spatstat v1.18-1

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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. 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
Kest K-function
Kdot.inhom Inhomogeneous Multitype K Dot Function
chorley Chorley-Ribble Cancer Data
bounding.box Bounding Box of a Window or Point Pattern
areaGain Difference of Disc Areas
areaLoss Difference of Disc Areas
coef.ppm Coefficients of Fitted Point Process Model
Softcore The Soft Core Point Process Model
ants Harkness-Isham ants' nests data
Kmeasure Reduced Second Moment Measure
Gest Nearest Neighbour Distance Function G
Extract.ppp Extract or Replace Subset of Point Pattern
colourmap Colour Lookup Tables
as.mask Pixel Image Approximation of a Window
blur Apply Gaussian Blur to a Pixel Image
Iest Estimate the I-function
Ldot Multitype L-function (i-to-any)
AreaInter The Area Interaction Point Process Model
collapse.fv Collapse Several Function Tables into One
betacells Beta Ganglion Cells in Cat Retina
Ldot.inhom Inhomogeneous Multitype L Dot Function
convexhull.xy Convex Hull of Points
bdist.points Distance to Boundary of Window
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
eval.im Evaluate Expression Involving Pixel Images
dirichlet Dirichlet Tessellation of Point Pattern
affine.ppp Apply Affine Transformation To Point Pattern
Geyer Geyer's Saturation Point Process Model
Extract.quad Subset of Quadrature Scheme
as.hyperframe.ppx Extract coordinates and marks of multidimensional point pattern
append.psp Combine Two Line Segment Patterns
affine.psp Apply Affine Transformation To Line Segment Pattern
bdist.pixels Distance to Boundary of Window
Kcross.inhom Inhomogeneous Cross K Function
bramblecanes Hutchings' Bramble Canes data
copper Berman-Huntington points and lines data
Extract.listof Extract or Replace Subset of a List of Things
crossdist Pairwise distances
DiggleGratton Diggle-Gratton model
as.ppp Convert Data To Class ppp
Strauss The Strauss Point Process Model
crossdist.pp3 Pairwise distances between two different three-dimensional point patterns
delaunay Delaunay Triangulation of Point Pattern
Lest L-function
inside.owin Test Whether Points Are Inside A Window
Fest Estimate the empty space function F
is.marked.ppm Test Whether A Point Process Model is Marked
cells Biological Cells Point Pattern
amacrine Hughes' Amacrine Cell Data
integral.im Integral of a Pixel Image
Kmulti Marked K-Function
Extract.fasp Extract Subset of Function Array
angles.psp Orientation Angles of Line Segments
is.multitype Test whether Object is Multitype
Pairwise Generic Pairwise Interaction model
interp.im Interpolate a Pixel Image
Lcross Multitype L-function (cross-type)
allstats Calculate four standard summary functions of a point pattern.
kaplan.meier Kaplan-Meier Estimator using Histogram Data
lansing Lansing Woods Point Pattern
levelset Level Set of a Pixel Image
as.polygonal Convert a Window to a Polygonal Window
pixellate.owin Convert Window to Pixel Image
Extract.psp Extract Subset of Line Segment Pattern
clickpoly Interactively Define a Polygon
centroid.owin Centroid of a window
as.matrix.im Convert Pixel Image to Matrix
Extract.fv Extract Subset of Function Values
K3est K-function of a Three-Dimensional Point Pattern
ppp.object Class of Point Patterns
quadratresample Resample a Point Pattern by Resampling Quadrats
as.psp Convert Data To Class psp
concatxy Concatenate x,y Coordinate Vectors
diameter Diameter of a Window
kppm Fit cluster point process model
discretise Safely Convert Point Pattern Window to Binary Mask
crossdist.default Pairwise distances between two different sets of points
lengths.psp Lengths of Line Segments
eval.fv Evaluate Expression Involving Functions
Kcross Multitype K Function (Cross-type)
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
diameter.box3 Geometrical Calculations for Three-Dimensional Box
latest.news Print News About Latest Version of Package
LennardJones The Lennard-Jones Potential
Extract.tess Extract or Replace Subset of Tessellation
quadscheme Generate a Quadrature Scheme from a Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
complement.owin Take Complement of a Window
hamster Aherne's hamster tumour data
