spatstat v1.17-2

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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
BadGey Hybrid Geyer Point Process Model
chop.tess Subdivide a Window or Tessellation using a Set of Lines
clickpoly Interactively Define a Polygon
bramblecanes Hutchings' Bramble Canes data
crossdist.ppp Pairwise distances between two different point patterns
dirichlet Dirichlet Tessellation of Point Pattern
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
distmap.psp Distance Map of Line Segment Pattern
as.box3 Convert Data to Three-Dimensional Box
border Border Region of a Window
Extract.fv Extract Subset of Function Values
clip.infline Intersect Infinite Straight Lines with a Window
Extract.im Extract Subset of Image
Ldot Multitype L-function (i-to-any)
MultiStrauss The Multitype Strauss Point Process Model
eroded.areas Areas of Morphological Erosions
eval.fv Evaluate Expression Involving Functions
fasp.object Function Arrays for Spatial Patterns
Lest L-function
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
ewcdf Weighted Empirical Cumulative Distribution Function
crossdist Pairwise distances
Kmeasure Reduced Second Moment Measure
as.matrix.im Convert Pixel Image to Matrix
Extract.splitppp Extract or Replace Sub-Patterns
Ldot.inhom Inhomogeneous Multitype L Dot Function
Gmulti Marked Nearest Neighbour Distance Function
Softcore The Soft Core Point Process Model
applynbd Apply Function to Every Neighbourhood in a Point Pattern
affine.ppp Apply Affine Transformation To Point Pattern
AreaInter The Area Interaction Point Process Model
Kest.fft K-function using FFT
affine.psp Apply Affine Transformation To Line Segment Pattern
compatible.fv Test Whether Two Function Objects Are Compatible
as.polygonal Convert a Window to a Polygonal Window
betacells Beta Ganglion Cells in Cat Retina
convexhull Convex Hull
envelope Simulation envelopes of summary function
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
affine Apply Affine Transformation
angles.psp Orientation Angles of Line Segments
G3est Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
Extract.quad Subset of Quadrature Scheme
gpc2owin Convert Polygonal Region into Different Format
as.hyperframe Convert Data to Hyperframe
markconnect Mark Connection Function
K3est K-function of a Three-Dimensional Point Pattern
Iest Estimate the I-function
area.owin Area of a Window
ants Harkness-Isham ants' nests data
StraussHard The Strauss / Hard Core Point Process Model
markvario Mark Variogram
compatible.im Test Whether Two Pixel Images Are Compatible
methods.ppx Methods for Multidimensional Space-Time Point Patterns
is.convex Test Whether a Window is Convex
areaLoss Difference of Disc Areas
complement.owin Take Complement of a Window
nbfires Point Patterns of New Brunswick Forest Fires
bdist.pixels Distance to Boundary of Window
Emark Diagnostics for random marking
demopat Artificial Data Point Pattern
bdist.points Distance to Boundary of Window
DiggleGratton Diggle-Gratton model
Extract.ppp Extract or Replace Subset of Point Pattern
Kcross.inhom Inhomogeneous Cross K Function
Lcross Multitype L-function (cross-type)
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
Jmulti Marked J Function
Extract.listof Extract or Replace Subset of a List of Things
as.tess Convert Data To Tessellation
dilation Morphological Dilation
Lcross.inhom Inhomogeneous Cross Type L Function
Hest Spherical Contact Distribution Function
Fest Estimate the empty space function F
Replace.im Reset Values in Subset of Image
Jcross Multitype J Function (i-to-j)
pcf Pair Correlation Function
coords Extract Coordinates of a Spatial or Spatiotemporal Point Pattern
expand.owin Expand Window By Factor
plot.ppp plot a Spatial Point Pattern
F3est Empty Space Function of a Three-Dimensional Point Pattern
Jest Estimate the J-function
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
print.im Print Brief Details of an Image
Kdot Multitype K Function (i-to-any)
anemones Beadlet Anemones Data
as.ppp Convert Data To Class ppp
convexhull.xy Convex Hull of Points
Geyer Geyer's Saturation Point Process Model
inside.owin Test Whether Points Are Inside A Window
amacrine Hughes' Amacrine Cell Data
opening Morphological Opening
harmonic Basis for Harmonic Functions
Strauss The Strauss Point Process Model
Linhom L-function
