spatstat v1.18-2

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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
ants Harkness-Isham ants' nests data
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
clarkevans Clark and Evans Aggregation Index
Jest Estimate the J-function
coords Extract Coordinates of a Spatial or Spatiotemporal Point Pattern
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
StraussHard The Strauss / Hard Core Point Process Model
as.hyperframe.ppx Extract coordinates and marks of multidimensional point pattern
cut.ppp Classify Points in a Point Pattern
Emark Diagnostics for random marking
as.psp Convert Data To Class psp
Fest Estimate the empty space function F
im.object Class of Images
eval.fasp Evaluate Expression Involving Function Arrays
interp.im Interpolate a Pixel Image
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
centroid.owin Centroid of a window
Jdot Multitype J Function (i-to-any)
crossdist Pairwise distances
intersect.tess Intersection of Two Tessellations
Geyer Geyer's Saturation Point Process Model
distmap.ppp Distance Map of Point Pattern
Kcross.inhom Inhomogeneous Cross K Function
Kcross Multitype K Function (Cross-type)
as.owin Convert Data To Class owin
fitted.ppm Fitted Conditional Intensity for Point Process Model
nztrees New Zealand Trees Point Pattern
complement.owin Take Complement of a Window
Kest.fft K-function using FFT
Linhom L-function
latest.news Print News About Latest Version of Package
Strauss The Strauss Point Process Model
as.hyperframe Convert Data to Hyperframe
pairdist Pairwise distances
gpc2owin Convert Polygonal Region into Different Format
predict.ppm Prediction from a Fitted Point Process Model
print.im Print Brief Details of an Image
hyperframe Hyper Data Frame
as.tess Convert Data To Tessellation
Lcross Multitype L-function (cross-type)
Lest L-function
MultiStrauss The Multitype Strauss Point Process Model
DiggleGratton Diggle-Gratton model
is.marked.ppm Test Whether A Point Process Model is Marked
istat Point and Click Interface for Exploratory Analysis of Point Pattern
chorley Chorley-Ribble Cancer Data
Saturated Saturated Pairwise Interaction model
ppp Create a Point Pattern
Poisson Poisson Point Process Model
crossing.psp Crossing Points of Two Line Segment Patterns
distmap.psp Distance Map of Line Segment Pattern
pcf Pair Correlation Function
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
pcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)
AreaInter The Area Interaction Point Process Model
Extract.fv Extract Subset of Function Values
Extract.fasp Extract Subset of Function Array
as.mask.psp Convert Line Segment Pattern to Binary Pixel Mask
Replace.im Reset Values in Subset of Image
areaLoss Difference of Disc Areas
Gest Nearest Neighbour Distance Function G
selfcrossing.psp Crossing Points in a Line Segment Pattern
eval.im Evaluate Expression Involving Pixel Images
lengths.psp Lengths of Line Segments
G3est Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
markcorr Mark Correlation Function
Lcross.inhom Inhomogeneous Cross Type L Function
gridweights Compute Quadrature Weights Based on Grid Counts
Extract.im Extract Subset of Image
Hest Spherical Contact Distribution Function
Pairwise Generic Pairwise Interaction model
as.data.frame.ppp Coerce Point Pattern to a Data Frame
bounding.box Bounding Box of a Window or Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
chop.tess Subdivide a Window or Tessellation using a Set of Lines
rlabel Random Re-Labelling of Point Pattern
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
rpoint Generate N Random Points
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
affine Apply Affine Transformation
as.im Convert to Pixel Image
area.owin Area of a Window
miplot Morishita Index Plot
Softcore The Soft Core Point Process Model
as.box3 Convert Data to Three-Dimensional Box
Gfox Foxall's Distance Functions
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
Ldot Multitype L-function (i-to-any)
Ord Generic Ord Interaction model
mincontrast Method of Minimum Contrast
as.rectangle Window Frame
rsyst Simulate systematic random point pattern
shift.owin Apply Vector Translation To Window
bramblecanes Hutchings' Bramble Canes data
collapse.fv Collapse Several Function Tables into One
