spatstat v1.16-3

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

Date 28 August 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2009-10-13 20:42:22 UTC; adrian
Repository CRAN
Date/Publication 2009-10-13 08:54:43

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