spatstat v1.17-5

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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. 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
Strauss The Strauss Point Process Model
cells Biological Cells Point Pattern
areaGain Difference of Disc Areas
Extract.listof Extract or Replace Subset of a List of Things
DiggleGratton Diggle-Gratton model
Ord Generic Ord Interaction model
K3est K-function of a Three-Dimensional Point Pattern
Emark Diagnostics for random marking
distmap.psp Distance Map of Line Segment Pattern
bdist.pixels Distance to Boundary of Window
append.psp Combine Two Line Segment Patterns
fryplot Fry Plot of Point Pattern
diameter Diameter of a Window
Jmulti Marked J Function
distmap.owin Distance Map of Window
applynbd Apply Function to Every Neighbourhood in a Point Pattern
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
delaunay Delaunay Triangulation of Point Pattern
as.im Convert to Pixel Image
affine.ppp Apply Affine Transformation To Point Pattern
Kest.fft K-function using FFT
is.ppp Test Whether An Object Is A Point Pattern
Lest L-function
anova.ppm ANOVA for Fitted Point Process Models
Fest Estimate the empty space function F
as.mask Pixel Image Approximation of a Window
is.marked Test Whether Marks Are Present
Saturated Saturated Pairwise Interaction model
Gmulti Marked Nearest Neighbour Distance Function
Extract.quad Subset of Quadrature Scheme
Lcross.inhom Inhomogeneous Cross Type L Function
data.ppm Extract Original Data from a Fitted Point Process Model
Geyer Geyer's Saturation Point Process Model
hamster Aherne's hamster tumour data
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
affine.psp Apply Affine Transformation To Line Segment Pattern
Pairwise Generic Pairwise Interaction model
Extract.im Extract Subset of Image
clickpoly Interactively Define a Polygon
Kdot.inhom Inhomogeneous Multitype K Dot Function
as.matrix.im Convert Pixel Image to Matrix
pcfcross Multitype pair correlation function (cross-type)
as.box3 Convert Data to Three-Dimensional Box
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
allstats Calculate four standard summary functions of a point pattern.
Poisson Poisson Point Process Model
Kcross Multitype K Function (Cross-type)
compatible.fasp Test Whether Two Function Arrays Are Compatible
disc Circular Window
interp.im Interpolate a Pixel Image
clickppp Interactively Add Points
by.im Apply Function to Image Broken Down by Factor
Ldot.inhom Inhomogeneous Multitype L Dot Function
dilation Morphological Dilation
MultiStrauss The Multitype Strauss Point Process Model
distmap Distance Map
pairdist Pairwise distances
lurking Lurking variable plot
G3est Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
as.hyperframe Convert Data to Hyperframe
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Extract.fasp Extract Subset of Function Array
plot.tess Plot a tessellation
discretise Safely Convert Point Pattern Window to Binary Mask
Extract.tess Extract or Replace Subset of Tessellation
as.polygonal Convert a Window to a Polygonal Window
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
eroded.areas Areas of Morphological Erosions
amacrine Hughes' Amacrine Cell Data
as.psp Convert Data To Class psp
F3est Empty Space Function of a Three-Dimensional Point Pattern
cut.im Convert Pixel Image from Numeric to Factor
concatxy Concatenate x,y Coordinate Vectors
demopat Artificial Data Point Pattern
Jcross Multitype J Function (i-to-j)
is.empty Test Whether An Object Is Empty
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
area.owin Area of a Window
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
as.tess Convert Data To Tessellation
is.convex Test Whether a Window is Convex
angles.psp Orientation Angles of Line Segments
ants Harkness-Isham ants' nests data
affine.owin Apply Affine Transformation To Window
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
compatible.im Test Whether Two Pixel Images Are Compatible
midpoints.psp Midpoints of Line Segment Pattern
BadGey Hybrid Geyer Point Process Model
connected Connected components of an image or window
Replace.im Reset Values in Subset of Image
