spatstat v1.18-4


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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 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. Point process models can be fitted to point pattern data. Cluster type models are fitted by the method of minimum contrast. Very general Gibbs point process models can be fitted to point pattern data using a function ppm similar to lm or glm. Models may include dependence on covariates, interpoint interaction and dependence on marks. Fitted models can be simulated automatically. Also provides facilities for formal inference (such as chi-squared tests) and model diagnostics (including simulation envelopes, residuals, residual plots and Q-Q plots).

Functions in spatstat

Name Description
BadGey Hybrid Geyer Point Process Model
affine.ppp Apply Affine Transformation To Point Pattern
Ldot.inhom Inhomogeneous Multitype L Dot Function
Ldot Multitype L-function (i-to-any) Coerce Line Segment Pattern to a Data Frame
AreaInter The Area Interaction Point Process Model Convert to Pixel Image
border Border Region of a Window
chop.tess Subdivide a Window or Tessellation using a Set of Lines
diameter.boxx Geometrical Calculations for Multi-Dimensional Box
bdist.pixels Distance to Boundary of Window
Jmulti Marked J Function
DiggleGratton Diggle-Gratton model
envelope.pp3 Simulation Envelopes of Summary Function for 3D Point Pattern
as.polygonal Convert a Window to a Polygonal Window
Linhom L-function
deltametric Delta Metric
boxx Multi-Dimensional Box
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
Kest.fft K-function using FFT
Poisson Poisson Point Process Model
data.ppm Extract Original Data from a Fitted Point Process Model
fitin.ppm Extract the Interaction from a Fitted Point Process Model
distfun Distance Map as a Function
Strauss The Strauss Point Process Model
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
erosion Morphological Erosion
angles.psp Orientation Angles of Line Segments
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
lengths.psp Lengths of Line Segments
methods.ppx Methods for Multidimensional Space-Time Point Patterns
applynbd Apply Function to Every Neighbourhood in a Point Pattern
fitted.ppm Fitted Conditional Intensity for Point Process Model
nnwhich.ppx Nearest Neighbours in Any Dimensions
fryplot Fry Plot of Point Pattern
areaLoss Difference of Disc Areas
Geyer Geyer's Saturation Point Process Model Convert Pixel Image to Data Frame
as.owin Convert Data To Class owin
bind.fv Combine Function Value Tables
bramblecanes Hutchings' Bramble Canes data
compatible.fv Test Whether Two Function Objects Are Compatible
finpines Pine saplings in Finland.
demopat Artificial Data Point Pattern
plot.listof Plot a List of Things
complement.owin Take Complement of a Window
crossdist.ppp Pairwise distances between two different point patterns
gpc2owin Convert Polygonal Region into Different Format
anova.ppm ANOVA for Fitted Point Process Models
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
pairdist.pp3 Pairwise distances in Three Dimensions
humberside Humberside Data on Childhood Leukaemia and Lymphoma
Gfox Foxall's Distance Functions
Extract.fv Extract Subset of Function Values
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
endpoints.psp Endpoints of Line Segment Pattern
Softcore The Soft Core Point Process Model
Extract.listof Extract or Replace Subset of a List of Things
pixellate Convert Spatial Object to Pixel Image
incircle Find Largest Circle Inside Window
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
as.hyperframe Convert Data to Hyperframe
gridweights Compute Quadrature Weights Based on Grid Counts
pointsOnLines Place Points Evenly Along Specified Lines
Ord Generic Ord Interaction model Convert Pixel Image to Matrix
affine.psp Apply Affine Transformation To Line Segment Pattern
markcorrint Mark Correlation Integral
lut Lookup Tables Apply Function to Image Broken Down by Factor
dilated.areas Areas of Morphological Dilations
discpartarea Area of Part of Disc
ants Harkness-Isham ants' nests data
reach Interaction Distance of a Point Process
as.mask Pixel Image Approximation of a Window
coef.ppm Coefficients of Fitted Point Process Model
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
stieltjes Compute Integral of Function Against Cumulative Distribution
nnclean Nearest Neighbour Clutter Removal
connected Connected components of an image or window
whist Weighted Histogram