Kmeasure Reduced Second Moment Measure
angles.psp Orientation Angles of Line Segments
bind.fv Combine Function Value Tables
pcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-Type)
summary.ppp Summary of a Point Pattern Dataset
OrdThresh Ord's Interaction model
nndist.pp3 Nearest neighbour distances in three dimensions
contour.im Contour plot of pixel image
bdist.pixels Distance to Boundary of Window
pcfinhom Inhomogeneous Pair Correlation Function
coef.ppm Coefficients of Fitted Point Process Model
by.im Apply Function to Image Broken Down by Factor
diameter.box3 Geometrical Calculations for Three-Dimensional Box
delaunay Delaunay Triangulation of Point Pattern
plot.hyperframe Plot Entries in a Hyperframe
pairwise.family Pairwise Interaction Process Family
convexhull.xy Convex Hull of Points
plot.plotppm Plot a plotppm Object Created by plot.ppm
plot.owin Plot a Spatial Window
owin Create a Window
cut.im Convert Pixel Image from Numeric to Factor
Ldot.inhom Inhomogeneous Multitype L Dot Function
density.ppp Kernel Smoothed Intensity of Point Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
clickpoly Interactively Define a Polygon
spatstat-deprecated Deprecated spatstat functions
Extract.psp Extract Subset of Line Segment Pattern
with.hyperframe Evaluate an Expression in Each Row of a Hyperframe
periodify Make Periodic Copies of a Spatial Pattern
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
betacells Beta Ganglion Cells in Cat Retina
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
ewcdf Weighted Empirical Cumulative Distribution Function
connected Connected components of an image or window
disc Circular Window
plot.listof Plot a List of Things
default.dummy Generate a Default Pattern of Dummy Points
crossdist.default Pairwise distances between two different sets of points
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
concatxy Concatenate x,y Coordinate Vectors
clickppp Interactively Add Points
copper Berman-Huntington points and lines data
density.psp Kernel Smoothing of Line Segment Pattern
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
discretise Safely Convert Point Pattern Window to Binary Mask
diameter Diameter of a Window
pp3 Three Dimensional Point Pattern
data.ppm Extract Original Data from a Fitted Point Process Model
box3 Three-Dimensional Box
envelope.pp3 Simulation Envelopes of Summary Function for 3D Point Pattern
discpartarea Area of Part of Disc
rpoisline Generate Poisson Random Line Process
kppm Fit cluster point process model
envelope Simulation Envelopes of Summary Function
fv Create a Function Value Table
erosion Morphological Erosion
endpoints.psp Endpoints of Line Segment Pattern
crossdist.psp Pairwise distances between two different line segment patterns
model.matrix.ppm Extract Design Matrix from Point Process Model
distmap Distance Map
expand.owin Expand Window By Factor
dilated.areas Areas of Morphological Dilations
fasp.object Function Arrays for Spatial Patterns
inforder.family Infinite Order Interaction Family
fitin.ppm Extract the Interaction from a Fitted Point Process Model
is.multitype.ppm Test Whether A Point Process Model is Multitype
methods.box3 Methods for Three-Dimensional Box
is.ppm Test Whether An Object Is A Fitted Point Process Model
plot.kppm Plot a fitted cluster point process
ord.family Ord Interaction Process Family
hist.im Histogram of Pixel Values in an Image
incircle Find Largest Circle Inside Window
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
longleaf Longleaf Pines Point Pattern
mean.im Mean, Median and Range of Pixel Values in an Image
print.ppp Print Brief Details of a Point Pattern Dataset
fv.object Data Frames of Function Values
nearest.raster.point Find Pixel Nearest to a Given Point
nearestsegment Find Line Segment Nearest to Each Point
iplot Point and Click Interface for Displaying a Point Pattern
print.owin Print Brief Details of a Spatial Window
predict.kppm Prediction from a Fitted Cluster Point Process Model
ppx Multidimensional Space-Time Point Pattern
print.ppm Print a Fitted Point Process Model
multiplicity.ppp Count Multiplicity of Duplicate Points
murchison Murchison gold deposits
lansing Lansing Woods Point Pattern
nnclean Nearest Neighbour Clutter Removal
is.subset.owin Determine Whether One Window is Contained In Another