eval.im Evaluate Expression Involving Pixel Images
ganglia Beta Ganglion Cells in Cat Retina, Old Version
Iest Estimate the I-function
bermantest Berman's Tests for Point Process Model
methods.box3 Methods for Three-Dimensional Box
coef.ppm Coefficients of Fitted Point Process Model
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
fitted.ppm Fitted Conditional Intensity for Point Process Model
ppm Fit Point Process Model to Data
discpartarea Area of Part of Disc
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
levelset Level Set of a Pixel Image
OrdThresh Ord's Interaction model
bounding.box Bounding Box of a Window or Point Pattern
colourmap Colour Lookup Tables
Kmulti Marked K-Function
default.dummy Generate a Default Pattern of Dummy Points
as.owin Convert Data To Class owin
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
Extract.fv Extract Subset of Function Values
im Create a Pixel Image Object
crossdist.pp3 Pairwise distances between two different three-dimensional point patterns
AreaInter The Area Interaction Point Process Model
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
bdist.points Distance to Boundary of Window
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
Kmeasure Reduced Second Moment Measure
crossdist.ppp Pairwise distances between two different point patterns
Jest Estimate the J-function
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
envelope Simulation envelopes of summary function
endpoints.psp Endpoints of Line Segment Pattern
nndist Nearest neighbour distances
crossing.psp Crossing Points of Two Line Segment Patterns
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
Gest Nearest Neighbour Distance Function G
crossdist Pairwise distances
pcf.ppp Pair Correlation Function of Point Pattern
Kest K-function
areaLoss Difference of Disc Areas
gridcentres Rectangular grid of points
eem Exponential Energy Marks
plot.ppp plot a Spatial Point Pattern
Kdot Multitype K Function (i-to-any)
Linhom L-function
clip.infline Intersect Infinite Straight Lines with a Window
Lcross Multitype L-function (cross-type)
density.psp Kernel Smoothing of Line Segment Pattern
density.ppp Kernel Smoothed Intensity of Point Pattern
chop.tess Subdivide a Window or Tessellation using a Set of Lines
bronzefilter Bronze gradient filter data
is.multitype Test whether Object is Multitype
Jdot Multitype J Function (i-to-any)
rGaussPoisson Simulate Gauss-Poisson Process
is.marked.ppm Test Whether A Point Process Model is Marked
gridweights Compute Quadrature Weights Based on Grid Counts
distfun Distance Map as a Function
spatstat-deprecated Deprecated spatstat functions
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
rMosaicSet Mosaic Random Set
letterR Window in Shape of Letter R
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
mincontrast Method of Minimum Contrast
as.ppp Convert Data To Class ppp
is.im Test Whether An Object Is A Pixel Image
nearest.raster.point Find Pixel Nearest to a Given Point
localK Neighbourhood density function
intersect.tess Intersection of Two Tessellations
istat Point and Click Interface for Exploratory Analysis of Point Pattern
kppm Fit cluster point process model
is.owin Test Whether An Object Is A Window
fv.object Data Frames of Function Values
hyperframe Hyper Data Frame
pppmatching Create a Point Matching
rlinegrid Generate grid of parallel lines with random displacement
convexhull Convex Hull
LennardJones The Lennard-Jones Potential
lengths.psp Lengths of Line Segments
Ldot Multitype L-function (i-to-any)
pcf.fv Pair Correlation Function obtained from K Function
nearestsegment Find Line Segment Nearest to Each Point
box3 Three-Dimensional Box
plot.hyperframe Plot Entries in a Hyperframe
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
longleaf Longleaf Pines Point Pattern
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
Kcross.inhom Inhomogeneous Cross K Function
blur Apply Gaussian Blur to a Pixel Image
markconnect Mark Connection Function
centroid.owin Centroid of a window
expand.owin Expand Window By Factor
gpc2owin Convert Polygonal Region into Different Format
compatible.fv Test Whether Two Function Objects Are Compatible
