on Linear Network
is.marked.ppp Test Whether A Point Pattern is Marked
model.frame.ppm Extract the Variables in a Point Process Model
im Create a Pixel Image Object
rMatClust Simulate Matern Cluster Process
midpoints.psp Midpoints of Line Segment Pattern
istat Point and Click Interface for Exploratory Analysis of Point Pattern
influence.ppm Influence Measure for Spatial Point Process Model
gordon People in Gordon Square
maxnndist Compute Minimum or Maximum Nearest-Neighbour Distance
plot.symbolmap Plot a Graphics Symbol Map
nnclean Nearest Neighbour Clutter Removal
logLik.slrm Loglikelihood of Spatial Logistic Regression
methods.linnet Methods for Linear Networks
methods.units Methods for Units
msr Signed or Vector-Valued Measure
plot.colourmap Plot a Colour Map
linearpcf Linear Pair Correlation Function
is.multitype.ppm Test Whether A Point Process Model is Multitype
as.solist Convert List of Two-Dimensional Spatial Objects
compatible.fv Test Whether Function Objects Are Compatible
nnwhich Nearest neighbour
linearpcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Dot-type) for Linear Point Pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
nndist.lpp Nearest neighbour distances on a linear network
nncross.lpp Nearest Neighbours on a Linear Network
linearpcfdot Multitype Pair Correlation Function (Dot-type) for Linear Point Pattern
nsegments Number of Line Segments in a Line Segment Pattern
methods.layered Methods for Layered Objects
plot.texturemap Plot a Texture Map
nztrees New Zealand Trees Point Pattern
cut.im Convert Pixel Image from Numeric to Factor
grow.rectangle Add margins to rectangle
kaplan.meier Kaplan-Meier Estimator using Histogram Data
pool.envelope Pool Data from Several Envelopes
linfun Function on a Linear Network
dirichletVertices Vertices and Edges of Dirichlet Tessellation
murchison Murchison gold deposits
parameters Extract Model Parameters in Understandable Form
pcfinhom Inhomogeneous Pair Correlation Function
disc Circular Window
lgcp.estpcf Fit a Log-Gaussian Cox Point Process by Minimum Contrast
pp3 Three Dimensional Point Pattern
pcfcross Multitype pair correlation function (cross-type)
gridcentres Rectangular grid of points
pcf Pair Correlation Function
hierpair.family Hierarchical Pairwise Interaction Process Family
linim Create Pixel Image on Linear Network
nnfun.lpp Nearest Neighbour Map on Linear Network
profilepl Profile Maximum Pseudolikelihood or AIC
is.owin Test Whether An Object Is A Window
print.quad Print a Quadrature Scheme
mppm Fit Point Process Model to Several Point Patterns
plot.psp plot a Spatial Line Segment Pattern
pairsat.family Saturated Pairwise Interaction Point Process Family
nnwhich.pp3 Nearest neighbours in three dimensions
pixellate Convert Spatial Object to Pixel Image
pcfdot Multitype pair correlation function (i-to-any)
diameter.box3 Geometrical Calculations for Three-Dimensional Box
plot.quadratcount Plot Quadrat Counts
marks Marks of a Point Pattern
plot.fasp Plot a Function Array
lut Lookup Tables
psp.object Class of Line Segment Patterns
nearest.raster.point Find Pixel Nearest to a Given Point
perimeter Perimeter Length of Window
eem Exponential Energy Marks
rpoislinetess Poisson Line Tessellation
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
matclust.estpcf Fit the Matern Cluster Point Process by Minimum Contrast Using Pair Correlation
quadrat.test.mppm Chi-Squared Test for Multiple Point Process Model Based on Quadrat Counts
interp.colourmap Interpolate smoothly between specified colours
rshift.splitppp Randomly Shift a List of Point Patterns
plot.slrm Plot a Fitted Spatial Logistic Regression