quantile.im Sample Quantiles of Pixel Image
as.im Convert to Pixel Image
MultiStrauss The Multitype Strauss Point Process Model
summary.im Summarizing a Pixel Image
G3est Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Jdot Multitype J Function (i-to-any)
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
is.owin Test Whether An Object Is A Window
is.multitype.ppp Test Whether A Point Pattern is Multitype
matchingdist Distance for a Point Pattern Matching
logLik.ppm Log Likelihood for Poisson Point Process Model
Extract.splitppp Extract or Replace Sub-Patterns
expand.owin Expand Window By Factor
Hardcore The Hard Core Point Process Model
fryplot Fry Plot of Point Pattern
gpc2owin Convert Polygonal Region into Different Format
compatible.fv Test Whether Two Function Objects Are Compatible
Jmulti Marked J Function
discpartarea Area of Part of Disc
convexhull Convex Hull
incircle Find Largest Circle Inside Window
ppp Create a Point Pattern
corners Corners of a rectangle
istat Point and Click Interface for Exploratory Analysis of Point Pattern
pcf.ppp Pair Correlation Function of Point Pattern
nndist.psp Nearest neighbour distances between line segments
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
localK Neighbourhood density function
longleaf Longleaf Pines Point Pattern
pcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-Type)
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
as.box3 Convert Data to Three-Dimensional Box
fitted.ppm Fitted Conditional Intensity for Point Process Model
im.object Class of Images
fitin.ppm Extract the Interaction from a Fitted Point Process Model
affine.owin Apply Affine Transformation To Window
plot.quad plot a Spatial Quadrature Scheme
japanesepines Japanese Pines Point Pattern
is.marked Test Whether Marks Are Present
closing Morphological Closing
Replace.im Reset Values in Subset of Image
StraussHard The Strauss / Hard Core Point Process Model
by.im Apply Function to Image Broken Down by Factor
thomas.estK Fit the Thomas Point Process by Minimum Contrast
rMatClust Simulate Matern Cluster Process
finpines Pine saplings in Finland.
is.marked.ppp Test Whether A Point Pattern is Marked
distfun Distance Map as a Function
rThomas Simulate Thomas Process
bermantest Berman's Tests for Point Process Model
pairdist.default Pairwise distances
is.im Test Whether An Object Is A Pixel Image
pppmatching Create a Point Matching
OrdThresh Ord's Interaction model
plot.owin Plot a Spatial Window
markconnect Mark Connection Function
letterR Window in Shape of Letter R
mean.im Mean, Median and Range of Pixel Values in an Image
vertices Vertices of a Window
murchison Murchison gold deposits
eroded.areas Areas of Morphological Erosions
Saturated Saturated Pairwise Interaction model
as.tess Convert Data To Tessellation
Emark Diagnostics for random marking
deltametric Delta Metric
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
pcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)
clickppp Interactively Add Points
distmap.owin Distance Map of Window
data.ppm Extract Original Data from a Fitted Point Process Model
pp3 Three Dimensional Point Pattern
nearestsegment Find Line Segment Nearest to Each Point
lurking Lurking variable plot
pcf Pair Correlation Function
markcorr Mark Correlation Function
pcfinhom Inhomogeneous Pair Correlation Function
Kest.fft K-function using FFT
unique.ppp Extract Unique Points from a Spatial Point Pattern
Ord Generic Ord Interaction model
rotate Rotate
is.empty Test Whether An Object Is Empty
connected Connected components of an image or window
rescale.im Convert Pixel Image to Another Unit of Length
pixellate.ppp Convert Point Pattern to Pixel Image
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
pairdist Pairwise distances
simulate.kppm Simulate a Fitted Cluster Point Process Model
ganglia Beta Ganglion Cells in Cat Retina, Old Version
owin Create a Window
rpoisline Generate Poisson Random Line Process
tiles Extract List of Tiles in a Tessellation
is.convex Test Whether a Window is Convex
Lcross.inhom Inhomogeneous Cross Type L Function
rcell Simulate Baddeley-Silverman Cell Process
gridweights Compute Quadrature Weights Based on Grid Counts
plot.im Plot a Pixel Image
iplot Point and Click Interface for Displaying a Point Pattern
