spatstat v1.17-0

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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. 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
Gmulti Marked Nearest Neighbour Distance Function
Kcross Multitype K Function (Cross-type)
Kdot Multitype K Function (i-to-any)
Iest Estimate the I-function
Emark Diagnostics for random marking
Extract.splitppp Extract or Replace Sub-Patterns
BadGey Hybrid Geyer Point Process Model
Hest Spherical Contact Distribution Function
Kinhom Inhomogeneous K-function
Lcross Multitype L-function (cross-type)
Kcross.inhom Inhomogeneous Cross K Function
Extract.im Extract Subset of Image
Saturated Saturated Pairwise Interaction model
Extract.tess Extract or Replace Subset of Tessellation
Extract.fv Extract Subset of Function Values
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
Gest Nearest Neighbour Distance Function G
Kmulti Marked K-Function
Lcross.inhom Inhomogeneous Cross Type L Function
Extract.listof Extract or Replace Subset of a List of Things
clickppp Interactively Add Points
Pairwise Generic Pairwise Interaction model
Jdot Multitype J Function (i-to-any)
as.matrix.im Convert Pixel Image to Matrix
Fest Estimate the empty space function F
Kest.fft K-function using FFT
angles.psp Orientation Angles of Line Segments
Kdot.inhom Inhomogeneous Multitype K Dot Function
affine Apply Affine Transformation
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Geyer Geyer's Saturation Point Process Model
Extract.fasp Extract Subset of Function Array
Jcross Multitype J Function (i-to-j)
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Ord Generic Ord Interaction model
complement.owin Take Complement of a Window
as.polygonal Convert a Window to a Polygonal Window
Ldot Multitype L-function (i-to-any)
areaLoss Difference of Disc Areas
Strauss The Strauss Point Process Model
demopat Artificial Data Point Pattern
cells Biological Cells Point Pattern
deltametric Delta Metric
AreaInter The Area Interaction Point Process Model
Kmeasure Reduced Second Moment Measure
closing Morphological Closing
DiggleGratton Diggle-Gratton model
Linhom L-function
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
Jmulti Marked J Function
envelope Simulation envelopes of summary function
as.tess Convert Data To Tessellation
affine.psp Apply Affine Transformation To Line Segment Pattern
betacells Beta Ganglion Cells in Cat Retina
anova.ppm ANOVA for Fitted Point Process Models
eval.fv Evaluate Expression Involving Functions
bramblecanes Hutchings' Bramble Canes data
Softcore The Soft Core Point Process Model
Lest L-function
as.data.frame.ppp Coerce Point Pattern to a Data Frame
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
MultiStrauss The Multitype Strauss Point Process Model
as.mask Pixel Image Approximation of a Window
areaGain Difference of Disc Areas
default.dummy Generate a Default Pattern of Dummy Points
bounding.box.xy Convex Hull of Points
compatible.fasp Test Whether Two Function Arrays Are Compatible
Extract.quad Subset of Quadrature Scheme
by.im Apply Function to Image Broken Down by Factor
anemones Beadlet Anemones Data
amacrine Hughes' Amacrine Cell Data
affine.owin Apply Affine Transformation To Window
bronzefilter Bronze gradient filter data
LennardJones The Lennard-Jones Potential
ants Harkness-Isham ants' nests data
as.rectangle Window Frame
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
colourmap Colour Lookup Tables
fasp.object Function Arrays for Spatial Patterns
expand.owin Expand Window By Factor
affine.ppp Apply Affine Transformation To Point Pattern
as.im Convert to Pixel Image
OrdThresh Ord's Interaction model
as.ppp Convert Data To Class ppp
bdist.points Distance to Boundary of Window
allstats Calculate four standard summary functions of a point pattern.
