spatstat v1.18-3

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

Date 2010-04-19
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2010-04-19 09:28:23 UTC; adrian
Repository CRAN
Date/Publication 2010-04-19 12:23:42

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