is.marked.ppm Test Whether A Point Process Model is Marked
linnet Create a Linear Network
print.im Print Brief Details of an Image
layerplotargs Extract or Replace the Plot Arguments of a Layered Object
model.images Compute Images of Constructed Covariates
project.ppm Force Point Process Model to be Valid
ippm Fit Point Process Model Involving Irregular Trend Parameters
project2set Find Nearest Point in a Region
intensity.ppm Intensity of Fitted Point Process Model
progressreport Print Progress Reports
is.multitype Test whether Object is Multitype
integral.im Integral of a Pixel Image
npoints Number of Points in a Point Pattern
linearKcross.inhom Inhomogeneous multitype K Function (Cross-type) for Linear Point Pattern
perspPoints Draw Points or Lines on a Surface Viewed in Perspective
methods.fii Methods for Fitted Interactions
nnwhich.ppx Nearest Neighbours in Any Dimensions
nestsplit Nested Split
methods.linim Methods for Images on a Linear Network
methods.rhohat Methods for Intensity Functions of Spatial Covariate
rLGCP Simulate Log-Gaussian Cox Process
model.matrix.slrm Extract Design Matrix from Spatial Logistic Regression Model
rescue.rectangle Convert Window Back To Rectangle
pcfmulti Marked pair correlation function
nndist Nearest neighbour distances
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
longleaf Longleaf Pines Point Pattern
project2segment Move Point To Nearest Line
finpines Pine saplings in Finland.
iplot Point and Click Interface for Displaying Spatial Data
crossdist.ppx Pairwise Distances Between Two Different Multi-Dimensional Point Patterns
mergeLevels Merge Levels of a Factor
pcf3est Pair Correlation Function of a Three-Dimensional Point Pattern
pcf.fv Pair Correlation Function obtained from K Function
psst Pseudoscore Diagnostic For Fitted Model against General Alternative
logLik.ppm Log Likelihood and AIC for Point Process Model
plot.imlist Plot a List of Images
rMosaicSet Mosaic Random Set
pairorient Point Pair Orientation Distribution
pairdist.ppp Pairwise distances
plot.lpp Plot Point Pattern on Linear Network
methods.pp3 Methods for three-dimensional point patterns
plot.im Plot a Pixel Image
persp.im Perspective Plot of Pixel Image
residuals.ppm Residuals for Fitted Point Process Model
nndist.pp3 Nearest neighbour distances in three dimensions
quadrats Divide Region into Quadrats
gridweights Compute Quadrature Weights Based on Grid Counts
mucosa Cells in Gastric Mucosa
model.matrix.ppm Extract Design Matrix from Point Process Model
plot.anylist Plot a List of Things
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
relrisk.ppp Nonparametric Estimate of Spatially-Varying Relative Risk
rshift Random Shift
infline Infinite Straight Lines
runifpoint Generate N Uniform Random Points
plot.layered Layered Plot
pool.rat Pool Data from Several Ratio Objects
pppmatching.object Class of Point Matchings
nnmap K-th Nearest Point Map
quadscheme.logi Generate a Logistic Regression Quadrature Scheme from a Point Pattern
lohboot Bootstrap Confidence Bands for Summary Function
plot.textstring Plot a Text String
scalardilate Apply Scalar Dilation
opening Morphological Opening
solist List of Two-Dimensional Spatial Objects
rsyst Simulate systematic random point pattern
ppx Multidimensional Space-Time Point Pattern
residuals.mppm Residuals for Point Process Model Fitted to Multiple Point Patterns
latest.news Print News About Latest Version of Package
plot.lppm Plot a Fitted Point Process Model on a Linear Network
pool.fasp Pool Data from Several Function Arrays
padimage Pad the Border of a Pixel Image
plot.quadrattest Display the result of a quadrat counting test.
