spatstat v1.16-1

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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.tess Extract or Replace Subset of Tessellation
Jest Estimate the J-function
Ldot Multitype L-function (i-to-any)
Emark Diagnostics for random marking
DiggleGratton Diggle-Gratton model
Extract.im Extract Subset of Image
Extract.fasp Extract Subset of Function Array
Gmulti Marked Nearest Neighbour Distance Function
Fest Estimate the empty space function F
Kcross.inhom Inhomogeneous Cross K Function
affine.owin Apply Affine Transformation To Window
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
OrdThresh Ord's Interaction model
anova.ppm ANOVA for Fitted Point Process Models
Extract.listof Extract or Replace Subset of a List of Things
Kmulti Marked K-Function
spatstat The Spatstat Package
Kdot.inhom Inhomogeneous Multitype K Dot Function
area.owin Area of a Window
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
clip.infline Intersect Infinite Straight Lines with a Window
anemones Beadlet Anemones Data
AreaInter The Area Interaction Point Process Model
Jmulti Marked J Function
affine Apply Affine Transformation
Extract.ppp Extract or Replace Subset of Point Pattern
as.ppp Convert Data To Class ppp
bdist.points Distance to Boundary of Window
Kinhom Inhomogeneous K-function
allstats Calculate four standard summary functions of a point pattern.
complement.owin Take Complement of a Window
Ldot.inhom Inhomogeneous Multitype L Dot Function
Kdot Multitype K Function (i-to-any)
as.im Convert to Pixel Image
Linhom L-function
Lcross.inhom Inhomogeneous Cross Type L Function
Lest L-function
delaunay Delaunay Triangulation of Point Pattern
amacrine Hughes' Amacrine Cell Data
corners Corners of a rectangle
angles.psp Orientation Angles of Line Segments
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
connected Connected components of an image or window
betacells Beta Ganglion Cells in Cat Retina
BadGey Hybrid Geyer Point Process Model
Kmeasure Reduced Second Moment Measure
clickppp Interactively Add Points
blur Apply Gaussian Blur to a Pixel Image
Extract.quad Subset of Quadrature Scheme
Kest.fft K-function using FFT
as.owin Convert Data To Class owin
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
cut.im Convert Pixel Image from Numeric to Factor
convexhull Convex Hull
Kcross Multitype K Function (Cross-type)
Extract.fv Extract Subset of Function Values
Kest K-function
finpines Pine saplings in Finland.
Replace.im Reset Values in Subset of Image
bei Tropical rain forest trees
concatxy Concatenate x,y Coordinate Vectors
erosion Morphological Erosion
Softcore The Soft Core Point Process Model
compatible.im Test Whether Two Pixel Images Are Compatible
Hest Spherical Contact Distribution Function
Iest Estimate the I-function
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
crossdist.ppp Pairwise distances between two different point patterns
LennardJones The Lennard-Jones Potential
crossdist.psp Pairwise distances between two different line segment patterns
as.rectangle Window Frame
crossing.psp Crossing Points of Two Line Segment Patterns
Ord Generic Ord Interaction model
Geyer Geyer's Saturation Point Process Model
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
is.convex Test Whether a Window is Convex
crossdist Pairwise distances
StraussHard The Strauss / Hard Core Point Process Model
as.tess Convert Data To Tessellation
areadiff Difference of Disc Areas
Extract.psp Extract Subset of Line Segment Pattern
diameter Diameter of a Window
distmap.psp Distance Map of Line Segment Pattern
applynbd Apply Function to Every Neighbourhood in a Point Pattern
Gest Nearest Neighbour Distance Function G
as.psp Convert Data To Class psp
ants Harkness-Isham ants' nests data
eval.im Evaluate Expression Involving Pixel Images
Extract.splitppp Extract or Replace Sub-Patterns
by.im Apply Function to Image Broken Down by Factor
affine.ppp Apply Affine Transformation To Point Pattern
discretise Safely Convert Point Pattern Window to Binary Mask
append.psp Combine Two Line Segment Patterns
bermantest Berman's Tests for Point Process Model
Pairwise Generic Pairwise Interaction model
crossdist.default Pairwise distances between two different sets of points
Strauss The Strauss Point Process Model
clarkevans Clark and Evans Aggregation Index
is.marked Test Whether Marks Are Present
harmonic Basis for Harmonic Functions
compatible.fasp Test Whether Two Function Arrays Are Compatible
owin Create a Window
bramblecanes Hutchings' Bramble Canes data
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
ganglia Beta Ganglion Cells in Cat Retina, Old Version
Poisson Poisson Point Process Model
