spatstat v1.16-2

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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. 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
convexhull Convex Hull
crossdist.ppp Pairwise distances between two different point patterns
distmap Distance Map
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
im Create a Pixel Image Object
print.quad Print a Quadrature Scheme
pixellate.owin Convert Window to Pixel Image
disc Circular Window
rMaternII Simulate Matern Model II
density.ppp Kernel Smoothed Intensity of Point Pattern
copper Berman-Huntington points and lines data
logLik.ppm Log Likelihood for Poisson Point Process Model
is.owin Test Whether An Object Is A Window
intersect.owin Intersection or Union of Two Windows
markconnect Mark Connection Function
crossdist Pairwise distances
pcf.fasp Pair Correlation Function obtained from array of K functions
shift.owin Apply Vector Translation To Window
pairdist.default Pairwise distances
matchingdist Distance for a Point Pattern Matching
summary.listof Summary of a List of Things
dilated.areas Areas of Morphological Dilations
lansing Lansing Woods Point Pattern
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
nndist.psp Nearest neighbour distances between line segments
nearestsegment Find Line Segment Nearest to Each Point
is.subset.owin Determine Whether One Window is Contained In Another
rescale.owin Convert Window to Another Unit of Length
nncross Nearest Neighbours Between Two Patterns
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
suffstat Sufficient Statistic of Point Process Model
kaplan.meier Kaplan-Meier Estimator using Histogram Data
plot.im Plot a Pixel Image
opening Morphological Opening
ppp.object Class of Point Patterns
is.marked.ppp Test Whether A Point Pattern is Marked
plot.quad plot a Spatial Quadrature Scheme
tess Create a Tessellation
markcorr Mark Correlation Function
rescale.im Convert Pixel Image to Another Unit of Length
concatxy Concatenate x,y Coordinate Vectors
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
plot.psp plot a Spatial Line Segment Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
ppp Create a Point Pattern
im.object Class of Images
pcf.ppp Pair Correlation Function of Point Pattern
residualspaper Data and Code From JRSS Discussion Paper on Residuals
nearest.raster.point Find Pixel Nearest to a Given Point
pcfcross Multitype pair correlation function
quadratresample Resample a Point Pattern by Resampling Quadrats
rescale.psp Convert Line Segment Pattern to Another Unit of Length
is.ppm Test Whether An Object Is A Fitted Point Process Model
is.multitype.ppm Test Whether A Point Process Model is Multitype
rMosaicField Mosaic Random Field
rSSI Simulate Simple Sequential Inhibition
crossing.psp Crossing Points of Two Line Segment Patterns
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
project2segment Move Point To Nearest Line
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
lut Lookup Tables
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
shift.psp Apply Vector Translation To Line Segment Pattern
is.convex Test Whether a Window is Convex
nndist Nearest neighbour distances
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
rMosaicSet Mosaic Random Set
convexhull.xy Convex Hull of Points
istat Point and Click Interface for Exploratory Analysis of Point Pattern
rotate.ppp Rotate a Point Pattern
markcorrint Mark Correlation Integral
owin.object Class owin
compatible.fasp Test Whether Two Function Arrays Are Compatible
vertices Vertices of a Window
kppm Fit cluster point process model
delaunay Delaunay Triangulation of Point Pattern
clip.infline Intersect Infinite Straight Lines with a Window
cut.ppp Classify Points in a Point Pattern
compatible.fv Test Whether Two Function Objects Are Compatible
pcf.fv Pair Correlation Function obtained from K Function
reach Interaction Distance of a Point Process
is.empty Test Whether An Object Is Empty
redwoodfull California Redwoods Point Pattern (Entire Dataset)
owin Create a Window
density.psp Kernel Smoothing of Line Segment Pattern
superimposePSP Superimpose Several Line Segment Patterns
plot.splitppp Plot a List of Point Patterns
predict.kppm Prediction from a Fitted Cluster Point Process Model
is.multitype Test whether Object is Multitype
plot.kppm Plot a fitted cluster point process
is.im Test Whether An Object Is A Pixel Image
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
plot.fasp Plot a Function Array
colourmap Colour Lookup Tables
plot.fv Plot Function Values
complement.owin Take Complement of a Window
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rGaussPoisson Simulate Gauss-Poisson Process