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
nnfun Nearest Neighbour Index Map as a Function
fv Create a Function Value Table
raster.x Cartesian Coordinates for a Pixel Raster
rjitter Random Perturbation of a Point Pattern
linearK Linear K Function
identify.psp Identify Segments in a Line Segment Pattern
pcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)
quantile.im Sample Quantiles of Pixel Image
plot.linnet Plot a linear network
quantile.ewcdf Quantiles of Weighted Empirical Cumulative Distribution Function
shift Apply Vector Translation
plot.hyperframe Plot Entries in a Hyperframe
runifpoint3 Generate N Uniform Random Points in Three Dimensions
rotate Rotate
plot.kppm Plot a fitted cluster point process
quasirandom Quasirandom Patterns
owin Create a Window
miplot Morisita Index Plot
rose Rose Diagram
intensity Intensity of a Dataset or a Model
multiplicity.ppp Count Multiplicity of Duplicate Points
plot.cdftest Plot a Spatial Distribution Test
suffstat Sufficient Statistic of Point Process Model
nearestsegment Find Line Segment Nearest to Each Point
panel.contour Panel Plots using Colour Image or Contour Lines
rgbim Create Colour-Valued Pixel Image
hybrid.family Hybrid Interaction Family
leverage.ppm Leverage Measure for Spatial Point Process Model
spatstat-deprecated Deprecated spatstat functions
is.lpp Test Whether An Object Is A Point Pattern on a Linear Network
nncross Nearest Neighbours Between Two Patterns
rknn Theoretical Distribution of Nearest Neighbour Distance
plot.envelope Plot a Simulation Envelope
linearpcfcross Multitype Pair Correlation Function (Cross-type) for Linear Point Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
pppdist Distance Between Two Point Patterns
rGaussPoisson Simulate Gauss-Poisson Process
owin.object Class owin
nndist.psp Nearest neighbour distances between line segments
selfcut.psp Cut Line Segments Where They Intersect
lengths.psp Lengths of Line Segments
plot.leverage.ppm Plot Leverage Function
periodify Make Periodic Copies of a Spatial Pattern
rotate.ppp Rotate a Point Pattern
pairdist.lpp Pairwise shortest-path distances between points on a linear network
split.im Divide Image Into Sub-images
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
nnmark Mark of Nearest Neighbour
pointsOnLines Place Points Evenly Along Specified Lines
ppm Fit Point Process Model to Data
npfun Dummy Function Returns Number of Points
rstrat Simulate Stratified Random Point Pattern
vcov.kppm Variance-Covariance Matrix for a Fitted Cluster Point Process Model
pool.anylist Pool Data from a List of Objects
scanLRTS Likelihood Ratio Test Statistic for Scan Test
rThomas Simulate Thomas Process
pixelquad Quadrature Scheme Based on Pixel Grid
integral.linim Integral on a Linear Network
reload.or.compute Compute Unless Previously Saved
inforder.family Infinite Order Interaction Family
ponderosa Ponderosa Pine Tree Point Pattern
rQuasi Generate Quasirandom Point Pattern in Given Window
predict.lppm Predict Point Process Model on Linear Network
rMosaicField Mosaic Random Field
interp.im Interpolate a Pixel Image
pcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-Type)
sharpen Data Sharpening of Point Pattern
simulate.ppm Simulate a Fitted Gibbs Point Process Model
split.ppp Divide Point Pattern into Sub-patterns
plot.pp3 Plot a Three-Dimensional Point Pattern
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
print.ppm Print a Fitted Point Process Model
quad.object Class of Quadrature Schemes
rpoisppx Generate Poisson Point Pattern in Any Dimensions
spiders Spider Webs on Mortar Lines of a Brick Wall
ppm.ppp Fit Point Process Model to Point Pattern Data
subset.ppp Subset of Point Pattern Satisfying A Condition
vertices Vertices of a Window
print.ppp Print Brief Details of a Point Pattern Dataset
rSSI Simulate Simple Sequential Inhibition
zapsmall.im Rounding of Pixel Values
ppp.object Class of Point Patterns
spatstat-internal Internal spatstat functions
plot.onearrow Plot an Arrow
summary.ppm Summarizing a Fitted Point Process Model
is.ppp Test Whether An Object Is A Point Pattern
plot.splitppp Plot a List of Point Patterns
tilenames Names of Tiles in a Tessellation
will.expand Test Expansion Rule
pool.quadrattest Pool Several Quadrat Tests
rcell Simulate Baddeley-Silverman Cell Process
vargamma.estpcf Fit the Neyman-Scott Cluster Point Process with Variance Gamma kernel
plot.ppp plot a Spatial Point Pattern
plot.yardstick Plot a Yardstick or Scale Bar
summary.splitppp Summary of a Split Point Pattern
quadratcount Quadrat counting for a point pattern
layout.boxes Generate a Row or Column Arrangement of Rectangles.
