spatstat v1.19-0


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by Adrian Baddeley

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

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


Date 2010-05-14
License GPL (>= 2)
Packaged 2010-05-14 09:23:40 UTC; adrian
Repository CRAN
Date/Publication 2010-05-16 16:21:34

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