bdist.tiles Distance to Boundary of Window
Extract.splitppp Extract or Replace Sub-Patterns
as.rectangle Window Frame
Kinhom Inhomogeneous K-function
Extract.psp Extract Subset of Line Segment Pattern
betacells Beta Ganglion Cells in Cat Retina
inside.owin Test Whether Points Are Inside A Window
crossdist.default Pairwise distances between two different sets of points
nndist.pp3 Nearest neighbour distances in three dimensions
rknn Theoretical Distribution of Nearest Neighbour Distance
is.ppm Test Whether An Object Is A Fitted Point Process Model
as.hyperframe.ppx Extract coordinates and marks of multidimensional point pattern
project2segment Move Point To Nearest Line
is.subset.owin Determine Whether One Window is Contained In Another
closing Morphological Closing
corners Corners of a rectangle
complement.owin Take Complement of a Window
predict.kppm Prediction from a Fitted Cluster Point Process Model
integral.im Integral of a Pixel Image
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
opening Morphological Opening
pixellate Convert Spatial Object to Pixel Image
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
ewcdf Weighted Empirical Cumulative Distribution Function
markvario Mark Variogram
is.multitype.ppm Test Whether A Point Process Model is Multitype
logLik.ppm Log Likelihood for Poisson Point Process Model
crossdist.psp Pairwise distances between two different line segment patterns
eval.fv Evaluate Expression Involving Functions
quantile.im Sample Quantiles of Pixel Image
StraussHard The Strauss / Hard Core Point Process Model
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
raster.x Cartesian Coordinates for a Pixel Raster
contour.im Contour plot of pixel image
bounding.box.xy Convex Hull of Points
eval.fasp Evaluate Expression Involving Function Arrays
pixellate.owin Convert Window to Pixel Image
pcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-Type)
fitin.ppm Extract the Interaction from a Fitted Point Process Model
rStrauss Perfect Simulation of the Strauss Process
as.data.frame.ppp Coerce Point Pattern to a Data Frame
Hest Spherical Contact Distribution Function
nncross Nearest Neighbours Between Two Patterns
pp3 Three Dimensional Point Pattern
im.object Class of Images
nnwhich.pp3 Nearest neighbours in three dimensions
diameter.box3 Geometrical Calculations for Three-Dimensional Box
inforder.family Infinite Order Interaction Family
perimeter Perimeter Length of Window
miplot Morishita Index Plot
pcfinhom Inhomogeneous Pair Correlation Function
plot.fasp Plot a Function Array
Softcore The Soft Core Point Process Model
markcorr Mark Correlation Function
affine Apply Affine Transformation
is.multitype.ppp Test Whether A Point Pattern is Multitype
nnwhich Nearest neighbour
print.psp Print Brief Details of a Line Segment Pattern Dataset
finpines Pine saplings in Finland.
pcf.fasp Pair Correlation Function obtained from array of K functions
plot.fv Plot Function Values
chorley Chorley-Ribble Cancer Data
matchingdist Distance for a Point Pattern Matching
model.images Compute Images of Constructed Covariates
plot.colourmap Plot a Colour Map
redwood California Redwoods Point Pattern (Ripley's Subset)
fasp.object Function Arrays for Spatial Patterns
print.im Print Brief Details of an Image
pcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)
ponderosa Ponderosa Pine Tree Point Pattern
harmonic Basis for Harmonic Functions
ppx Multidimensional Space-Time Point Pattern
bramblecanes Hutchings' Bramble Canes data
rescale.psp Convert Line Segment Pattern to Another Unit of Length
ppm.object Class of Fitted Point Process Models
kaplan.meier Kaplan-Meier Estimator using Histogram Data
plot.owin Plot a Spatial Window
dilated.areas Areas of Morphological Dilations
superimpose Superimpose Several Point Patterns
plot.ppm plot a Fitted Point Process Model
print.quad Print a Quadrature Scheme
iplot Point and Click Interface for Displaying a Point Pattern
erosion Morphological Erosion
rescue.rectangle Convert Window Back To Rectangle
murchison Murchison gold deposits
quadscheme Generate a Quadrature Scheme from a Point Pattern
rshift Random Shift
plot.kppm Plot a fitted cluster point process