plot.quad Plot a Spatial Quadrature Scheme
tweak.colourmap Change Colour Values in a Colour Map
plot.fv Plot Function Values
tess Create a Tessellation
plot.mppm plot a Fitted Multiple Point Process Model
simulate.kppm Simulate a Fitted Cluster Point Process Model
rotate.owin Rotate a Window
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
quantess Quantile Tessellation
pool Pool Data
mean.im Maximum, Minimum, Mean, Median, Range or Sum of Pixel Values in an Image
rescale Convert dataset to another unit of length
print.psp Print Brief Details of a Line Segment Pattern Dataset
rescale.psp Convert Line Segment Pattern to Another Unit of Length
rshift.ppp Randomly Shift a Point Pattern
methods.boxx Methods for Multi-Dimensional Box
nndist.ppx Nearest Neighbour Distances in Any Dimensions
summary.solist Summary of a List of Spatial Objects
residualspaper Data and Code From JRSS Discussion Paper on Residuals
pyramidal Pyramidal Neurons in Cingulate Cortex
spokes Spokes pattern of dummy points
pool.fv Pool Several Functions
superimpose Superimpose Several Geometric Patterns
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
ppm.object Class of Fitted Point Process Models
pcf.ppp Pair Correlation Function of Point Pattern
shift.psp Apply Vector Translation To Line Segment Pattern
psstA Pseudoscore Diagnostic For Fitted Model against Area-Interaction Alternative
stienen Stienen Diagram
rotate.im Rotate a Pixel Image
sporophores Sporophores Data
osteo Osteocyte Lacunae Data: Replicated Three-Dimensional Point Patterns
pixellate.psp Convert Line Segment Pattern to Pixel Image
predict.mppm Prediction for Fitted Multiple Point Process Model
psstG Pseudoscore Diagnostic For Fitted Model against Saturation Alternative
selfcrossing.psp Crossing Points in a Line Segment Pattern
vesicles Vesicles Data
predict.ppm Prediction from a Fitted Point Process Model
sessionLibs Print Names and Version Numbers of Libraries Loaded
setcov Set Covariance of a Window
plot.linim Plot Pixel Image on Linear Network
plot.influence.ppm Plot Influence Measure
psp Create a Line Segment Pattern
plot.plotppm Plot a plotppm Object Created by plot.ppm
triplet.family Triplet Interaction Family
nnwhich.lpp Identify Nearest Neighbours on a Linear Network
reach Interaction Distance of a Point Process
waterstriders Waterstriders data. Three independent replications of a point pattern formed by insects.
moribund Outdated Functions
rat Ratio object
rounding Detect Numerical Rounding
rescale.ppp Convert Point Pattern to Another Unit of Length
plot.scan.test Plot Result of Scan Test
rlabel Random Re-Labelling of Point Pattern
rNeymanScott Simulate Neyman-Scott Process
rCauchy Simulate Neyman-Scott Point Process with Cauchy cluster kernel
nnorient Nearest Neighbour Orientation Distribution
residuals.kppm Residuals for Fitted Cox or Cluster Point Process Model
simdat Simulated Point Pattern
simulate.slrm Simulate a Fitted Spatial Logistic Regression Model
range.fv Range of Function Values
pairdist Pairwise distances
update.symbolmap Update a Graphics Symbol Map.
