spatstat v1.17-6

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

Date 2010-02-08
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2010-02-10 01:41:32 UTC; adrian
Repository CRAN
Date/Publication 2010-02-09 11:07:38

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