nnwhich.pp3 Nearest neighbours in three dimensions
hyperframe Hyper Data Frame
pcf Pair Correlation Function
eval.fv Evaluate Expression Involving Functions
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
distmap.ppp Distance Map of Point Pattern
intersect.owin Intersection, Union or Set Subtraction of Two Windows Integral of a Pixel Image
perimeter Perimeter Length of Window
pcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)
is.multitype.ppm Test Whether A Point Process Model is Multitype
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
spokes Spokes pattern of dummy points
plot.ppp plot a Spatial Point Pattern
methods.boxx Methods for Multi-Dimensional Box
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
as.ppp Convert Data To Class ppp
append.psp Combine Two Line Segment Patterns
dirichlet Dirichlet Tessellation of Point Pattern
Jdot Multitype J Function (i-to-any)
coords Extract Coordinates of a Spatial or Spatiotemporal Point Pattern
owin.object Class owin
longleaf Longleaf Pines Point Pattern
Extract.psp Extract Subset of Line Segment Pattern
amacrine Hughes' Amacrine Cell Data
Lcross.inhom Inhomogeneous Cross Type L Function
as.rectangle Window Frame
anemones Beadlet Anemones Data
plot.pp3 Plot a three-dimensional point pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
chorley Chorley-Ribble Cancer Data
thomas.estK Fit the Thomas Point Process by Minimum Contrast
nearestsegment Find Line Segment Nearest to Each Point
Gmulti Marked Nearest Neighbour Distance Function
clickppp Interactively Add Points Saturated Pairwise Interaction Point Process Family
Jcross Multitype J Function (i-to-j) Ord Interaction Process Family
distmap.psp Distance Map of Line Segment Pattern
K3est K-function of a Three-Dimensional Point Pattern
pppdist Distance Between Two Point Patterns
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
Kest K-function
harmonic Basis for Harmonic Functions
fasp.object Function Arrays for Spatial Patterns
mincontrast Method of Minimum Contrast
im Create a Pixel Image Object Reset Values in Subset of Image
rcell Simulate Baddeley-Silverman Cell Process
print.ppm Print a Fitted Point Process Model
bdist.points Distance to Boundary of Window
affine.owin Apply Affine Transformation To Window
convexhull Convex Hull
as.tess Convert Data To Tessellation
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
profilepl Profile Maximum Pseudolikelihood
Pairwise Generic Pairwise Interaction model
convexhull.xy Convex Hull of Points
plot.colourmap Plot a Colour Map
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
cells Biological Cells Point Pattern
print.quad Print a Quadrature Scheme
pairdist.psp Pairwise distances between line segments
F3est Empty Space Function of a Three-Dimensional Point Pattern
psp.object Class of Line Segment Patterns
as.mask.psp Convert Line Segment Pattern to Binary Pixel Mask
rSSI Simulate Simple Sequential Inhibition
Fest Estimate the empty space function F
centroid.owin Centroid of a window
closing Morphological Closing
plot.ppm plot a Fitted Point Process Model
Extract.tess Extract or Replace Subset of Tessellation
compatible.fasp Test Whether Two Function Arrays Are Compatible
rpoispp Generate Poisson Point Pattern
rthin Random Thinning
ppm Fit Point Process Model to Data
crossdist.default Pairwise distances between two different sets of points Perspective Plot of Pixel Image
Iest Estimate the I-function
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
corners Corners of a rectangle
nndist.pp3 Nearest neighbour distances in three dimensions
diameter.owin Diameter of a Window
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
density.psp Kernel Smoothing of Line Segment Pattern
rThomas Simulate Thomas Process
delaunay Delaunay Triangulation of Point Pattern
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern Extract Subset of Image
plot.owin Plot a Spatial Window Pairwise Interaction Process Family
betacells Beta Ganglion Cells in Cat Retina
model.matrix.ppm Extract Design Matrix from Point Process Model
rescale.owin Convert Window to Another Unit of Length
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
Lest L-function
default.dummy Generate a Default Pattern of Dummy Points
rshift.psp Randomly Shift a Line Segment Pattern
residuals.ppm Residuals for Fitted Point Process Model
cut.ppp Classify Points in a Point Pattern
periodify Make Periodic Copies of a Spatial Pattern
rjitter Random Perturbation of a Point Pattern
