spatstat v1.17-1

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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. 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, and pixel images. 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
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
DiggleGratton Diggle-Gratton model
Lcross.inhom Inhomogeneous Cross Type L Function
closing Morphological Closing
Extract.im Extract Subset of Image
Geyer Geyer's Saturation Point Process Model
Kinhom Inhomogeneous K-function
density.psp Kernel Smoothing of Line Segment Pattern
append.psp Combine Two Line Segment Patterns
Linhom L-function
bermantest Berman's Tests for Point Process Model
Kest K-function
connected Connected components of an image or window
applynbd Apply Function to Every Neighbourhood in a Point Pattern
Hest Spherical Contact Distribution Function
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
as.rectangle Window Frame
Extract.quad Subset of Quadrature Scheme
as.box3 Convert Data to Three-Dimensional Box
Extract.tess Extract or Replace Subset of Tessellation
gridweights Compute Quadrature Weights Based on Grid Counts
hyperframe Hyper Data Frame
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
Gest Nearest Neighbour Distance Function G
bronzefilter Bronze gradient filter data
coords Extract Coordinates of a Spatial or Spatiotemporal Point Pattern
F3est Empty Space Function of a Three-Dimensional Point Pattern
BadGey Hybrid Geyer Point Process Model
allstats Calculate four standard summary functions of a point pattern.
deltametric Delta Metric
Kmeasure Reduced Second Moment Measure
Emark Diagnostics for random marking
pppmatching.object Class of Point Matchings
Jest Estimate the J-function
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
cells Biological Cells Point Pattern
Poisson Poisson Point Process Model
chorley Chorley-Ribble Cancer Data
expand.owin Expand Window By Factor
diameter.box3 Geometrical Calculations for Three-Dimensional Box
clickpoly Interactively Define a Polygon
default.dummy Generate a Default Pattern of Dummy Points
Replace.im Reset Values in Subset of Image
areaLoss Difference of Disc Areas
fasp.object Function Arrays for Spatial Patterns
heather Diggle's Heather Data
pairsat.family Saturated Pairwise Interaction Point Process Family
nztrees New Zealand Trees Point Pattern
nndist.psp Nearest neighbour distances between line segments
Extract.fv Extract Subset of Function Values
dilation Morphological Dilation
Jcross Multitype J Function (i-to-j)
Pairwise Generic Pairwise Interaction model
hist.im Histogram of Pixel Values in an Image
predict.kppm Prediction from a Fitted Cluster Point Process Model
spatstat-internal Internal spatstat functions
pcf.fv Pair Correlation Function obtained from K Function
Saturated Saturated Pairwise Interaction model
rstrat Simulate Stratified Random Point Pattern
Ldot.inhom Inhomogeneous Multitype L Dot Function
compatible.fv Test Whether Two Function Objects Are Compatible
rotate Rotate
complement.owin Take Complement of a Window
affine Apply Affine Transformation
runifdisc Generate N Uniform Random Points in a Disc
as.polygonal Convert a Window to a Polygonal Window
clip.infline Intersect Infinite Straight Lines with a Window
diameter Diameter of a Window
area.owin Area of a Window
data.ppm Extract Original Data from a Fitted Point Process Model
bounding.box.xy Convex Hull of Points
rthin Random Thinning
bei Tropical rain forest trees
Strauss The Strauss Point Process Model
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
is.marked.ppp Test Whether A Point Pattern is Marked
box3 Three-Dimensional Box
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
pcf Pair Correlation Function
Fest Estimate the empty space function F
Kdot.inhom Inhomogeneous Multitype K Dot Function
StraussHard The Strauss / Hard Core Point Process Model
humberside Humberside Data on Childhood Leukaemia and Lymphoma
is.im Test Whether An Object Is A Pixel Image
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