intersect.owin Intersection, Union or Set Subtraction of Two Windows
bdist.tiles Distance to Boundary of Window
npoints Number of Points in a Point Pattern
quadratcount Quadrat counting for a point pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
endpoints.psp Endpoints of Line Segment Pattern
harmonic Basis for Harmonic Functions
dilation Morphological Dilation
demopat Artificial Data Point Pattern
pcfdot Multitype pair correlation function (i-to-any)
coords Extract Coordinates of a Spatial or Spatiotemporal Point Pattern
heather Diggle's Heather Data
rmpoispp Generate Multitype Poisson Point Pattern
spruces Spruces Point Pattern
plot.fasp Plot a Function Array
distmap Distance Map
nearest.raster.point Find Pixel Nearest to a Given Point
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
crossdist.ppp Pairwise distances between two different point patterns
split.ppp Divide Point Pattern into Sub-patterns
F3est Empty Space Function of a Three-Dimensional Point Pattern
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
distmap.ppp Distance Map of Point Pattern
model.images Compute Images of Constructed Covariates
is.subset.owin Determine Whether One Window is Contained In Another
as.mask.psp Convert Line Segment Pattern to Binary Pixel Mask
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
crossing.psp Crossing Points of Two Line Segment Patterns
compatible.fasp Test Whether Two Function Arrays Are Compatible
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
scanpp Read Point Pattern From Data File
pcf.fasp Pair Correlation Function obtained from array of K functions
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
unitname Name for Unit of Length
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
is.ppm Test Whether An Object Is A Fitted Point Process Model
rMaternI Simulate Matern Model I
as.owin Convert Data To Class owin
selfcrossing.psp Crossing Points in a Line Segment Pattern
nbfires Point Patterns of New Brunswick Forest Fires
update.ppm Update a Fitted Point Process Model
hist.im Histogram of Pixel Values in an Image
density.ppp Kernel Smoothed Intensity of Point Pattern
ord.family Ord Interaction Process Family
bronzefilter Bronze gradient filter data
with.fv Evaluate an Expression in a Function Table
is.ppp Test Whether An Object Is A Point Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
print.owin Print Brief Details of a Spatial Window
Linhom L-function
pixellate Convert Spatial Object to Pixel Image
is.multitype.ppm Test Whether A Point Process Model is Multitype
as.data.frame.im Convert Pixel Image to Data Frame
print.im Print Brief Details of an Image
print.ppm Print a Fitted Point Process Model
infline Infinite Straight Lines
pairdist.psp Pairwise distances between line segments
nndist Nearest neighbour distances
summary.ppm Summarizing a Fitted Point Process Model
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
methods.pp3 Methods for three-dimensional point patterns
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
multiplicity.ppp Count Multiplicity of Duplicate Points
markcorrint Mark Correlation Integral
shift.ppp Apply Vector Translation To Point Pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
union.quad Union of Data and Dummy Points
ppm Fit Point Process Model to Data
anemones Beadlet Anemones Data
raster.x Cartesian Coordinates for a Pixel Raster
rStrauss Perfect Simulation of the Strauss Process
ppx Multidimensional Space-Time Point Pattern
envelope Simulation Envelopes of Summary Function
pixellate.psp Convert Line Segment Pattern to Pixel Image
persp.im Perspective Plot of Pixel Image
humberside Humberside Data on Childhood Leukaemia and Lymphoma
plot.splitppp Plot a List of Point Patterns
identify.ppp Identify Points in a Point Pattern
plot.psp plot a Spatial Line Segment Pattern
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
smooth.ppp Spatial smoothing of observations at irregular points
plot.ppp plot a Spatial Point Pattern
Extract.im Extract Subset of Image
fv.object Data Frames of Function Values
urkiola Urkiola Woods Point Pattern
disc Circular Window
rpoislinetess Poisson Line Tessellation
inforder.family Infinite Order Interaction Family