hamster Aherne's hamster tumour data
setcov Set Covariance of a Window
Extract.fasp Extract Subset of Function Array
bermantest Berman's Tests for Point Process Model
pcf.fv Pair Correlation Function obtained from K Function Maximum, Minimum, Mean, Median, Range or Sum of Pixel Values in an Image
spatstat-package The Spatstat Package
summary.ppm Summarizing a Fitted Point Process Model
markconnect Mark Connection Function Print Brief Details of an Image
Extract.splitppp Extract or Replace Sub-Patterns
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
crossdist.ppx Pairwise Distances Between Two Different Multi-Dimensional Point Patterns
crossing.psp Crossing Points of Two Line Segment Patterns Divide Image Into Sub-images
MultiStrauss The Multitype Strauss Point Process Model
disc Circular Window
plot.tess Plot a tessellation Convert Pixel Image from Numeric to Factor
nnwhich Nearest neighbour
rMosaicField Mosaic Random Field Evaluate Expression Involving Pixel Images
diameter.box3 Geometrical Calculations for Three-Dimensional Box Bounding Box of a Window or Point Pattern
distmap.owin Distance Map of Window
bdist.tiles Distance to Boundary of Window
unitname Name for Unit of Length
OrdThresh Ord's Interaction model
eval.fasp Evaluate Expression Involving Function Arrays
is.marked.ppp Test Whether A Point Pattern is Marked
tess Create a Tessellation
predict.kppm Prediction from a Fitted Cluster Point Process Model
Kcross.inhom Inhomogeneous Cross K Function
rotate Rotate
project2segment Move Point To Nearest Line
as.psp Convert Data To Class psp
Kinhom Inhomogeneous K-function
Gest Nearest Neighbour Distance Function G
plot.kppm Plot a fitted cluster point process
plot.plotppm Plot a plotppm Object Created by plot.ppm
clickpoly Interactively Define a Polygon
ponderosa Ponderosa Pine Tree Point Pattern Kaplan-Meier and Reduced Sample Estimator using Histograms
update.kppm Update a Fitted Cluster Point Process Model Print News About Latest Version of Package
collapse.fv Collapse Several Function Tables into One
urkiola Urkiola Woods Point Pattern
concatxy Concatenate x,y Coordinate Vectors
im.object Class of Images
plot.psp plot a Spatial Line Segment Pattern
update.ppm Update a Fitted Point Process Model
is.owin Test Whether An Object Is A Window
ppm.object Class of Fitted Point Process Models
envelope Simulation Envelopes of Summary Function
quadratcount Quadrat counting for a point pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
Kmeasure Reduced Second Moment Measure
Kmulti Marked K-Function
is.subset.owin Determine Whether One Window is Contained In Another
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
smooth.fv Apply Smoothing to Function Values
allstats Calculate four standard summary functions of a point pattern. Sample Quantiles of Pixel Image
rotate.owin Rotate a Window
clarkevans Clark and Evans Aggregation Index
methods.pp3 Methods for three-dimensional point patterns
letterR Window in Shape of Letter R
rmpoint Generate N Random Multitype Points
rmh.ppm Simulate from a Fitted Point Process Model
Emark Diagnostics for random marking
rsyst Simulate systematic random point pattern
istat Point and Click Interface for Exploratory Analysis of Point Pattern
ewcdf Weighted Empirical Cumulative Distribution Function
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
area.owin Area of a Window
ppx Multidimensional Space-Time Point Pattern
pppmatching.object Class of Point Matchings
plot.quad plot a Spatial Quadrature Scheme
is.marked.ppm Test Whether A Point Process Model is Marked
nearest.raster.point Find Pixel Nearest to a Given Point
nncross Nearest Neighbours Between Two Patterns
affine Apply Affine Transformation
scanpp Read Point Pattern From Data File
Jest Estimate the J-function
union.quad Union of Data and Dummy Points
simplify.owin Approximate a Polygon by a Simpler Polygon
areaGain Difference of Disc Areas
pairdist.default Pairwise distances
rotate.ppp Rotate a Point Pattern
Kdot.inhom Inhomogeneous Multitype K Dot Function
fv.object Data Frames of Function Values
pcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-Type)
print.ppp Print Brief Details of a Point Pattern Dataset Coerce Point Pattern to a Data Frame
matchingdist Distance for a Point Pattern Matching
bronzefilter Bronze gradient filter data
Kcross Multitype K Function (Cross-type)
Extract.quad Subset of Quadrature Scheme
heather Diggle's Heather Data Convex Hull of Points
