spatstat v1.39-0

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

Nickname Smoke and Mirrors
Date 2014-10-23
License GPL (>= 2)
URL http://www.spatstat.org
LazyData true
NeedsCompilation yes
ByteCompile true
Packaged 2014-10-23 01:47:26 UTC; adrian
Repository CRAN
Date/Publication 2014-10-23 08:43:49

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