reduced.sample Reduced Sample Estimator using Histogram Data
nztrees New Zealand Trees Point Pattern
midpoints.psp Midpoints of Line Segment Pattern
quadrats Divide Region into Quadrats
gridcentres Rectangular grid of points
rescale.ppp Convert Point Pattern to Another Unit of Length
redwoodfull California Redwoods Point Pattern (Entire Dataset)
summary.psp Summary of a Line Segment Pattern Dataset
bounding.box.xy Convex Hull of Points
runifpoint Generate N Uniform Random Points
area.owin Area of a Window
with.hyperframe Evaluate an Expression in Each Row of a Hyperframe
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
ripras Estimate window from points alone
default.dummy Generate a Default Pattern of Dummy Points
square Square Window
crossdist.psp Pairwise distances between two different line segment patterns
pcf.fv Pair Correlation Function obtained from K Function
rSSI Simulate Simple Sequential Inhibition
markvario Mark Variogram
plot.bermantest Plot Result of Berman Test
density.psp Kernel Smoothing of Line Segment Pattern
rpoispp3 Generate Poisson Point Pattern in Three Dimensions
setcov Set Covariance of a Window
distmap.psp Distance Map of Line Segment Pattern
project2segment Move Point To Nearest Line
spatstat-internal Internal spatstat functions
plot.ppm plot a Fitted Point Process Model
rescale.owin Convert Window to Another Unit of Length
residualspaper Data and Code From JRSS Discussion Paper on Residuals
fv Create a Function Value Table
Hest Spherical Contact Distribution Function
pointsOnLines Place Points Evenly Along Specified Lines
rpoint Generate N Random Points
pixelquad Quadrature Scheme Based on Pixel Grid
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
plot.listof Plot a List of Things
methods.ppx Methods for Multidimensional Space-Time Point Patterns
Poisson Poisson Point Process Model
Kdot Multitype K Function (i-to-any)
rknn Theoretical Distribution of Nearest Neighbour Distance
mincontrast Method of Minimum Contrast
print.psp Print Brief Details of a Line Segment Pattern Dataset
rjitter Random Perturbation of a Point Pattern
predict.kppm Prediction from a Fitted Cluster Point Process Model
plot.kppm Plot a fitted cluster point process
psp Create a Line Segment Pattern
bind.fv Combine Function Value Tables
shift Apply Vector Translation
clarkevans Clark and Evans Aggregation Index
miplot Morishita Index Plot
runifdisc Generate N Uniform Random Points in a Disc
trim.rectangle Cut margins from rectangle
plot.plotppm Plot a plotppm Object Created by plot.ppm
predict.ppm Prediction from a Fitted Point Process Model
quad.object Class of Quadrature Schemes
pairwise.family Pairwise Interaction Process Family
rMosaicField Mosaic Random Field
plot.colourmap Plot a Colour Map
as.rectangle Window Frame
nnwhich Nearest neighbour
rstrat Simulate Stratified Random Point Pattern
reach Interaction Distance of a Point Process
psp.object Class of Line Segment Patterns
rMaternII Simulate Matern Model II
rsyst Simulate systematic random point pattern
plot.pp3 Plot a three-dimensional point pattern
nncross Nearest Neighbours Between Two Patterns
spatstat.options Internal Options in Spatstat Package
perimeter Perimeter Length of Window
box3 Three-Dimensional Box
contour.im Contour plot of pixel image
rMosaicSet Mosaic Random Set
rlabel Random Re-Labelling of Point Pattern
summary.owin Summary of a Spatial Window
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
methods.box3 Methods for Three-Dimensional Box
lut Lookup Tables
runifpoint3 Generate N Uniform Random Points in Three Dimensions
rshift.psp Randomly Shift a Line Segment Pattern
plot.hyperframe Plot Entries in a Hyperframe
hyperframe Hyper Data Frame
pppmatching.object Class of Point Matchings
rlinegrid Generate grid of parallel lines with random displacement
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
bei Tropical rain forest trees
rmh.ppm Simulate from a Fitted Point Process Model
marks Marks of a Point Pattern
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
print.quad Print a Quadrature Scheme
plot.tess Plot a tessellation
rescale Convert dataset to another unit of length
runifpointOnLines Generate N Uniform Random Points On Line Segments
rNeymanScott Simulate Neyman-Scott Process