Extract.psp Extract Subset of Line Segment Pattern
Ldot.inhom Inhomogeneous Multitype L Dot Function
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
StraussHard The Strauss / Hard Core Point Process Model
as.psp Convert Data To Class psp
Kest K-function
Extract.ppp Extract or Replace Subset of Point Pattern
Jest Estimate the J-function
intersect.tess Intersection of Two Tessellations
applynbd Apply Function to Every Neighbourhood in a Point Pattern
hyperframe Hyper Data Frame
dilation Morphological Dilation
Replace.im Reset Values in Subset of Image
distmap.ppp Distance Map of Point Pattern
clickpoly Interactively Define a Polygon
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
copper Berman-Huntington points and lines data
bei Tropical rain forest trees
spatstat-internal Internal spatstat functions
corners Corners of a rectangle
area.owin Area of a Window
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
pppmatching Create a Point Matching
Poisson Poisson Point Process Model
cut.im Convert Pixel Image from Numeric to Factor
lengths.psp Lengths of Line Segments
chorley Chorley-Ribble Cancer Data
discpartarea Area of Part of Disc
contour.im Contour plot of pixel image
append.psp Combine Two Line Segment Patterns
bdist.pixels Distance to Boundary of Window
data.ppm Extract Original Data from a Fitted Point Process Model
endpoints.psp Endpoints of Line Segment Pattern
convexhull Convex Hull
levelset Level Set of a Pixel Image
spatstat-deprecated Deprecated spatstat functions
eval.fasp Evaluate Expression Involving Function Arrays
crossdist.default Pairwise distances between two different sets of points
compatible.fv Test Whether Two Function Objects Are Compatible
diameter Diameter of a Window
as.owin Convert Data To Class owin
ord.family Ord Interaction Process Family
bermantest Berman's Tests for Point Process Model
iplot Point and Click Interface for Displaying a Point Pattern
density.ppp Kernel Smoothed Intensity of Point Pattern
distmap.owin Distance Map of Window
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
gridweights Compute Quadrature Weights Based on Grid Counts
mean.im Mean, Median and Range of Pixel Values in an Image
centroid.owin Centroid of a window
clarkevans Clark and Evans Aggregation Index
is.owin Test Whether An Object Is A Window
ewcdf Weighted Empirical Cumulative Distribution Function
heather Diggle's Heather Data
crossdist Pairwise distances
delaunay Delaunay Triangulation of Point Pattern
psp.object Class of Line Segment Patterns
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
plot.ppm plot a Fitted Point Process Model
gpc2owin Convert Polygonal Region into Different Format
eval.im Evaluate Expression Involving Pixel Images
bounding.box Bounding Box of a Window or Point Pattern
rStrauss Perfect Simulation of the Strauss Process
compatible.im Test Whether Two Pixel Images Are Compatible
distmap.psp Distance Map of Line Segment Pattern
markvario Mark Variogram
logLik.ppm Log Likelihood for Poisson Point Process Model
plot.hyperframe Plot Entries in a Hyperframe
nndist Nearest neighbour distances
nncross Nearest Neighbours Between Two Patterns
eem Exponential Energy Marks
chop.tess Subdivide a Window or Tessellation using a Set of Lines
discretise Safely Convert Point Pattern Window to Binary Mask
quadratcount Quadrat counting for a point pattern
is.empty Test Whether An Object Is Empty
finpines Pine saplings in Finland.
pcf.fasp Pair Correlation Function obtained from array of K functions
crossing.psp Crossing Points of Two Line Segment Patterns
inside.owin Test Whether Points Are Inside A Window
pcf.ppp Pair Correlation Function of Point Pattern
concatxy Concatenate x,y Coordinate Vectors
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
plot.colourmap Plot a Colour Map
clip.infline Intersect Infinite Straight Lines with a Window
nndist.psp Nearest neighbour distances between line segments
rthin Random Thinning
persp.im Perspective Plot of Pixel Image
plot.im Plot a Pixel Image
rSSI Simulate Simple Sequential Inhibition
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
infline Infinite Straight Lines
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
connected Connected components of an image or window
dirichlet Dirichlet Tessellation of Point Pattern
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
density.psp Kernel Smoothing of Line Segment Pattern
plot.fasp Plot a Function Array
harmonic Basis for Harmonic Functions
erosion Morphological Erosion
kppm Fit cluster point process model
lurking Lurking variable plot
letterR Window in Shape of Letter R
rpoislinetess Poisson Line Tessellation
print.ppm Print a Fitted Point Process Model
kaplan.meier Kaplan-Meier Estimator using Histogram Data
fryplot Fry Plot of Point Pattern
profilepl Profile Maximum Pseudolikelihood
pcf Pair Correlation Function
pairdist Pairwise distances
hamster Aherne's hamster tumour data
is.convex Test Whether a Window is Convex
is.marked Test Whether Marks Are Present
japanesepines Japanese Pines Point Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
is.ppm Test Whether An Object Is A Fitted Point Process Model