Kdot Multitype K Function (i-to-any)
pppmatching Create a Point Matching
colourmap Colour Lookup Tables
expand.owin Expand Window By Factor
predict.ppm Prediction from a Fitted Point Process Model
rlinegrid Generate grid of parallel lines with random displacement
pairdist.ppp Pairwise distances
simulate.kppm Simulate a Fitted Cluster Point Process Model
rlabel Random Re-Labelling of Point Pattern
Lcross Multitype L-function (cross-type)
rmpoispp Generate Multitype Poisson Point Pattern
rpoisppx Generate Poisson Point Pattern in Any Dimensions
blur Apply Gaussian Blur to a Pixel Image
pairdist.ppx Pairwise Distances in Any Dimensions
runifpoint3 Generate N Uniform Random Points in Three Dimensions
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
runifpoint Generate N Uniform Random Points Summarizing a Pixel Image
fv Create a Function Value Table
quad.object Class of Quadrature Schemes
as.hyperframe.ppx Extract coordinates and marks of multidimensional point pattern
rMaternII Simulate Matern Model II
StraussHard The Strauss / Hard Core Point Process Model
is.multitype.ppp Test Whether A Point Pattern is Multitype
plot.splitppp Plot a List of Point Patterns
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
infline Infinite Straight Lines
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
murchison Murchison gold deposits
localK Neighbourhood density function
nndist.psp Nearest neighbour distances between line segments
unique.ppp Extract Unique Points from a Spatial Point Pattern
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
clip.infline Intersect Infinite Straight Lines with a Window
LennardJones The Lennard-Jones Potential
kaplan.meier Kaplan-Meier Estimator using Histogram Data
lansing Lansing Woods Point Pattern
shift Apply Vector Translation
shift.owin Apply Vector Translation To Window
lurking Lurking variable plot
crossdist Pairwise distances
summary.ppp Summary of a Point Pattern Dataset Test Whether Two Pixel Images Are Compatible
rshift.splitppp Randomly Shift a List of Point Patterns
crossdist.pp3 Pairwise distances between two different three-dimensional point patterns
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
as.box3 Convert Data to Three-Dimensional Box
nztrees New Zealand Trees Point Pattern
box3 Three-Dimensional Box
rescale.psp Convert Line Segment Pattern to Another Unit of Length
spruces Spruces Point Pattern
plot.bermantest Plot Result of Berman Test
crossdist.psp Pairwise distances between two different line segment patterns
Extract.ppp Extract or Replace Subset of Point Pattern
pixellate.ppp Convert Point Pattern to Pixel Image
quadrats Divide Region into Quadrats
markcorr Mark Correlation Function
residualspaper Data and Code From JRSS Discussion Paper on Residuals
superimposePSP Superimpose Several Line Segment Patterns
density.ppp Kernel Smoothed Intensity of Point Pattern
tiles Extract List of Tiles in a Tessellation
miplot Morishita Index Plot
copper Berman-Huntington points and lines data
summary.owin Summary of a Spatial Window
marks Marks of a Point Pattern
discretise Safely Convert Point Pattern Window to Binary Mask
bei Tropical rain forest trees
swedishpines Swedish Pines Point Pattern
rStrauss Perfect Simulation of the Strauss Process
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
redwood California Redwoods Point Pattern (Ripley's Subset)
superimpose Superimpose Several Point Patterns
smooth.ppp Spatial smoothing of observations at irregular points
runifdisc Generate N Uniform Random Points in a Disc
eem Exponential Energy Marks
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
npoints Number of Points in a Point Pattern
G3est Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
diameter Diameter of an Object
inside.owin Test Whether Points Are Inside A Window
eroded.areas Areas of Morphological Erosions
ganglia Beta Ganglion Cells in Cat Retina, Old Version
Hest Spherical Contact Distribution Function
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
pcfinhom Inhomogeneous Pair Correlation Function
spatstat-internal Internal spatstat functions
runifpointOnLines Generate N Uniform Random Points On Line Segments
plot.fasp Plot a Function Array
distmap Distance Map
progressreport Print Progress Reports
rMaternI Simulate Matern Model I
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
rGaussPoisson Simulate Gauss-Poisson Process
simdat Simulated Point Pattern
pixellate.psp Convert Line Segment Pattern to Pixel Image