spatstat.options Internal Options in Spatstat Package
as.matrix.im Convert Pixel Image to Matrix
distmap.psp Distance Map of Line Segment Pattern
by.im Apply Function to Image Broken Down by Factor
Ldot Multitype L-function (i-to-any)
residualspaper Data and Code From JRSS Discussion Paper on Residuals
crossdist.default Pairwise distances between two different sets of points
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
OrdThresh Ord's Interaction model
Kest.fft K-function using FFT
Kcross.inhom Inhomogeneous Cross K Function
spatstat-deprecated Deprecated spatstat functions
pixellate.owin Convert Window to Pixel Image
ppx Multidimensional Space-Time Point Pattern
crossing.psp Crossing Points of Two Line Segment Patterns
rlabel Random Re-Labelling of Point Pattern
distmap Distance Map
Jmulti Marked J Function
setmarks Set or Reset the Marks in a Point Pattern
nearestsegment Find Line Segment Nearest to Each Point
contour.im Contour plot of pixel image
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
density.ppp Kernel Smoothed Intensity of Point Pattern
as.ppp Convert Data To Class ppp
summary.listof Summary of a List of Things
inforder.family Infinite Order Interaction Family
lansing Lansing Woods Point Pattern
as.mask Pixel Image Approximation of a Window
anemones Beadlet Anemones Data
rmh.ppm Simulate from a Fitted Point Process Model
delaunay Delaunay Triangulation of Point Pattern
finpines Pine saplings in Finland.
intersect.owin Intersection, Union or Set Subtraction of Two Windows
is.ppp Test Whether An Object Is A Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
as.hyperframe.ppx Extract coordinates and marks of multidimensional point pattern
Extract.listof Extract or Replace Subset of a List of Things
Ord Generic Ord Interaction model
endpoints.psp Endpoints of Line Segment Pattern
Extract.ppp Extract or Replace Subset of Point Pattern
crossdist Pairwise distances
dirichlet Dirichlet Tessellation of Point Pattern
superimposePSP Superimpose Several Line Segment Patterns
angles.psp Orientation Angles of Line Segments
betacells Beta Ganglion Cells in Cat Retina
pp3 Three Dimensional Point Pattern
gridcentres Rectangular grid of points
redwoodfull California Redwoods Point Pattern (Entire Dataset)
is.marked Test Whether Marks Are Present
shift Apply Vector Translation
reach Interaction Distance of a Point Process
as.im Convert to Pixel Image
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
pairwise.family Pairwise Interaction Process Family
as.owin Convert Data To Class owin
cut.im Convert Pixel Image from Numeric to Factor
as.tess Convert Data To Tessellation
disc Circular Window
miplot Morishita Index Plot
Softcore The Soft Core Point Process Model
concatxy Concatenate x,y Coordinate Vectors
kaplan.meier Kaplan-Meier Estimator using Histogram Data
as.data.frame.ppp Coerce Point Pattern to a Data Frame
distmap.ppp Distance Map of Point Pattern
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
Extract.psp Extract Subset of Line Segment Pattern
eroded.areas Areas of Morphological Erosions
print.ppp Print Brief Details of a Point Pattern Dataset
interp.im Interpolate a Pixel Image
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
Extract.splitppp Extract or Replace Sub-Patterns
nndist Nearest neighbour distances
convexhull.xy Convex Hull of Points
cut.ppp Classify Points in a Point Pattern
K3est K-function of a Three-Dimensional Point Pattern
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
progressreport Print Progress Reports
eval.fv Evaluate Expression Involving Functions
copper Berman-Huntington points and lines data
fitin.ppm Extract the Interaction from a Fitted Point Process Model
affine.psp Apply Affine Transformation To Line Segment Pattern
anova.ppm ANOVA for Fitted Point Process Models
vertices Vertices of a Window
rGaussPoisson Simulate Gauss-Poisson Process
rescue.rectangle Convert Window Back To Rectangle
rmpoint Generate N Random Multitype Points
as.hyperframe Convert Data to Hyperframe
colourmap Colour Lookup Tables