rotmean Rotational Average of a Pixel Image
simplepanel Simple Point-and-Click Interface Panels
vcov.mppm Calculate Variance-Covariance Matrix for Fitted Multiple Point Process Model
yardstick Text, Arrow or Scale Bar in a Diagram
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
ppp Create a Point Pattern
vargamma.estK Fit the Neyman-Scott Cluster Point Process with Variance Gamma kernel
pppmatching Create a Point Matching
volume Volume of an Object
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
rStrauss Perfect Simulation of the Strauss Process
slrm Spatial Logistic Regression
rMaternII Simulate Matern Model II
with.msr Evaluate Expression Involving Components of a Measure
quadratresample Resample a Point Pattern by Resampling Quadrats
rshift.psp Randomly Shift a Line Segment Pattern
reduced.sample Reduced Sample Estimator using Histogram Data
predict.slrm Predicted or Fitted Values from Spatial Logistic Regression
scan.test Spatial Scan Test
redwood California Redwoods Point Pattern (Ripley's Subset)
spatstat.options Internal Options in Spatstat Package
stieltjes Compute Integral of Function Against Cumulative Distribution
square Square Window
rVarGamma Simulate Neyman-Scott Point Process with Variance Gamma cluster kernel
quadrat.test.splitppp Dispersion Test of CSR for Split Point Pattern Based on Quadrat Counts
summary.psp Summary of a Line Segment Pattern Dataset
transect.im Pixel Values Along a Transect
textureplot Plot Image or Tessellation Using Texture Fill
relrisk Estimate of Spatially-Varying Relative Risk
thomas.estK Fit the Thomas Point Process by Minimum Contrast
pairdist.ppx Pairwise Distances in Any Dimensions
whist Weighted Histogram
treebranchlabels Label Vertices of a Tree by Branch Membership
simba Simulated data from a two-group experiment with replication within each group.
quadscheme Generate a Quadrature Scheme from a Point Pattern
rmpoispp Generate Multitype Poisson Point Pattern
rmhexpand Specify Simulation Window or Expansion Rule
update.kppm Update a Fitted Cluster Point Process Model
rcellnumber Generate Random Numbers of Points for Cell Process
rDGS Perfect Simulation of the Diggle-Gates-Stibbard Process
rhohat Smoothing Estimate of Covariate Transformation
split.hyperframe Divide Hyperframe Into Subsets and Reassemble
rescale.im Convert Pixel Image to Another Unit of Length
unnormdensity Weighted kernel smoother
split.ppx Divide Multidimensional Point Pattern into Sub-patterns
plot.listof Plot a List of Things
rMaternI Simulate Matern Model I
rescale.owin Convert Window to Another Unit of Length
reflect Reflect In Origin
superimpose.lpp Superimpose Several Point Patterns on Linear Network
tiles Extract List of Tiles in a Tessellation
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
runiflpp Uniform Random Points on a Linear Network
summary.ppp Summary of a Point Pattern Dataset
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
solapply Apply a Function Over a List and Obtain a List of Objects
ripras Estimate window from points alone
runifpointx Generate N Uniform Random Points in Any Dimensions
rpoisline Generate Poisson Random Line Process
rotate.psp Rotate a Line Segment Pattern
segregation.test Test of Spatial Segregation of Types
plot.tess Plot a tessellation
thomas.estpcf Fit the Thomas Point Process by Minimum Contrast
spruces Spruces Point Pattern
with.fv Evaluate an Expression in a Function Table
symbolmap Graphics Symbol Map
rmh.ppm Simulate from a Fitted Point Process Model
studpermu.test Studentised Permutation Test
stratrand Stratified random point pattern
summary.anylist Summary of a List of Things