is.empty Test Whether An Object Is Empty Histogram of Pixel Values in an Image
is.multitype Test whether Object is Multitype
Hardcore The Hard Core Point Process Model
identify.ppp Identify Points in a Point Pattern Infinite Order Interaction Family
is.ppm Test Whether An Object Is A Fitted Point Process Model
iplot Point and Click Interface for Displaying a Point Pattern
pixellate.owin Convert Window to Pixel Image
rshift Random Shift Apply Vector Translation To Pixel Image
shapley Galaxies in the Shapley Supercluster
is.convex Test Whether a Window is Convex
methods.box3 Methods for Three-Dimensional Box
logLik.ppm Log Likelihood for Poisson Point Process Model Convert Pixel Image to Another Unit of Length
Saturated Saturated Pairwise Interaction model
shift.psp Apply Vector Translation To Line Segment Pattern
ppp.object Class of Point Patterns Contour plot of pixel image
spatstat.options Internal Options in Spatstat Package
summary.listof Summary of a List of Things
psp Create a Line Segment Pattern
shift.ppp Apply Vector Translation To Point Pattern
is.marked Test Whether Marks Are Present
owin Create a Window
midpoints.psp Midpoints of Line Segment Pattern
japanesepines Japanese Pines Point Pattern
nndist Nearest neighbour distances
model.images Compute Images of Constructed Covariates
with.fv Evaluate an Expression in a Function Table
spatstat-deprecated Deprecated spatstat functions
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
dilation Morphological Dilation Test Whether An Object Is A Pixel Image
plot.hyperframe Plot Entries in a Hyperframe
simulate.ppm Simulate a Fitted Gibbs Point Process Model
unmark Remove Marks
levelset Level Set of a Pixel Image
with.hyperframe Evaluate an Expression in Each Row of a Hyperframe
rNeymanScott Simulate Neyman-Scott Process
multiplicity.ppp Count Multiplicity of Duplicate Points
pcf.fasp Pair Correlation Function obtained from array of K functions
rescale.ppp Convert Point Pattern to Another Unit of Length
print.owin Print Brief Details of a Spatial Window
gridcentres Rectangular grid of points
rMatClust Simulate Matern Cluster Process
pairdist Pairwise distances
rescue.rectangle Convert Window Back To Rectangle
split.ppp Divide Point Pattern into Sub-patterns
plot.fv Plot Function Values
raster.x Cartesian Coordinates for a Pixel Raster
pcf.ppp Pair Correlation Function of Point Pattern Interpolate a Pixel Image
pixelquad Quadrature Scheme Based on Pixel Grid
summary.quad Summarizing a Quadrature Scheme
nndist.ppx Nearest Neighbour Distances in Any Dimensions
rknn Theoretical Distribution of Nearest Neighbour Distance
intersect.tess Intersection of Two Tessellations
summary.psp Summary of a Line Segment Pattern Dataset
is.ppp Test Whether An Object Is A Point Pattern
pcfdot Multitype pair correlation function (i-to-any)
pcfcross Multitype pair correlation function (cross-type)
volume Volume of an Object
quadratresample Resample a Point Pattern by Resampling Quadrats
rshift.ppp Randomly Shift a Point Pattern
kppm Fit cluster point process model
rMosaicSet Mosaic Random Set
pp3 Three Dimensional Point Pattern
print.psp Print Brief Details of a Line Segment Pattern Dataset
ppp Create a Point Pattern
nbfires Point Patterns of New Brunswick Forest Fires
runifpointx Generate N Uniform Random Points in Any Dimensions
rescale Convert dataset to another unit of length
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
markvario Mark Variogram
opening Morphological Opening
ripras Estimate window from points alone Plot a Pixel Image
rpoint Generate N Random Points
summary.splitppp Summary of a Split Point Pattern
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rotate.psp Rotate a Line Segment Pattern
quadscheme Generate a Quadrature Scheme from a Point Pattern
rpoispp3 Generate Poisson Point Pattern in Three Dimensions
rstrat Simulate Stratified Random Point Pattern
square Square Window
rpoislinetess Poisson Line Tessellation
reduced.sample Reduced Sample Estimator using Histogram Data
rpoisline Generate Poisson Random Line Process
vertices Vertices of a Window
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
suffstat Sufficient Statistic of Point Process Model
trim.rectangle Cut margins from rectangle
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Last month downloads


Date 2010-05-02
License GPL (>= 2)
Packaged 2010-05-02 01:41:47 UTC; adrian
Repository CRAN
Date/Publication 2010-05-02 07:04:41

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