multiplicity.ppp Count Multiplicity of Duplicate Points
model.matrix.ppm Extract Design Matrix from Point Process Model
Kmulti Marked K-Function
square Square Window
shift.owin Apply Vector Translation To Window
chop.tess Subdivide a Window or Tessellation using a Set of Lines
fitted.ppm Fitted Conditional Intensity for Point Process Model
Kcross Multitype K Function (Cross-type)
border Border Region of a Window
midpoints.psp Midpoints of Line Segment Pattern
opening Morphological Opening
bramblecanes Hutchings' Bramble Canes data
quadratcount Quadrat counting for a point pattern
rMatClust Simulate Matern Cluster Process
plot.owin Plot a Spatial Window
murchison Murchison gold deposits
pcfcross Multitype pair correlation function
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
centroid.owin Centroid of a window
harmonic Basis for Harmonic Functions
quadratresample Resample a Point Pattern by Resampling Quadrats
rshift Random Shift
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
compatible.im Test Whether Two Pixel Images Are Compatible
kppm Fit cluster point process model
pcf.ppp Pair Correlation Function of Point Pattern
discpartarea Area of Part of Disc
intersect.tess Intersection of Two Tessellations
psp Create a Line Segment Pattern
methods.box3 Methods for Three-Dimensional Box
spatstat-package The Spatstat Package
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
is.multitype.ppp Test Whether A Point Pattern is Multitype
plot.fv Plot Function Values
summary.splitppp Summary of a Split Point Pattern
Lest L-function
hamster Aherne's hamster tumour data
with.hyperframe Evaluate an Expression in Each Row of a Hyperframe
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
tiles Extract List of Tiles in a Tessellation
lurking Lurking variable plot
lengths.psp Lengths of Line Segments
bdist.points Distance to Boundary of Window
eval.im Evaluate Expression Involving Pixel Images
Iest Estimate the I-function
nnwhich Nearest neighbour
crossdist.ppp Pairwise distances between two different point patterns
plot.quad plot a Spatial Quadrature Scheme
markcorrint Mark Correlation Integral
iplot Point and Click Interface for Displaying a Point Pattern
rescale.ppp Convert Point Pattern to Another Unit of Length
pairdist.default Pairwise distances
LennardJones The Lennard-Jones Potential
discretise Safely Convert Point Pattern Window to Binary Mask
print.im Print Brief Details of an Image
AreaInter The Area Interaction Point Process Model
plot.ppm plot a Fitted Point Process Model
gpc2owin Convert Polygonal Region into Different Format
distfun Distance Map as a Function
Lcross Multitype L-function (cross-type)
union.quad Union of Data and Dummy Points
markcorr Mark Correlation Function
as.psp Convert Data To Class psp
pppmatching Create a Point Matching
rpoint Generate N Random Points
coef.ppm Coefficients of Fitted Point Process Model
clarkevans Clark and Evans Aggregation Index
matchingdist Distance for a Point Pattern Matching
MultiStrauss The Multitype Strauss Point Process Model
model.images Compute Images of Constructed Covariates
rmpoispp Generate Multitype Poisson Point Pattern
is.convex Test Whether a Window is Convex
pppdist Distance Between Two Point Patterns
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
is.multitype Test whether Object is Multitype
is.subset.owin Determine Whether One Window is Contained In Another
rThomas Simulate Thomas Process
pixellate.ppp Convert Point Pattern to Pixel Image
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
print.psp Print Brief Details of a Line Segment Pattern Dataset
ewcdf Weighted Empirical Cumulative Distribution Function
profilepl Profile Maximum Pseudolikelihood
split.im Divide Image Into Sub-images
ppm Fit Point Process Model to Data
bounding.box Bounding Box of a Window or Point Pattern
redwood California Redwoods Point Pattern (Ripley's Subset)
amacrine Hughes' Amacrine Cell Data
owin.object Class owin
identify.ppp Identify Points in a Point Pattern
rMosaicSet Mosaic Random Set