opening Morphological Opening
affine Apply Affine Transformation
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
erosion Morphological Erosion
profilepl Profile Maximum Pseudolikelihood
rthin Random Thinning
pppdist Distance Between Two Point Patterns
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
redwood California Redwoods Point Pattern (Ripley's Subset)
update.kppm Update a Fitted Cluster Point Process Model
rotate.ppp Rotate a Point Pattern
shift.psp Apply Vector Translation To Line Segment Pattern
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
spokes Spokes pattern of dummy points
superimposePSP Superimpose Several Line Segment Patterns
print.ppp Print Brief Details of a Point Pattern Dataset
shapley Galaxies in the Shapley Supercluster
simulate.ppm Simulate a Fitted Gibbs Point Process Model
rpoispp Generate Poisson Point Pattern
cut.ppp Classify Points in a Point Pattern
rotate.psp Rotate a Line Segment Pattern
dilated.areas Areas of Morphological Dilations
rshift Random Shift
pairdist.ppp Pairwise distances
plot.fv Plot Function Values
whist Weighted Histogram
ppm.object Class of Fitted Point Process Models
unmark Remove Marks
eval.fasp Evaluate Expression Involving Function Arrays
eem Exponential Energy Marks
ponderosa Ponderosa Pine Tree Point Pattern
summary.ppp Summary of a Point Pattern Dataset
ewcdf Weighted Empirical Cumulative Distribution Function
rshift.splitppp Randomly Shift a List of Point Patterns
progressreport Print Progress Reports
shift.im Apply Vector Translation To Pixel Image
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
rGaussPoisson Simulate Gauss-Poisson Process
nnwhich.pp3 Nearest neighbours in three dimensions
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
cut.im Convert Pixel Image from Numeric to Factor
pairsat.family Saturated Pairwise Interaction Point Process Family
simdat Simulated Point Pattern
rmpoint Generate N Random Multitype Points
fasp.object Function Arrays for Spatial Patterns
superimpose Superimpose Several Point Patterns
rescue.rectangle Convert Window Back To Rectangle
residuals.ppm Residuals for Fitted Point Process Model
split.im Divide Image Into Sub-images
intersect.tess Intersection of Two Tessellations
nndist.pp3 Nearest neighbour distances in three dimensions
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
summary.quad Summarizing a Quadrature Scheme
Jcross Multitype J Function (i-to-j)
model.matrix.ppm Extract Design Matrix from Point Process Model
tess Create a Tessellation
swedishpines Swedish Pines Point Pattern
shift.owin Apply Vector Translation To Window
summary.splitppp Summary of a Split Point Pattern
anova.ppm ANOVA for Fitted Point Process Models
BadGey Hybrid Geyer Point Process Model
summary.listof Summary of a List of Things
as.data.frame.ppp Coerce Point Pattern to a Data Frame
Jest Estimate the J-function
border Border Region of a Window
Kinhom Inhomogeneous K-function
as.hyperframe Convert Data to Hyperframe
chop.tess Subdivide a Window or Tessellation using a Set of Lines
clip.infline Intersect Infinite Straight Lines with a Window
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
spatstat-deprecated Deprecated spatstat functions
envelope.pp3 Simulation Envelopes of Summary Function for 3D Point Pattern
nnclean Nearest Neighbour Clutter Removal
pcfcross Multitype pair correlation function (cross-type)
periodify Make Periodic Copies of a Spatial Pattern
owin.object Class owin
rescale.psp Convert Line Segment Pattern to Another Unit of Length
suffstat Sufficient Statistic of Point Process Model
applynbd Apply Function to Every Neighbourhood in a Point Pattern
rshift.ppp Randomly Shift a Point Pattern
stieltjes Compute Integral of Function Against Cumulative Distribution
spatstat-package The Spatstat Package
simplify.owin Approximate a Polygon by a Simpler Polygon
rotate.owin Rotate a Window
im Create a Pixel Image Object
pairdist.pp3 Pairwise distances in Three Dimensions
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Date 2010-03-19
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2010-03-19 04:19:48 UTC; adrian
Repository CRAN
Date/Publication 2010-03-19 07:31:32

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