Saturated Saturated Pairwise Interaction model
areaGain Difference of Disc Areas
as.hyperframe.ppx Extract coordinates and marks of multidimensional point pattern
colourmap Colour Lookup Tables
clarkevans Clark and Evans Aggregation Index
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
is.marked.ppm Test Whether A Point Process Model is Marked
as.data.frame.ppp Coerce Point Pattern to a Data Frame
compatible.fasp Test Whether Two Function Arrays Are Compatible
as.im Convert to Pixel Image
levelset Level Set of a Pixel Image
erosion Morphological Erosion
default.dummy Generate a Default Pattern of Dummy Points
Kmulti Marked K-Function
identify.ppp Identify Points in a Point Pattern
LennardJones The Lennard-Jones Potential
Extract.psp Extract Subset of Line Segment Pattern
bronzefilter Bronze gradient filter data
intersect.tess Intersection of Two Tessellations
hist.im Histogram of Pixel Values in an Image
blur Apply Gaussian Blur to a Pixel Image
markcorr Mark Correlation Function
Gest Nearest Neighbour Distance Function G
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
is.multitype.ppp Test Whether A Point Pattern is Multitype
bounding.box Bounding Box of a Window or Point Pattern
Poisson Poisson Point Process Model
quadrats Divide Region into Quadrats
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
is.ppp Test Whether An Object Is A Point Pattern
copper Berman-Huntington points and lines data
contour.im Contour plot of pixel image
model.matrix.ppm Extract Design Matrix from Point Process Model
box3 Three-Dimensional Box
is.ppm Test Whether An Object Is A Fitted Point Process Model
diameter Diameter of a Window
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
hamster Aherne's hamster tumour data
persp.im Perspective Plot of Pixel Image
as.rectangle Window Frame
shift.ppp Apply Vector Translation To Point Pattern
concatxy Concatenate x,y Coordinate Vectors
chorley Chorley-Ribble Cancer Data
Kinhom Inhomogeneous K-function
Jdot Multitype J Function (i-to-any)
miplot Morishita Index Plot
rescale.psp Convert Line Segment Pattern to Another Unit of Length
distfun Distance Map as a Function
append.psp Combine Two Line Segment Patterns
eval.im Evaluate Expression Involving Pixel Images
istat Point and Click Interface for Exploratory Analysis of Point Pattern
plot.im Plot a Pixel Image
letterR Window in Shape of Letter R
gridweights Compute Quadrature Weights Based on Grid Counts
hyperframe Hyper Data Frame
Kcross Multitype K Function (Cross-type)
plot.psp plot a Spatial Line Segment Pattern
rStrauss Perfect Simulation of the Strauss Process
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
nztrees New Zealand Trees Point Pattern
Extract.tess Extract or Replace Subset of Tessellation
endpoints.psp Endpoints of Line Segment Pattern
eval.fasp Evaluate Expression Involving Function Arrays
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
discpartarea Area of Part of Disc
clickppp Interactively Add Points
Kdot.inhom Inhomogeneous Multitype K Dot Function
redwoodfull California Redwoods Point Pattern (Entire Dataset)
midpoints.psp Midpoints of Line Segment Pattern
by.im Apply Function to Image Broken Down by Factor
delaunay Delaunay Triangulation of Point Pattern
update.ppm Update a Fitted Point Process Model
disc Circular Window
is.multitype.ppm Test Whether A Point Process Model is Multitype
crossing.psp Crossing Points of Two Line Segment Patterns
anova.ppm ANOVA for Fitted Point Process Models
pcfcross Multitype pair correlation function
Pairwise Generic Pairwise Interaction model
owin.object Class owin
ponderosa Ponderosa Pine Tree Point Pattern
closing Morphological Closing
as.owin Convert Data To Class owin
spatstat-deprecated Deprecated spatstat functions
crossdist.default Pairwise distances between two different sets of points
distmap.ppp Distance Map of Point Pattern
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
ppp.object Class of Point Patterns
eem Exponential Energy Marks
coef.ppm Coefficients of Fitted Point Process Model
discretise Safely Convert Point Pattern Window to Binary Mask
dilated.areas Areas of Morphological Dilations
stieltjes Compute Integral of Function Against Cumulative Distribution
bei Tropical rain forest trees
is.empty Test Whether An Object Is Empty
finpines Pine saplings in Finland.