plot.ppp plot a Spatial Point Pattern
rescale.ppp Convert Point Pattern to Another Unit of Length
psp.object Class of Line Segment Patterns
is.marked Test Whether Marks Are Present
envelope Simulation envelopes of summary function
miplot Morishita Index Plot
quadscheme Generate a Quadrature Scheme from a Point Pattern
rlabel Random Re-Labelling of Point Pattern
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
japanesepines Japanese Pines Point Pattern
rmpoispp Generate Multitype Poisson Point Pattern
closing Morphological Closing
runifpoint Generate N Uniform Random Points
rthin Random Thinning
swedishpines Swedish Pines Point Pattern
plot.bermantest Plot Result of Berman Test
ppm.object Class of Fitted Point Process Models
compatible.im Test Whether Two Pixel Images Are Compatible
inside.owin Test Whether Points Are Inside A Window
cut.im Convert Pixel Image from Numeric to Factor
pcf Pair Correlation Function
print.owin Print Brief Details of a Spatial Window
redwood California Redwoods Point Pattern (Ripley's Subset)
is.ppp Test Whether An Object Is A Point Pattern
quantile.im Sample Quantiles of Pixel Image
progressreport Print Progress Reports
pppmatching Create a Point Matching
rescale Convert dataset to another unit of length
demopat Artificial Data Point Pattern
levelset Level Set of a Pixel Image
simulate.kppm Simulate a Fitted Cluster Point Process Model
lengths.psp Lengths of Line Segments
model.matrix.ppm Extract Design Matrix from Point Process Model
pixellate Convert Spatial Object to Pixel Image
intersect.tess Intersection of Two Tessellations
inforder.family Infinite Order Interaction Family
mincontrast Method of Minimum Contrast
iplot Point and Click Interface for Displaying a Point Pattern
pixellate.ppp Convert Point Pattern to Pixel Image
rjitter Random Perturbation of a Point Pattern
infline Infinite Straight Lines
plot.tess Plot a tessellation
rotate.owin Rotate a Window
pairdist.psp Pairwise distances between line segments
rmh.ppm Simulate from a Fitted Point Process Model
simplify.owin Approximate a Polygon by a Simpler Polygon
plot.plotppm Plot a plotppm Object Created by plot.ppm
rshift.ppp Randomly Shift a Point Pattern
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
nbfires Point Patterns of New Brunswick Forest Fires
rshift.splitppp Randomly Shift a List of Point Patterns
persp.im Perspective Plot of Pixel Image
rlinegrid Generate grid of parallel lines with random displacement
dilation Morphological Dilation
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
ripras Estimate window from points alone
profilepl Profile Maximum Pseudolikelihood
split.im Divide Image Into Sub-images
pppmatching.object Class of Point Matchings
rotate.psp Rotate a Line Segment Pattern
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rMaternI Simulate Matern Model I
discpartarea Area of Part of Disc
scanpp Read Point Pattern From Data File
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
pixelquad Quadrature Scheme Based on Pixel Grid
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
ppm Fit Point Process Model to Data
print.im Print Brief Details of an Image
nztrees New Zealand Trees Point Pattern
plot.listof Plot a List of Things
setcov Set Covariance of a Window
spatstat-internal Internal spatstat functions
lurking Lurking variable plot
shift Apply Vector Translation
interp.im Interpolate a Pixel Image
ord.family Ord Interaction Process Family
plot.ppm plot a Fitted Point Process Model
summary.splitppp Summary of a Split Point Pattern
rshift Random Shift
spruces Spruces Point Pattern
psp Create a Line Segment Pattern
rNeymanScott Simulate Neyman-Scott Process
rpoint Generate N Random Points
rstrat Simulate Stratified Random Point Pattern
rMatClust Simulate Matern Cluster Process
split.ppp Divide Point Pattern into Sub-patterns
rpoispp Generate Poisson Point Pattern
discretise Safely Convert Point Pattern Window to Binary Mask
rshift.psp Randomly Shift a Line Segment Pattern
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
perimeter Perimeter Length of Window
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
is.marked.ppm Test Whether A Point Process Model is Marked
summary.quad Summarizing a Quadrature Scheme
unique.ppp Extract Unique Points from a Spatial Point Pattern
incircle Find Largest Circle Inside Window
with.fv Evaluate an Expression in a Function Table
pppdist Distance Between Two Point Patterns
pairdist Pairwise distances
ponderosa Ponderosa Pine Tree Point Pattern
union.quad Union of Data and Dummy Points
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
tiles Extract List of Tiles in a Tessellation
update.kppm Update a Fitted Cluster Point Process Model
spokes Spokes pattern of dummy points