rmpoispp Generate Multitype Poisson Point Pattern
is.multitype.ppp Test Whether A Point Pattern is Multitype
pairdist.default Pairwise distances
humberside Humberside Data on Childhood Leukaemia and Lymphoma
is.marked.ppp Test Whether A Point Pattern is Marked
midpoints.psp Midpoints of Line Segment Pattern
plot.owin Plot a Spatial Window
hist.im Histogram of Pixel Values in an Image
ppm Fit Point Process Model to Data
distmap Distance Map
coef.ppm Coefficients of Fitted Point Process Model
im Create a Pixel Image Object
is.im Test Whether An Object Is A Pixel Image
is.marked.ppm Test Whether A Point Process Model is Marked
spatstat.options Internal Options in Spatstat Package
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
pcf.fv Pair Correlation Function obtained from K Function
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
intersect.owin Intersection or Union of Two Windows
distfun Distance Map as a Function
model.images Compute Images of Constructed Covariates
rsyst Simulate systematic random point pattern
tess Create a Tessellation
gridcentres Rectangular grid of points
blur Apply Gaussian Blur to a Pixel Image
fv.object Data Frames of Function Values
identify.ppp Identify Points in a Point Pattern
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
ponderosa Ponderosa Pine Tree Point Pattern
inforder.family Infinite Order Interaction Family
fitted.ppm Fitted Conditional Intensity for Point Process Model
convexhull.xy Convex Hull of Points
plot.kppm Plot a fitted cluster point process
ppp Create a Point Pattern
summary.quad Summarizing a Quadrature Scheme
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
murchison Murchison gold deposits
reach Interaction Distance of a Point Process
shapley Galaxies in the Shapley Supercluster
nbfires Point Patterns of New Brunswick Forest Fires
nztrees New Zealand Trees Point Pattern
is.subset.owin Determine Whether One Window is Contained In Another
rpoisline Generate Poisson Random Line Process
interp.im Interpolate a Pixel Image
plot.quad plot a Spatial Quadrature Scheme
cut.ppp Classify Points in a Point Pattern
rMosaicSet Mosaic Random Set
disc Circular Window
crossdist.ppp Pairwise distances between two different point patterns
model.matrix.ppm Extract Design Matrix from Point Process Model
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
is.multitype Test whether Object is Multitype
runifdisc Generate N Uniform Random Points in a Disc
pairsat.family Saturated Pairwise Interaction Point Process Family
ppp.object Class of Point Patterns
pointsOnLines Place Points Evenly Along Specified Lines
fitin.ppm Extract the Interaction from a Fitted Point Process Model
markcorr Mark Correlation Function
rGaussPoisson Simulate Gauss-Poisson Process
rThomas Simulate Thomas Process
quadrats Divide Region into Quadrats
dilated.areas Areas of Morphological Dilations
quadscheme Generate a Quadrature Scheme from a Point Pattern
rshift.ppp Randomly Shift a Point Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
mincontrast Method of Minimum Contrast
predict.ppm Prediction from a Fitted Point Process Model
runifpointOnLines Generate N Uniform Random Points On Line Segments
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
rcell Simulate Baddeley-Silverman Cell Process
crossdist.psp Pairwise distances between two different line segment patterns
pairdist.ppp Pairwise distances
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
im.object Class of Images
rMaternII Simulate Matern Model II
localK Neighbourhood density function
summary.owin Summary of a Spatial Window
rNeymanScott Simulate Neyman-Scott Process
pppmatching.object Class of Point Matchings
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
progressreport Print Progress Reports
incircle Find Largest Circle Inside Window
ppm.object Class of Fitted Point Process Models
miplot Morishita Index Plot
raster.x Cartesian Coordinates for a Pixel Raster
ganglia Beta Ganglion Cells in Cat Retina, Old Version
lansing Lansing Woods Point Pattern
print.owin Print Brief Details of a Spatial Window
owin.object Class owin
print.psp Print Brief Details of a Line Segment Pattern Dataset
owin Create a Window
plot.tess Plot a tessellation
redwood California Redwoods Point Pattern (Ripley's Subset)
eroded.areas Areas of Morphological Erosions
project2segment Move Point To Nearest Line
plot.listof Plot a List of Things
spokes Spokes pattern of dummy points
nearestsegment Find Line Segment Nearest to Each Point
superimposePSP Superimpose Several Line Segment Patterns
unique.ppp Extract Unique Points from a Spatial Point Pattern
simulate.kppm Simulate a Fitted Cluster Point Process Model
rotate.ppp Rotate a Point Pattern
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
is.ppp Test Whether An Object Is A Point Pattern
matchingdist Distance for a Point Pattern Matching
pppdist Distance Between Two Point Patterns
plot.psp plot a Spatial Line Segment Pattern
print.ppp Print Brief Details of a Point Pattern Dataset
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
shift.psp Apply Vector Translation To Line Segment Pattern