matchingdist Distance for a Point Pattern Matching
identify.ppp Identify Points in a Point Pattern
pairdist.psp Pairwise distances between line segments
quadscheme Generate a Quadrature Scheme from a Point Pattern
pixelquad Quadrature Scheme Based on Pixel Grid
quadratcount Quadrat counting for a point pattern
is.owin Test Whether An Object Is A Window
gridcentres Rectangular grid of points
pcf.ppp Pair Correlation Function of Point Pattern
eval.fv Evaluate Expression Involving Functions
plot.fasp Plot a Function Array
localK Neighbourhood density function
BadGey Hybrid Geyer Point Process Model
nndist.psp Nearest neighbour distances between line segments
lurking Lurking variable plot
pixellate.psp Convert Line Segment Pattern to Pixel Image
quadratresample Resample a Point Pattern by Resampling Quadrats
japanesepines Japanese Pines Point Pattern
markconnect Mark Connection Function
perimeter Perimeter Length of Window
rMaternII Simulate Matern Model II
levelset Level Set of a Pixel Image
pairdist.pp3 Pairwise distances in Three Dimensions
rStrauss Perfect Simulation of the Strauss Process
rmh.ppm Simulate from a Fitted Point Process Model
plot.bermantest Plot Result of Berman Test
ppm.object Class of Fitted Point Process Models
pointsOnLines Place Points Evenly Along Specified Lines
pixellate Convert Spatial Object to Pixel Image
rMosaicField Mosaic Random Field
pppmatching Create a Point Matching
rshift.ppp Randomly Shift a Point Pattern
ponderosa Ponderosa Pine Tree Point Pattern
F3est Empty Space Function of a Three-Dimensional Point Pattern
opening Morphological Opening
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
plot.pp3 Plot a three-dimensional point pattern
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
Hardcore The Hard Core Point Process Model
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
pixellate.owin Convert Window to Pixel Image
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
project2segment Move Point To Nearest Line
rpoispp3 Generate Poisson Point Pattern in Three Dimensions
owin.object Class owin
rSSI Simulate Simple Sequential Inhibition
runifpoint3 Generate N Uniform Random Points in Three Dimensions
quadrats Divide Region into Quadrats
rescale.im Convert Pixel Image to Another Unit of Length
rjitter Random Perturbation of a Point Pattern
rGaussPoisson Simulate Gauss-Poisson Process
pixellate.ppp Convert Point Pattern to Pixel Image
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
Jcross Multitype J Function (i-to-j)
raster.x Cartesian Coordinates for a Pixel Raster
psp.object Class of Line Segment Patterns
rmpoint Generate N Random Multitype Points
pppdist Distance Between Two Point Patterns
quantile.im Sample Quantiles of Pixel Image
rescale.owin Convert Window to Another Unit of Length
simdat Simulated Point Pattern
rThomas Simulate Thomas Process
affine.owin Apply Affine Transformation To Window
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
rshift.psp Randomly Shift a Line Segment Pattern
rescale Convert dataset to another unit of length
plot.im Plot a Pixel Image
union.quad Union of Data and Dummy Points
runifdisc Generate N Uniform Random Points in a Disc
split.ppp Divide Point Pattern into Sub-patterns
rescale.ppp Convert Point Pattern to Another Unit of Length
Kmulti Marked K-Function
rotate.psp Rotate a Line Segment Pattern
as.data.frame.im Convert Pixel Image to Data Frame
unmark Remove Marks
split.im Divide Image Into Sub-images
Kdot Multitype K Function (i-to-any)
suffstat Sufficient Statistic of Point Process Model
Extract.tess Extract or Replace Subset of Tessellation
crossdist.pp3 Pairwise distances between two different three-dimensional point patterns
Extract.quad Subset of Quadrature Scheme
border Border Region of a Window
runifpointOnLines Generate N Uniform Random Points On Line Segments
setcov Set Covariance of a Window
rlinegrid Generate grid of parallel lines with random displacement
rotate Rotate
compatible.fv Test Whether Two Function Objects Are Compatible
redwood California Redwoods Point Pattern (Ripley's Subset)
demopat Artificial Data Point Pattern
summary.quad Summarizing a Quadrature Scheme
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
pppmatching.object Class of Point Matchings