summary.owin Summary of a Spatial Window
superimpose Superimpose Several Point Patterns
shapley Galaxies in the Shapley Supercluster
plot.owin Plot a Spatial Window
model.images Compute Images of Constructed Covariates
summary.psp Summary of a Line Segment Pattern Dataset
raster.x Cartesian Coordinates for a Pixel Raster
unmark Remove Marks
midpoints.psp Midpoints of Line Segment Pattern
reduced.sample Reduced Sample Estimator using Histogram Data
rmpoint Generate N Random Multitype Points
runifdisc Generate N Uniform Random Points in a Disc
rStrauss Perfect Simulation of the Strauss Process
localK Neighbourhood density function
murchison Murchison gold deposits
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
simdat Simulated Point Pattern
shift.ppp Apply Vector Translation To Point Pattern
nnwhich Nearest neighbour
urkiola Urkiola Woods Point Pattern
runifpointOnLines Generate N Uniform Random Points On Line Segments
setmarks Set or Reset the Marks in a Point Pattern
affine.psp Apply Affine Transformation To Line Segment Pattern
rThomas Simulate Thomas Process
blur Apply Gaussian Blur to a Pixel Image
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
rescue.rectangle Convert Window Back To Rectangle
shift.im Apply Vector Translation To Pixel Image
rpoisline Generate Poisson Random Line Process
Lcross Multitype L-function (cross-type)
pairsat.family Saturated Pairwise Interaction Point Process Family
spatstat.options Internal Options in Spatstat Package
square Square Window
update.ppm Update a Fitted Point Process Model
print.ppm Print a Fitted Point Process Model
Extract.splitppp Extract or Replace Sub-Patterns
Kcross.inhom Inhomogeneous Cross K Function
Strauss The Strauss Point Process Model
unitname Name for Unit of Length
simulate.ppm Simulate a Fitted Gibbs Point Process Model
print.psp Print Brief Details of a Line Segment Pattern Dataset
applynbd Apply Function to Every Neighbourhood in a Point Pattern
spatstat-package The Spatstat Package
summary.im Summarizing a Pixel Image
bei Tropical rain forest trees
affine.ppp Apply Affine Transformation To Point Pattern
rpoislinetess Poisson Line Tessellation
selfcrossing.psp Crossing Points in a Line Segment Pattern
finpines Pine saplings in Finland.
crossdist.default Pairwise distances between two different sets of points
as.im Convert to Pixel Image
smooth.ppp Spatial smoothing of observations at irregular points
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
plot.colourmap Plot a Colour Map
Pairwise Generic Pairwise Interaction model
area.owin Area of a Window
letterR Window in Shape of Letter R
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
Replace.im Reset Values in Subset of Image
Linhom L-function
rotate Rotate
Saturated Saturated Pairwise Interaction model
as.data.frame.ppp Coerce Point Pattern to a Data Frame
StraussHard The Strauss / Hard Core Point Process Model
pairdist.ppp Pairwise distances
eval.fv Evaluate Expression Involving Functions
multiplicity.ppp Count Multiplicity of Duplicate Points
Kdot Multitype K Function (i-to-any)
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
stieltjes Compute Integral of Function Against Cumulative Distribution
gridweights Compute Quadrature Weights Based on Grid Counts
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
Emark Diagnostics for random marking
Kmeasure Reduced Second Moment Measure
LennardJones The Lennard-Jones Potential
MultiStrauss The Multitype Strauss Point Process Model
quadrats Divide Region into Quadrats
mean.im Mean, Median and Range of Pixel Values in an Image
connected Connected components of an image or window
affine.owin Apply Affine Transformation To Window
fitin.ppm Extract the Interaction from a Fitted Point Process Model
eval.fasp Evaluate Expression Involving Function Arrays
ants Harkness-Isham ants' nests data
ganglia Beta Ganglion Cells in Cat Retina, Old Version
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
residuals.ppm Residuals for Fitted Point Process Model
humberside Humberside Data on Childhood Leukaemia and Lymphoma
is.multitype.ppp Test Whether A Point Pattern is Multitype
as.matrix.im Convert Pixel Image to Matrix
Kest K-function
as.owin Convert Data To Class owin
as.psp Convert Data To Class psp
rcell Simulate Baddeley-Silverman Cell Process
Iest Estimate the I-function
AreaInter The Area Interaction Point Process Model
hyperframe Hyper Data Frame
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
Extract.psp Extract Subset of Line Segment Pattern
chop.tess Subdivide a Window or Tessellation using a Set of Lines
angles.psp Orientation Angles of Line Segments
allstats Calculate four standard summary functions of a point pattern.