bounding.box Bounding Box of a Window or Point Pattern
clickpoly Interactively Define a Polygon
MultiStrauss The Multitype Strauss Point Process Model
bdist.pixels Distance to Boundary of Window
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
convexhull.xy Convex Hull of Points
bounding.box.xy Convex Hull of Points
markvario Mark Variogram
gpc2owin Convert Polygonal Region into Different Format
pcf.fv Pair Correlation Function obtained from K Function
eval.fv Evaluate Expression Involving Functions
closing Morphological Closing
as.data.frame.ppp Coerce Point Pattern to a Data Frame
dilation Morphological Dilation
eem Exponential Energy Marks
as.matrix.im Convert Pixel Image to Matrix
residuals.ppm Residuals for Fitted Point Process Model
fv.object Data Frames of Function Values
hamster Aherne's hamster tumour data
density.psp Kernel Smoothing of Line Segment Pattern
is.owin Test Whether An Object Is A Window
eval.fasp Evaluate Expression Involving Function Arrays
levelset Level Set of a Pixel Image
interp.im Interpolate a Pixel Image
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
rescale.ppp Convert Point Pattern to Another Unit of Length
spatstat-deprecated Deprecated spatstat functions
copper Berman-Huntington points and lines data
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
fitted.ppm Fitted Conditional Intensity for Point Process Model
plot.owin Plot a Spatial Window
print.owin Print Brief Details of a Spatial Window
cut.ppp Classify Points in a Point Pattern
endpoints.psp Endpoints of Line Segment Pattern
pairdist.ppp Pairwise distances
im.object Class of Images
is.ppp Test Whether An Object Is A Point Pattern
ppp.object Class of Point Patterns
inside.owin Test Whether Points Are Inside A Window
intersect.owin Intersection or Union of Two Windows
spatstat-internal Internal spatstat functions
nndist.psp Nearest neighbour distances between line segments
print.psp Print Brief Details of a Line Segment Pattern Dataset
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
pppdist Distance Between Two Point Patterns
inforder.family Infinite Order Interaction Family
cells Biological Cells Point Pattern
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
demopat Artificial Data Point Pattern
pcf Pair Correlation Function
distmap Distance Map
as.mask Pixel Image Approximation of a Window
Saturated Saturated Pairwise Interaction model
plot.im Plot a Pixel Image
chorley Chorley-Ribble Cancer Data
as.polygonal Convert a Window to a Polygonal Window
is.subset.owin Determine Whether One Window is Contained In Another
predict.kppm Prediction from a Fitted Cluster Point Process Model
lengths.psp Lengths of Line Segments
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
incircle Find Largest Circle Inside Window
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
centroid.owin Centroid of a window
ppm Fit Point Process Model to Data
fasp.object Function Arrays for Spatial Patterns
pairsat.family Saturated Pairwise Interaction Point Process Family
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
mean.im Mean, Median and Range of Pixel Values in an Image
eroded.areas Areas of Morphological Erosions
heather Diggle's Heather Data
ewcdf Weighted Empirical Cumulative Distribution Function
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
density.ppp Kernel Smoothed Intensity of Point Pattern
is.multitype Test whether Object is Multitype
expand.owin Expand Window By Factor
gridweights Compute Quadrature Weights Based on Grid Counts
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
ppp Create a Point Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
hyperframe Hyper Data Frame
hist.im Histogram of Pixel Values in an Image
dirichlet Dirichlet Tessellation of Point Pattern
plot.fasp Plot a Function Array
gridcentres Rectangular grid of points
pairdist Pairwise distances
plot.plotppm Plot a plotppm Object Created by plot.ppm
is.multitype.ppp Test Whether A Point Pattern is Multitype
japanesepines Japanese Pines Point Pattern
ponderosa Ponderosa Pine Tree Point Pattern
miplot Morishita Index Plot
colourmap Colour Lookup Tables
murchison Murchison gold deposits
is.empty Test Whether An Object Is Empty
identify.ppp Identify Points in a Point Pattern
pppmatching Create a Point Matching
kppm Fit cluster point process model
rlinegrid Generate grid of parallel lines with random displacement
rGaussPoisson Simulate Gauss-Poisson Process
plot.ppm plot a Fitted Point Process Model
rlabel Random Re-Labelling of Point Pattern
rMosaicField Mosaic Random Field
humberside Humberside Data on Childhood Leukaemia and Lymphoma
is.multitype.ppm Test Whether A Point Process Model is Multitype