rpoislinetess Poisson Line Tessellation
applynbd Apply Function to Every Neighbourhood in a Point Pattern
plot.ppp plot a Spatial Point Pattern
as.polygonal Convert a Window to a Polygonal Window
amacrine Hughes' Amacrine Cell Data
stieltjes Compute Integral of Function Against Cumulative Distribution
distmap.owin Distance Map of Window
rshift Random Shift
dilation Morphological Dilation
vertices Vertices of a Window
rthin Random Thinning
shift.ppp Apply Vector Translation To Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
summary.im Summarizing a Pixel Image
rshift.splitppp Randomly Shift a List of Point Patterns
eroded.areas Areas of Morphological Erosions
is.multitype.ppp Test Whether A Point Pattern is Multitype
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
simplify.owin Approximate a Polygon by a Simpler Polygon
compatible.fasp Test Whether Two Function Arrays Are Compatible
shift Apply Vector Translation
urkiola Urkiola Woods Point Pattern
crossdist.ppp Pairwise distances between two different point patterns
as.ppp Convert Data To Class ppp
rNeymanScott Simulate Neyman-Scott Process
summary.owin Summary of a Spatial Window
rotate.owin Rotate a Window
affine.ppp Apply Affine Transformation To Point Pattern
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
smooth.ppp Spatial smoothing of observations at irregular points
areaGain Difference of Disc Areas
ganglia Beta Ganglion Cells in Cat Retina, Old Version
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
is.ppp Test Whether An Object Is A Point Pattern
as.mask Pixel Image Approximation of a Window
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
colourmap Colour Lookup Tables
nnwhich.pp3 Nearest neighbours in three dimensions
swedishpines Swedish Pines Point Pattern
distfun Distance Map as a Function
summary.listof Summary of a List of Things
pairdist.default Pairwise distances
harmonic Basis for Harmonic Functions
superimpose Superimpose Several Point Patterns
im Create a Pixel Image Object
ripras Estimate window from points alone
Kdot.inhom Inhomogeneous Multitype K Dot Function
bei Tropical rain forest trees
spatstat-internal Internal spatstat functions
letterR Window in Shape of Letter R
corners Corners of a rectangle
pairsat.family Saturated Pairwise Interaction Point Process Family
nbfires Point Patterns of New Brunswick Forest Fires
cells Biological Cells Point Pattern
pcfcross Multitype pair correlation function (cross-type)
heather Diggle's Heather Data
Extract.ppp Extract or Replace Subset of Point Pattern
is.empty Test Whether An Object Is Empty
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
intersect.owin Intersection, Union or Set Subtraction of Two Windows
append.psp Combine Two Line Segment Patterns
rMaternI Simulate Matern Model I
pcfdot Multitype pair correlation function (i-to-any)
eem Exponential Energy Marks
persp.im Perspective Plot of Pixel Image
is.marked Test Whether Marks Are Present
humberside Humberside Data on Childhood Leukaemia and Lymphoma
as.matrix.im Convert Pixel Image to Matrix
affine.psp Apply Affine Transformation To Line Segment Pattern
plot.colourmap Plot a Colour Map
markcorrint Mark Correlation Integral
print.quad Print a Quadrature Scheme
is.marked.ppp Test Whether A Point Pattern is Marked
is.multitype Test whether Object is Multitype
methods.ppx Methods for Multidimensional Space-Time Point Patterns
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
bounding.box.xy Convex Hull of Points
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
rmpoispp Generate Multitype Poisson Point Pattern
rstrat Simulate Stratified Random Point Pattern
model.images Compute Images of Constructed Covariates
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
thomas.estK Fit the Thomas Point Process by Minimum Contrast
nnwhich Nearest neighbour
ppp.object Class of Point Patterns
Extract.listof Extract or Replace Subset of a List of Things
profilepl Profile Maximum Pseudolikelihood
hamster Aherne's hamster tumour data
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
Extract.splitppp Extract or Replace Sub-Patterns
unique.ppp Extract Unique Points from a Spatial Point Pattern
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
shapley Galaxies in the Shapley Supercluster
rMosaicSet Mosaic Random Set