Jmulti Marked J Function
areaLoss Difference of Disc Areas
chorley Chorley-Ribble Cancer Data
Kinhom Inhomogeneous K-function
Kmulti Marked K-Function
distmap.ppp Distance Map of Point Pattern
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
Gmulti Marked Nearest Neighbour Distance Function
bermantest Berman's Tests for Point Process Model
bounding.box Bounding Box of a Window or Point Pattern
Extract.im Extract Subset of Image
bdist.points Distance to Boundary of Window
Gest Nearest Neighbour Distance Function G
DiggleGratton Diggle-Gratton model
bramblecanes Hutchings' Bramble Canes data
Extract.listof Extract or Replace Subset of a List of Things
corners Corners of a rectangle
Jdot Multitype J Function (i-to-any)
fitted.ppm Fitted Conditional Intensity for Point Process Model
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Ldot.inhom Inhomogeneous Multitype L Dot Function
bdist.pixels Distance to Boundary of Window
contour.im Contour plot of pixel image
gridcentres Rectangular grid of points
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
Extract.fasp Extract Subset of Function Array
summary.ppp Summary of a Point Pattern Dataset
identify.ppp Identify Points in a Point Pattern
default.dummy Generate a Default Pattern of Dummy Points
append.psp Combine Two Line Segment Patterns
Extract.ppp Extract or Replace Subset of Point Pattern
fv.object Data Frames of Function Values
Jest Estimate the J-function
Softcore The Soft Core Point Process Model
eem Exponential Energy Marks
cells Biological Cells Point Pattern
crossdist.psp Pairwise distances between two different line segment patterns
distmap.psp Distance Map of Line Segment Pattern
quad.object Class of Quadrature Schemes
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
gpc2owin Convert Polygonal Region into Different Format
fryplot Fry Plot of Point Pattern
Extract.quad Subset of Quadrature Scheme
erosion Morphological Erosion
data.ppm Extract Original Data from a Fitted Point Process Model
Hest Spherical Contact Distribution Function
endpoints.psp Endpoints of Line Segment Pattern
spatstat-deprecated Deprecated spatstat functions
as.polygonal Convert a Window to a Polygonal Window
betacells Beta Ganglion Cells in Cat Retina
Kest.fft K-function using FFT
Kcross Multitype K Function (Cross-type)
heather Diggle's Heather Data
diameter Diameter of a Window
fasp.object Function Arrays for Spatial Patterns
dirichlet Dirichlet Tessellation of Point Pattern
clarkevans Clark and Evans Aggregation Index
Ord Generic Ord Interaction model
Lest L-function
anova.ppm ANOVA for Fitted Point Process Models
amacrine Hughes' Amacrine Cell Data
by.im Apply Function to Image Broken Down by Factor
eroded.areas Areas of Morphological Erosions
hist.im Histogram of Pixel Values in an Image
Extract.fv Extract Subset of Function Values
areaGain Difference of Disc Areas
eval.im Evaluate Expression Involving Pixel Images
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
OrdThresh Ord's Interaction model
Poisson Poisson Point Process Model
Kdot.inhom Inhomogeneous Multitype K Dot Function
anemones Beadlet Anemones Data
Fest Estimate the empty space function F
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
Jcross Multitype J Function (i-to-j)
as.ppp Convert Data To Class ppp
rsyst Simulate systematic random point pattern
affine Apply Affine Transformation
Ldot Multitype L-function (i-to-any)
coef.ppm Coefficients of Fitted Point Process Model
harmonic Basis for Harmonic Functions
expand.owin Expand Window By Factor
ewcdf Weighted Empirical Cumulative Distribution Function
Extract.tess Extract or Replace Subset of Tessellation
BadGey Hybrid Geyer Point Process Model
hamster Aherne's hamster tumour data
clickppp Interactively Add Points
pairwise.family Pairwise Interaction Process Family
plot.hyperframe Plot Entries in a Hyperframe
print.ppp Print Brief Details of a Point Pattern Dataset
pointsOnLines Place Points Evenly Along Specified Lines
predict.ppm Prediction from a Fitted Point Process Model
longleaf Longleaf Pines Point Pattern
quadratcount Quadrat counting for a point pattern
trim.rectangle Cut margins from rectangle
thomas.estK Fit the Thomas Point Process by Minimum Contrast
markvario Mark Variogram
Geyer Geyer's Saturation Point Process Model
bounding.box.xy Convex Hull of Points
as.tess Convert Data To Tessellation
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
Lcross.inhom Inhomogeneous Cross Type L Function
centroid.owin Centroid of a window
as.rectangle Window Frame
clickpoly Interactively Define a Polygon
distmap.owin Distance Map of Window
as.mask Pixel Image Approximation of a Window
summary.ppm Summarizing a Fitted Point Process Model
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Date 22 August 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2009-08-23 22:41:44 UTC; adrian
Repository CRAN
Date/Publication 2009-08-23 15:40:20

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