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
nztrees New Zealand Trees Point Pattern
plot.listof Plot a List of Things
print.im Print Brief Details of an Image
longleaf Longleaf Pines Point Pattern
plot.quad plot a Spatial Quadrature Scheme
quadratcount Quadrat counting for a point pattern
istat Point and Click Interface for Exploratory Analysis of Point Pattern
rpoisline Generate Poisson Random Line Process
intersect.tess Intersection of Two Tessellations
markcorr Mark Correlation Function
rNeymanScott Simulate Neyman-Scott Process
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
rshift.psp Randomly Shift a Line Segment Pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
pointsOnLines Place Points Evenly Along Specified Lines
rThomas Simulate Thomas Process
print.ppp Print Brief Details of a Point Pattern Dataset
rmpoispp Generate Multitype Poisson Point Pattern
simulate.kppm Simulate a Fitted Cluster Point Process Model
rotate Rotate
rMaternI Simulate Matern Model I
pppmatching.object Class of Point Matchings
fryplot Fry Plot of Point Pattern
opening Morphological Opening
rpoispp Generate Poisson Point Pattern
nnwhich Nearest neighbour
thomas.estK Fit the Thomas Point Process by Minimum Contrast
pixellate Convert Point Pattern to Pixel Image
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
rthin Random Thinning
rotate.owin Rotate a Window
iplot Point and Click Interface for Displaying a Point Pattern
is.marked.ppm Test Whether A Point Process Model is Marked
nbfires Point Patterns of New Brunswick Forest Fires
rjitter Random Perturbation of a Point Pattern
rMosaicSet Mosaic Random Set
print.quad Print a Quadrature Scheme
runifdisc Generate N Uniform Random Points in a Disc
rotate.ppp Rotate a Point Pattern
quantile.im Sample Quantiles of Pixel Image
reduced.sample Reduced Sample Estimator using Histogram Data
disc Circular Window
quadscheme Generate a Quadrature Scheme from a Point Pattern
setmarks Set or Reset the Marks in a Point Pattern
rshift.ppp Randomly Shift a Point Pattern
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rmh.ppm Simulate from a Fitted Point Process Model
plot.hyperframe Plot Entries in a Hyperframe
pairdist.default Pairwise distances
ord.family Ord Interaction Process Family
suffstat Sufficient Statistic of Point Process Model
predict.ppm Prediction from a Fitted Point Process Model
rescale.im Convert Pixel Image to Another Unit of Length
psp Create a Line Segment Pattern
fitin.ppm Extract the Interaction from a Fitted Point Process Model
infline Infinite Straight Lines
rescue.rectangle Convert Window Back To Rectangle
letterR Window in Shape of Letter R
pairdist.psp Pairwise distances between line segments
plot.tess Plot a tessellation
rMaternII Simulate Matern Model II
summary.splitppp Summary of a Split Point Pattern
shift.owin Apply Vector Translation To Window
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
print.ppm Print a Fitted Point Process Model
plot.ppp plot a Spatial Point Pattern
lurking Lurking variable plot
psp.object Class of Line Segment Patterns
compatible.fv Test Whether Two Function Objects Are Compatible
owin.object Class owin
persp.im Perspective Plot of Pixel Image
rSSI Simulate Simple Sequential Inhibition
plot.kppm Plot a fitted cluster point process
quadratresample Resample a Point Pattern by Resampling Quadrats
redwoodfull California Redwoods Point Pattern (Entire Dataset)
plot.splitppp Plot a List of Point Patterns
nearestsegment Find Line Segment Nearest to Each Point
multiplicity.ppp Count Multiplicity of Duplicate Points
rescale.owin Convert Window to Another Unit of Length
localK Neighbourhood density function
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
is.im Test Whether An Object Is A Pixel Image
quadrats Divide Region into Quadrats
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
smooth.ppp Spatial smoothing of observations at irregular points
summary.im Summarizing a Pixel Image
model.images Compute Images of Constructed Covariates
pcfcross Multitype pair correlation function
rshift Random Shift
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
update.kppm Update a Fitted Cluster Point Process Model
quad.object Class of Quadrature Schemes
update.ppm Update a Fitted Point Process Model
logLik.ppm Log Likelihood for Poisson Point Process Model
square Square Window
envelope Simulation envelopes of summary function
nndist Nearest neighbour distances
split.im Divide Image Into Sub-images
markcorrint Mark Correlation Integral
selfcrossing.psp Crossing Points in a Line Segment Pattern
pcf.ppp Pair Correlation Function of Point Pattern
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