markvario Mark Variogram
Iest Estimate the I-function
rescue.rectangle Convert Window Back To Rectangle
rcell Simulate Baddeley-Silverman Cell Process
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
lut Lookup Tables
logLik.ppm Log Likelihood for Poisson Point Process Model
whist Weighted Histogram
Kinhom Inhomogeneous K-function
marks Marks of a Point Pattern
print.psp Print Brief Details of a Line Segment Pattern Dataset
quad.object Class of Quadrature Schemes
plot.fv Plot Function Values
midpoints.psp Midpoints of Line Segment Pattern
spatstat-package The Spatstat Package
summary.ppm Summarizing a Fitted Point Process Model
with.fv Evaluate an Expression in a Function Table
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
plot.splitppp Plot a List of Point Patterns
reach Interaction Distance of a Point Process
update.kppm Update a Fitted Cluster Point Process Model
bermantest Berman's Tests for Point Process Model
simulate.kppm Simulate a Fitted Cluster Point Process Model
psp Create a Line Segment Pattern
dirichlet Dirichlet Tessellation of Point Pattern
plot.ppm plot a Fitted Point Process Model
rknn Theoretical Distribution of Nearest Neighbour Distance
plot.quad plot a Spatial Quadrature Scheme
tess Create a Tessellation
nncross Nearest Neighbours Between Two Patterns
trim.rectangle Cut margins from rectangle
finpines Pine saplings in Finland.
Jmulti Marked J Function
inside.owin Test Whether Points Are Inside A Window
pcf.fasp Pair Correlation Function obtained from array of K functions
K3est K-function of a Three-Dimensional Point Pattern
spruces Spruces Point Pattern
residuals.ppm Residuals for Fitted Point Process Model
plot.tess Plot a tessellation
allstats Calculate four standard summary functions of a point pattern.
LennardJones The Lennard-Jones Potential
anemones Beadlet Anemones Data
summary.splitppp Summary of a Split Point Pattern
runifpoint Generate N Uniform Random Points
is.im Test Whether An Object Is A Pixel Image
tiles Extract List of Tiles in a Tessellation
ppm Fit Point Process Model to Data
scanpp Read Point Pattern From Data File
rotate.ppp Rotate a Point Pattern
update.ppm Update a Fitted Point Process Model
square Square Window
fryplot Fry Plot of Point Pattern
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
kaplan.meier Kaplan-Meier Estimator using Histogram Data
unitname Name for Unit of Length
anova.ppm ANOVA for Fitted Point Process Models
methods.pp3 Methods for three-dimensional point patterns
bdist.tiles Distance to Boundary of Window
bdist.points Distance to Boundary of Window
bronzefilter Bronze gradient filter data
clip.infline Intersect Infinite Straight Lines with a Window
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
pairdist.ppp Pairwise distances
rescale.psp Convert Line Segment Pattern to Another Unit of Length
shift.im Apply Vector Translation To Pixel Image
closing Morphological Closing
blur Apply Gaussian Blur to a Pixel Image
shift.psp Apply Vector Translation To Line Segment Pattern
convexhull Convex Hull
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
deltametric Delta Metric
spatstat.options Internal Options in Spatstat Package
spokes Spokes pattern of dummy points
infline Infinite Straight Lines
integral.im Integral of a Pixel Image
superimposePSP Superimpose Several Line Segment Patterns
residualspaper Data and Code From JRSS Discussion Paper on Residuals
is.convex Test Whether a Window is Convex
npoints Number of Points in a Point Pattern
nndist Nearest neighbour distances
pcf.fv Pair Correlation Function obtained from K Function
plot.psp plot a Spatial Line Segment Pattern
progressreport Print Progress Reports
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
rMatClust Simulate Matern Cluster Process
reduced.sample Reduced Sample Estimator using Histogram Data
redwoodfull California Redwoods Point Pattern (Entire Dataset)
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
simulate.ppm Simulate a Fitted Gibbs Point Process Model
rpoispp Generate Poisson Point Pattern
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Date 2010-04-09
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2010-04-09 13:44:39 UTC; adrian
Repository CRAN
Date/Publication 2010-04-10 06:33:10

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