raster.x Cartesian Coordinates for a Pixel Raster
simulate.ppm Simulate a Fitted Gibbs Point Process Model
is.empty Test Whether An Object Is Empty
infline Infinite Straight Lines
plot.splitppp Plot a List of Point Patterns
print.owin Print Brief Details of a Spatial Window
nearest.raster.point Find Pixel Nearest to a Given Point
G3est Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
runifpointOnLines Generate N Uniform Random Points On Line Segments
Jdot Multitype J Function (i-to-any)
plot.colourmap Plot a Colour Map
rMaternII Simulate Matern Model II
summary.quad Summarizing a Quadrature Scheme
pairdist.psp Pairwise distances between line segments
rsyst Simulate systematic random point pattern
print.quad Print a Quadrature Scheme
plot.psp plot a Spatial Line Segment Pattern
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
inside.owin Test Whether Points Are Inside A Window
runifpoint Generate N Uniform Random Points
plot.im Plot a Pixel Image
corners Corners of a rectangle
eem Exponential Energy Marks
plot.bermantest Plot Result of Berman Test
print.ppm Print a Fitted Point Process Model
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
rotate.psp Rotate a Line Segment Pattern
project2segment Move Point To Nearest Line
rshift.splitppp Randomly Shift a List of Point Patterns
Extract.fasp Extract Subset of Function Array
dilated.areas Areas of Morphological Dilations
rescale.im Convert Pixel Image to Another Unit of Length
superimpose Superimpose Several Point Patterns
distmap.owin Distance Map of Window
summary.ppm Summarizing a Fitted Point Process Model
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
setcov Set Covariance of a Window
pixellate Convert Spatial Object to Pixel Image
rescale.owin Convert Window to Another Unit of Length
quad.object Class of Quadrature Schemes
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
trim.rectangle Cut margins from rectangle
affine.owin Apply Affine Transformation To Window
rshift.ppp Randomly Shift a Point Pattern
urkiola Urkiola Woods Point Pattern
update.kppm Update a Fitted Cluster Point Process Model
rshift.psp Randomly Shift a Line Segment Pattern
simdat Simulated Point Pattern
levelset Level Set of a Pixel Image
plot.fasp Plot a Function Array
nbfires Point Patterns of New Brunswick Forest Fires
rpoislinetess Poisson Line Tessellation
plot.tess Plot a tessellation
crossdist.psp Pairwise distances between two different line segment patterns
rjitter Random Perturbation of a Point Pattern
ord.family Ord Interaction Process Family
rescale Convert dataset to another unit of length
fryplot Fry Plot of Point Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
unitname Name for Unit of Length
japanesepines Japanese Pines Point Pattern
im.object Class of Images
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
rotate.ppp Rotate a Point Pattern
markvario Mark Variogram
pcf.fasp Pair Correlation Function obtained from array of K functions
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
compatible.fasp Test Whether Two Function Arrays Are Compatible
shapley Galaxies in the Shapley Supercluster
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
rpoisline Generate Poisson Random Line Process
plot.pp3 Plot a three-dimensional point pattern
methods.ppx Methods for Multidimensional Space-Time Point Patterns
tess Create a Tessellation
shift.im Apply Vector Translation To Pixel Image
update.ppm Update a Fitted Point Process Model
with.fv Evaluate an Expression in a Function Table
scanpp Read Point Pattern From Data File
plot.ppp plot a Spatial Point Pattern
rcell Simulate Baddeley-Silverman Cell Process
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
unique.ppp Extract Unique Points from a Spatial Point Pattern
quadscheme Generate a Quadrature Scheme from a Point Pattern
logLik.ppm Log Likelihood for Poisson Point Process Model
markconnect Mark Connection Function
is.ppm Test Whether An Object Is A Fitted Point Process Model
summary.im Summarizing a Pixel Image
reduced.sample Reduced Sample Estimator using Histogram Data