urkiola Urkiola Woods Point Pattern
predict.kppm Prediction from a Fitted Cluster Point Process Model
update.ppm Update a Fitted Point Process Model
rPoissonCluster Simulate Poisson Cluster Process
rpoispp3 Generate Poisson Point Pattern in Three Dimensions
simulate.lppm Simulate a Fitted Point Process Model on a Linear Network
rDiggleGratton Perfect Simulation of the Diggle-Gratton Process
treeprune Prune Tree to Given Level
unmark Remove Marks
shift.owin Apply Vector Translation To Window
summary.owin Summary of a Spatial Window
roc Receiver Operating Characteristic
simplify.owin Approximate a Polygon by a Simpler Polygon
tile.areas Compute Areas of Tiles in a Tessellation
round.ppp Apply Numerical Rounding to Spatial Coordinates
rpoispp Generate Poisson Point Pattern
runifdisc Generate N Uniform Random Points in a Disc
rmpoint Generate N Random Multitype Points
run.simplepanel Run Point-and-Click Interface
shapley Galaxies in the Shapley Supercluster
rHardcore Perfect Simulation of the Hardcore Process
sumouter Compute Quadratic Forms
rthin Random Thinning
scanpp Read Point Pattern From Data File
rnoise Random Pixel Noise
summary.quad Summarizing a Quadrature Scheme
unique.ppp Extract Unique Points from a Spatial Point Pattern
texturemap Texture Map
update.rmhcontrol Update Control Parameters of Metropolis-Hastings Algorithm
rpoislpp Poisson Point Process on a Linear Network
subset.hyperframe Subset of Hyperframe Satisfying A Condition
plot.owin Plot a Spatial Window
relevel.im Reorder Levels of a Factor-Valued Image or Pattern
rho2hat Smoothed Relative Density of Pairs of Covariate Values
transmat Convert Pixel Array Between Different Conventions
vcov.slrm Variance-Covariance Matrix for a Fitted Spatial Logistic Regression
is.stationary Recognise Stationary and Poisson Point Process Models
rlinegrid Generate grid of parallel lines with random displacement
scaletointerval Rescale Data to Lie Between Specified Limits
sidelengths.owin Side Lengths of Enclosing Rectangle of a Window
summary.im Summarizing a Pixel Image
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
timed Record the Computation Time
spatialcdf Spatial Cumulative Distribution Function
runifpointOnLines Generate N Uniform Random Points On Line Segments
rpoint Generate N Random Points
valid.ppm Check Whether Point Process Model is Valid
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
spatstat-package The Spatstat Package
with.hyperframe Evaluate an Expression in Each Row of a Hyperframe
shift.im Apply Vector Translation To Pixel Image
plot.bermantest Plot Result of Berman Test
subfits Extract List of Individual Point Process Models
simplenet Simple Example of Linear Network
summary.listof Summary of a List of Things
summary.kppm Summarizing a Fitted Cox or Cluster Point Process Model
swedishpines Swedish Pines Point Pattern
varblock Estimate Variance of Summary Statistic by Subdivision
trim.rectangle Cut margins from rectangle
waka Trees in Waka national park
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Nickname Life, The Universe and Everything
Date 2015-05-27
License GPL (>= 2)
URL http://www.spatstat.org
LazyData true
NeedsCompilation yes
ByteCompile true
Packaged 2015-05-27 09:24:09 UTC; adrian
Repository CRAN
Date/Publication 2015-06-01 07:46:50
imports abind , deldir (>= 0.0-21) , goftest , Matrix , mgcv , polyclip (>= 1.3-0) , tensor
depends base (>= 3.2.0) , graphics , grDevices , R (>= 3.2.0) , stats , utils
suggests gsl , locfit , maptools , RandomFields (>= 3.0.0) , rpanel , sm , spatial , tkrplot
Contributors Rolf Turner, Adrian Baddeley, Ege Rubak

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