spatstat v1.18-0

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

Date 2010-03-10
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2010-03-10 02:55:09 UTC; adrian
Repository CRAN
Date/Publication 2010-03-10 10:20:21

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