Gmulti Marked Nearest Neighbour Distance Function
simulate.kppm Simulate a Fitted Cluster Point Process Model
rlinegrid Generate grid of parallel lines with random displacement
rMosaicField Mosaic Random Field
residuals.ppm Residuals for Fitted Point Process Model
rpoispp Generate Poisson Point Pattern
owin Create a Window
stieltjes Compute Integral of Function Against Cumulative Distribution
letterR Window in Shape of Letter R
predict.ppm Prediction from a Fitted Point Process Model
is.owin Test Whether An Object Is A Window
pixelquad Quadrature Scheme Based on Pixel Grid
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rStrauss Perfect Simulation of the Strauss Process
ppp Create a Point Pattern
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
rescale.psp Convert Line Segment Pattern to Another Unit of Length
psp.object Class of Line Segment Patterns
shift.ppp Apply Vector Translation To Point Pattern
localK Neighbourhood density function
incircle Find Largest Circle Inside Window
suffstat Sufficient Statistic of Point Process Model
spruces Spruces Point Pattern
nncross Nearest Neighbours Between Two Patterns
fv.object Data Frames of Function Values
summary.owin Summary of a Spatial Window
ppm.object Class of Fitted Point Process Models
shift.psp Apply Vector Translation To Line Segment Pattern
bdist.tiles Distance to Boundary of Window
split.ppp Divide Point Pattern into Sub-patterns
methods.pp3 Methods for three-dimensional point patterns
summary.psp Summary of a Line Segment Pattern Dataset
thomas.estK Fit the Thomas Point Process by Minimum Contrast
persp.im Perspective Plot of Pixel Image
im Create a Pixel Image Object
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
plot.listof Plot a List of Things
summary.ppp Summary of a Point Pattern Dataset
pointsOnLines Place Points Evenly Along Specified Lines
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
plot.hyperframe Plot Entries in a Hyperframe
rSSI Simulate Simple Sequential Inhibition
swedishpines Swedish Pines Point Pattern
longleaf Longleaf Pines Point Pattern
ppp.object Class of Point Patterns
ganglia Beta Ganglion Cells in Cat Retina, Old Version
plot.kppm Plot a fitted cluster point process
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
pairdist Pairwise distances
mincontrast Method of Minimum Contrast
Kdot Multitype K Function (i-to-any)
perimeter Perimeter Length of Window
is.marked.ppm Test Whether A Point Process Model is Marked
convexhull Convex Hull
areaGain Difference of Disc Areas
erosion Morphological Erosion
mean.im Mean, Median and Range of Pixel Values in an Image
envelope Simulation envelopes of summary function
affine.ppp Apply Affine Transformation To Point Pattern
bdist.pixels Distance to Boundary of Window
ants Harkness-Isham ants' nests data
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
clickppp Interactively Add Points
lut Lookup Tables
demopat Artificial Data Point Pattern
istat Point and Click Interface for Exploratory Analysis of Point Pattern
blur Apply Gaussian Blur to a Pixel Image
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
ponderosa Ponderosa Pine Tree Point Pattern
ripras Estimate window from points alone
smooth.ppp Spatial smoothing of observations at irregular points
simplify.owin Approximate a Polygon by a Simpler Polygon
quadrats Divide Region into Quadrats
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
quantile.im Sample Quantiles of Pixel Image
unmark Remove Marks
eval.fasp Evaluate Expression Involving Function Arrays
pairdist.ppp Pairwise distances
rNeymanScott Simulate Neyman-Scott Process
rotate.owin Rotate a Window
rMaternI Simulate Matern Model I
spokes Spokes pattern of dummy points
plot.plotppm Plot a plotppm Object Created by plot.ppm
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Date 04 november 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2009-11-06 03:02:06 UTC; adrian
Repository CRAN
Date/Publication 2009-11-06 10:18:11

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