ppm.object Class of Fitted Point Process Models
residualspaper Data and Code From JRSS Discussion Paper on Residuals
midpoints.psp Midpoints of Line Segment Pattern
setcov Set Covariance of a Window
progressreport Print Progress Reports
simdat Simulated Point Pattern
rotate.psp Rotate a Line Segment Pattern
rshift.splitppp Randomly Shift a List of Point Patterns
shapley Galaxies in the Shapley Supercluster
unique.ppp Extract Unique Points from a Spatial Point Pattern
rmpoint Generate N Random Multitype Points
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
simplify.owin Approximate a Polygon by a Simpler Polygon
shift.im Apply Vector Translation To Pixel Image
rpoislinetess Poisson Line Tessellation
runifpointOnLines Generate N Uniform Random Points On Line Segments
summary.ppm Summarizing a Fitted Point Process Model
rstrat Simulate Stratified Random Point Pattern
mincontrast Method of Minimum Contrast
project2segment Move Point To Nearest Line
unmark Remove Marks
markconnect Mark Connection Function
plot.psp plot a Spatial Line Segment Pattern
split.ppp Divide Point Pattern into Sub-patterns
rStrauss Perfect Simulation of the Strauss Process
tess Create a Tessellation
pairwise.family Pairwise Interaction Process Family
runifpoint Generate N Uniform Random Points
reach Interaction Distance of a Point Process
shift Apply Vector Translation
ripras Estimate window from points alone
perimeter Perimeter Length of Window
vertices Vertices of a Window
rpoint Generate N Random Points
spokes Spokes pattern of dummy points
superimpose Superimpose Several Point Patterns
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
unitname Name for Unit of Length
shift.ppp Apply Vector Translation To Point Pattern
rsyst Simulate systematic random point pattern
summary.psp Summary of a Line Segment Pattern Dataset
pixelquad Quadrature Scheme Based on Pixel Grid
urkiola Urkiola Woods Point Pattern
is.marked.ppp Test Whether A Point Pattern is Marked
stieltjes Compute Integral of Function Against Cumulative Distribution
rescale Convert dataset to another unit of length
summary.ppp Summary of a Point Pattern Dataset
plot.fv Plot Function Values
rescale.psp Convert Line Segment Pattern to Another Unit of Length
tiles Extract List of Tiles in a Tessellation
profilepl Profile Maximum Pseudolikelihood
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
summary.listof Summary of a List of Things
scanpp Read Point Pattern From Data File
summary.quad Summarizing a Quadrature Scheme
redwood California Redwoods Point Pattern (Ripley's Subset)
raster.x Cartesian Coordinates for a Pixel Raster
swedishpines Swedish Pines Point Pattern
shift.psp Apply Vector Translation To Line Segment Pattern
spruces Spruces Point Pattern
trim.rectangle Cut margins from rectangle
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
union.quad Union of Data and Dummy Points
superimposePSP Superimpose Several Line Segment Patterns
Jdot Multitype J Function (i-to-any)
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
coef.ppm Coefficients of Fitted Point Process Model
affine.psp Apply Affine Transformation To Line Segment Pattern
default.dummy Generate a Default Pattern of Dummy Points
distmap.ppp Distance Map of Point Pattern
kaplan.meier Kaplan-Meier Estimator using Histogram Data
lansing Lansing Woods Point Pattern
lut Lookup Tables
matchingdist Distance for a Point Pattern Matching
model.matrix.ppm Extract Design Matrix from Point Process Model
summary.owin Summary of a Spatial Window
nncross Nearest Neighbours Between Two Patterns
simulate.ppm Simulate a Fitted Gibbs Point Process Model
Jcross Multitype J Function (i-to-j)
Lcross Multitype L-function (cross-type)
chop.tess Subdivide a Window or Tessellation using a Set of Lines
data.ppm Extract Original Data from a Fitted Point Process Model
contour.im Contour plot of pixel image
distmap.owin Distance Map of Window
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
im Create a Pixel Image Object
plot.colourmap Plot a Colour Map
is.ppm Test Whether An Object Is A Fitted Point Process Model
pcf.fasp Pair Correlation Function obtained from array of K functions
rcell Simulate Baddeley-Silverman Cell Process
rMatClust Simulate Matern Cluster Process
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
with.fv Evaluate an Expression in a Function Table
spatstat.options Internal Options in Spatstat Package
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Date 27 July 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2009-07-28 01:07:11 UTC; adrian
Repository CRAN
Date/Publication 2009-07-27 19:54:06

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