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
print.im Print Brief Details of an Image
opening Morphological Opening
summary.psp Summary of a Line Segment Pattern Dataset
rescale.owin Convert Window to Another Unit of Length
istat Point and Click Interface for Exploratory Analysis of Point Pattern
pixellate.owin Convert Window to Pixel Image
plot.ppp plot a Spatial Point Pattern
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
multiplicity.ppp Count Multiplicity of Duplicate Points
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
rmpoint Generate N Random Multitype Points
pairwise.family Pairwise Interaction Process Family
perimeter Perimeter Length of Window
longleaf Longleaf Pines Point Pattern
plot.bermantest Plot Result of Berman Test
print.quad Print a Quadrature Scheme
reduced.sample Reduced Sample Estimator using Histogram Data
markcorrint Mark Correlation Integral
lut Lookup Tables
shift.ppp Apply Vector Translation To Point Pattern
union.quad Union of Data and Dummy Points
residuals.ppm Residuals for Fitted Point Process Model
rescale.im Convert Pixel Image to Another Unit of Length
pcfcross Multitype pair correlation function
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
pixelquad Quadrature Scheme Based on Pixel Grid
simulate.ppm Simulate a Fitted Gibbs Point Process Model
ripras Estimate window from points alone
rstrat Simulate Stratified Random Point Pattern
rotate.owin Rotate a Window
psp Create a Line Segment Pattern
rMosaicField Mosaic Random Field
nnwhich Nearest neighbour
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
rlinegrid Generate grid of parallel lines with random displacement
residualspaper Data and Code From JRSS Discussion Paper on Residuals
rescue.rectangle Convert Window Back To Rectangle
rpoint Generate N Random Points
plot.splitppp Plot a List of Point Patterns
rMatClust Simulate Matern Cluster Process
rpoispp Generate Poisson Point Pattern
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
rjitter Random Perturbation of a Point Pattern
setmarks Set or Reset the Marks in a Point Pattern
stieltjes Compute Integral of Function Against Cumulative Distribution
square Square Window
unitname Name for Unit of Length
rotate Rotate
spruces Spruces Point Pattern
simplify.owin Approximate a Polygon by a Simpler Polygon
thomas.estK Fit the Thomas Point Process by Minimum Contrast
quantile.im Sample Quantiles of Pixel Image
rshift Random Shift
markconnect Mark Connection Function
scanpp Read Point Pattern From Data File
rmh.ppm Simulate from a Fitted Point Process Model
rescale.ppp Convert Point Pattern to Another Unit of Length
summary.ppm Summarizing a Fitted Point Process Model
rshift.psp Randomly Shift a Line Segment Pattern
pixellate.ppp Convert Point Pattern to Pixel Image
summary.splitppp Summary of a Split Point Pattern
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
rlabel Random Re-Labelling of Point Pattern
split.ppp Divide Point Pattern into Sub-patterns
pixellate Convert Spatial Object to Pixel Image
quadratresample Resample a Point Pattern by Resampling Quadrats
runifpoint Generate N Uniform Random Points
shift.owin Apply Vector Translation To Window
shift Apply Vector Translation
tiles Extract List of Tiles in a Tessellation
swedishpines Swedish Pines Point Pattern
with.fv Evaluate an Expression in a Function Table
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
plot.plotppm Plot a plotppm Object Created by plot.ppm
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
pairdist.psp Pairwise distances between line segments
predict.kppm Prediction from a Fitted Cluster Point Process Model
redwoodfull California Redwoods Point Pattern (Entire Dataset)
rshift.splitppp Randomly Shift a List of Point Patterns
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
split.im Divide Image Into Sub-images
rotate.psp Rotate a Line Segment Pattern
summary.ppp Summary of a Point Pattern Dataset
rescale.psp Convert Line Segment Pattern to Another Unit of Length
trim.rectangle Cut margins from rectangle
spatstat-package The Spatstat Package
shift.im Apply Vector Translation To Pixel Image
unmark Remove Marks
simdat Simulated Point Pattern
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
setcov Set Covariance of a Window
summary.im Summarizing a Pixel Image
superimpose Superimpose Several Point Patterns
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
summary.listof Summary of a List of Things
suffstat Sufficient Statistic of Point Process Model
update.ppm Update a Fitted Point Process Model
update.kppm Update a Fitted Cluster Point Process Model
urkiola Urkiola Woods Point Pattern
plot.fv Plot Function Values
quad.object Class of Quadrature Schemes
rMaternI Simulate Matern Model I
rescale Convert dataset to another unit of length
smooth.ppp Spatial smoothing of observations at irregular points
vertices Vertices of a Window
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Date 22 october 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2009-10-22 20:51:58 UTC; adrian
Repository CRAN
Date/Publication 2009-10-22 18:37:53

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