japanesepines Japanese Pines Point Pattern
rMaternI Simulate Matern Model I
setmarks Set or Reset the Marks in a Point Pattern
infline Infinite Straight Lines
bei Tropical rain forest trees
rpoispp3 Generate Poisson Point Pattern in Three Dimensions
humberside Humberside Data on Childhood Leukaemia and Lymphoma
deltametric Delta Metric
spatstat-internal Internal spatstat functions
anemones Beadlet Anemones Data
dirichlet Dirichlet Tessellation of Point Pattern
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
heather Diggle's Heather Data
mean.im Mean, Median and Range of Pixel Values in an Image
hist.im Histogram of Pixel Values in an Image
rescale.owin Convert Window to Another Unit of Length
distmap.ppp Distance Map of Point Pattern
rMaternII Simulate Matern Model II
rSSI Simulate Simple Sequential Inhibition
lut Lookup Tables
ppp Create a Point Pattern
pairwise.family Pairwise Interaction Process Family
plot.listof Plot a List of Things
spruces Spruces Point Pattern
pairsat.family Saturated Pairwise Interaction Point Process Family
setcov Set Covariance of a Window
pcfdot Multitype pair correlation function (i-to-any)
rmpoispp Generate Multitype Poisson Point Pattern
convexhull.xy Convex Hull of Points
methods.pp3 Methods for three-dimensional point patterns
rshift.ppp Randomly Shift a Point Pattern
ripras Estimate window from points alone
rpoislinetess Poisson Line Tessellation
ppp.object Class of Point Patterns
shift Apply Vector Translation
print.ppp Print Brief Details of a Point Pattern Dataset
pppmatching.object Class of Point Matchings
periodify Make Periodic Copies of a Spatial Pattern
pppdist Distance Between Two Point Patterns
pixelquad Quadrature Scheme Based on Pixel Grid
cut.ppp Classify Points in a Point Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
quadratcount Quadrat counting for a point pattern
multiplicity.ppp Count Multiplicity of Duplicate Points
ord.family Ord Interaction Process Family
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
plot.pp3 Plot a three-dimensional point pattern
pairdist.pp3 Pairwise distances in Three Dimensions
copper Berman-Huntington points and lines data
pointsOnLines Place Points Evenly Along Specified Lines
rNeymanScott Simulate Neyman-Scott Process
reduced.sample Reduced Sample Estimator using Histogram Data
intersect.owin Intersection, Union or Set Subtraction of Two Windows
rcell Simulate Baddeley-Silverman Cell Process
quad.object Class of Quadrature Schemes
residualspaper Data and Code From JRSS Discussion Paper on Residuals
quadrats Divide Region into Quadrats
profilepl Profile Maximum Pseudolikelihood
methods.ppx Methods for Multidimensional Space-Time Point Patterns
redwoodfull California Redwoods Point Pattern (Entire Dataset)
pairdist.ppp Pairwise distances
split.ppp Divide Point Pattern into Sub-patterns
owin Create a Window
rescale.ppp Convert Point Pattern to Another Unit of Length
rMatClust Simulate Matern Cluster Process
plot.splitppp Plot a List of Point Patterns
rpoispp Generate Poisson Point Pattern
pairdist.default Pairwise distances
plot.psp plot a Spatial Line Segment Pattern
pixellate.ppp Convert Point Pattern to Pixel Image
plot.im Plot a Pixel Image
coords Extract Coordinates of a Spatial or Spatiotemporal Point Pattern
rThomas Simulate Thomas Process
is.marked.ppp Test Whether A Point Pattern is Marked
quadratresample Resample a Point Pattern by Resampling Quadrats
owin.object Class owin
swedishpines Swedish Pines Point Pattern
Extract.ppp Extract or Replace Subset of Point Pattern
rMosaicField Mosaic Random Field
pairdist.psp Pairwise distances between line segments
square Square Window
rotate.owin Rotate a Window
summary.listof Summary of a List of Things
superimposePSP Superimpose Several Line Segment Patterns
nndist.psp Nearest neighbour distances between line segments
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
identify.ppp Identify Points in a Point Pattern
residuals.ppm Residuals for Fitted Point Process Model
reach Interaction Distance of a Point Process
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rmh.ppm Simulate from a Fitted Point Process Model
rotate Rotate
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
shapley Galaxies in the Shapley Supercluster
incircle Find Largest Circle Inside Window
smooth.ppp Spatial smoothing of observations at irregular points
nbfires Point Patterns of New Brunswick Forest Fires
psp.object Class of Line Segment Patterns
persp.im Perspective Plot of Pixel Image
predict.ppm Prediction from a Fitted Point Process Model
model.matrix.ppm Extract Design Matrix from Point Process Model
nztrees New Zealand Trees Point Pattern
tiles Extract List of Tiles in a Tessellation
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
clarkevans Clark and Evans Aggregation Index
rescale.im Convert Pixel Image to Another Unit of Length
rotate.psp Rotate a Line Segment Pattern
rthin Random Thinning
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
runifpoint Generate N Uniform Random Points
selfcrossing.psp Crossing Points in a Line Segment Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
summary.ppp Summary of a Point Pattern Dataset
plot.plotppm Plot a plotppm Object Created by plot.ppm
rjitter Random Perturbation of a Point Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
unitname Name for Unit of Length
print.owin Print Brief Details of a Spatial Window
plot.bermantest Plot Result of Berman Test
unmark Remove Marks
rsyst Simulate systematic random point pattern
whist Weighted Histogram
plot.quad plot a Spatial Quadrature Scheme
border Border Region of a Window
simplify.owin Approximate a Polygon by a Simpler Polygon
simulate.ppm Simulate a Fitted Gibbs Point Process Model
spatstat-package The Spatstat Package
runifdisc Generate N Uniform Random Points in a Disc
progressreport Print Progress Reports
runifpointOnLines Generate N Uniform Random Points On Line Segments
rpoint Generate N Random Points
simdat Simulated Point Pattern
scanpp Read Point Pattern From Data File
with.fv Evaluate an Expression in a Function Table
rescale Convert dataset to another unit of length
rmpoint Generate N Random Multitype Points
unique.ppp Extract Unique Points from a Spatial Point Pattern
summary.ppm Summarizing a Fitted Point Process Model
tess Create a Tessellation
markcorrint Mark Correlation Integral
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
stieltjes Compute Integral of Function Against Cumulative Distribution
update.kppm Update a Fitted Cluster Point Process Model
summary.im Summarizing a Pixel Image
shift.owin Apply Vector Translation To Window
shift.psp Apply Vector Translation To Line Segment Pattern
shift.im Apply Vector Translation To Pixel Image
union.quad Union of Data and Dummy Points
shift.ppp Apply Vector Translation To Point Pattern
psp Create a Line Segment Pattern
urkiola Urkiola Woods Point Pattern
summary.owin Summary of a Spatial Window
split.im Divide Image Into Sub-images
update.ppm Update a Fitted Point Process Model
rshift.splitppp Randomly Shift a List of Point Patterns
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
summary.quad Summarizing a Quadrature Scheme
print.ppm Print a Fitted Point Process Model
simulate.kppm Simulate a Fitted Cluster Point Process Model
summary.psp Summary of a Line Segment Pattern Dataset
rotate.ppp Rotate a Point Pattern
vertices Vertices of a Window
spatstat.options Internal Options in Spatstat Package
rstrat Simulate Stratified Random Point Pattern
rshift.psp Randomly Shift a Line Segment Pattern
pcf Pair Correlation Function
rlabel Random Re-Labelling of Point Pattern
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
runifpoint3 Generate N Uniform Random Points in Three Dimensions
rpoisline Generate Poisson Random Line Process
suffstat Sufficient Statistic of Point Process Model
with.hyperframe Evaluate an Expression in Each Row of a Hyperframe
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
spokes Spokes pattern of dummy points
trim.rectangle Cut margins from rectangle
summary.splitppp Summary of a Split Point Pattern
lansing Lansing Woods Point Pattern
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Date 06 january 2010
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2010-01-06 16:46:37 UTC; adrian
Repository CRAN
Date/Publication 2010-01-06 12:12:10

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