is.multitype Test whether Object is Multitype
bounding.box.xy Convex Hull of Points
multiplicity.ppp Count Multiplicity of Duplicate Points
summary.im Summarizing a Pixel Image
markcorrint Mark Correlation Integral
data.ppm Extract Original Data from a Fitted Point Process Model
incircle Find Largest Circle Inside Window
fitin.ppm Extract the Interaction from a Fitted Point Process Model
thomas.estK Fit the Thomas Point Process by Minimum Contrast
pairdist Pairwise distances
pp3 Three Dimensional Point Pattern
longleaf Longleaf Pines Point Pattern
inforder.family Infinite Order Interaction Family
plot.kppm Plot a fitted cluster point process
plot.owin Plot a Spatial Window
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
nncross Nearest Neighbours Between Two Patterns
im.object Class of Images
bermantest Berman's Tests for Point Process Model
pairsat.family Saturated Pairwise Interaction Point Process Family
interp.im Interpolate a Pixel Image
rsyst Simulate systematic random point pattern
corners Corners of a rectangle
rotate.owin Rotate a Window
cut.ppp Classify Points in a Point Pattern
distmap Distance Map
nearestsegment Find Line Segment Nearest to Each Point
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
plot.fasp Plot a Function Array
spruces Spruces Point Pattern
print.quad Print a Quadrature Scheme
plot.plotppm Plot a plotppm Object Created by plot.ppm
rpoisline Generate Poisson Random Line Process
perimeter Perimeter Length of Window
iplot Point and Click Interface for Displaying a Point Pattern
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
rNeymanScott Simulate Neyman-Scott Process
quadscheme Generate a Quadrature Scheme from a Point Pattern
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
matchingdist Distance for a Point Pattern Matching
predict.ppm Prediction from a Fitted Point Process Model
tess Create a Tessellation
lansing Lansing Woods Point Pattern
cut.im Convert Pixel Image from Numeric to Factor
gridcentres Rectangular grid of points
im Create a Pixel Image Object
fv.object Data Frames of Function Values
swedishpines Swedish Pines Point Pattern
quantile.im Sample Quantiles of Pixel Image
residuals.ppm Residuals for Fitted Point Process Model
rMaternII Simulate Matern Model II
density.ppp Kernel Smoothed Intensity of Point Pattern
union.quad Union of Data and Dummy Points
shift.im Apply Vector Translation To Pixel Image
simplify.owin Approximate a Polygon by a Simpler Polygon
redwood California Redwoods Point Pattern (Ripley's Subset)
fryplot Fry Plot of Point Pattern
is.marked Test Whether Marks Are Present
distmap.owin Distance Map of Window
plot.bermantest Plot Result of Berman Test
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
mincontrast Method of Minimum Contrast
infline Infinite Straight Lines
summary.listof Summary of a List of Things
humberside Humberside Data on Childhood Leukaemia and Lymphoma
cells Biological Cells Point Pattern
lut Lookup Tables
localK Neighbourhood density function
kppm Fit cluster point process model
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
owin Create a Window
spatstat-internal Internal spatstat functions
pairdist.psp Pairwise distances between line segments
is.subset.owin Determine Whether One Window is Contained In Another
intersect.owin Intersection, Union or Set Subtraction of Two Windows
japanesepines Japanese Pines Point Pattern
density.psp Kernel Smoothing of Line Segment Pattern
progressreport Print Progress Reports
is.im Test Whether An Object Is A Pixel Image
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
psp.object Class of Line Segment Patterns
rshift.psp Randomly Shift a Line Segment Pattern
lengths.psp Lengths of Line Segments
project2segment Move Point To Nearest Line
methods.box3 Methods for Three-Dimensional Box
quad.object Class of Quadrature Schemes
plot.listof Plot a List of Things
shift.owin Apply Vector Translation To Window
tiles Extract List of Tiles in a Tessellation
plot.fv Plot Function Values
smooth.ppp Spatial smoothing of observations at irregular points
methods.pp3 Methods for three-dimensional point patterns
print.ppm Print a Fitted Point Process Model
raster.x Cartesian Coordinates for a Pixel Raster
rotate.ppp Rotate a Point Pattern
ppm.object Class of Fitted Point Process Models
nearest.raster.point Find Pixel Nearest to a Given Point
rescale.ppp Convert Point Pattern to Another Unit of Length
rescale Convert dataset to another unit of length
pairdist.ppp Pairwise distances
urkiola Urkiola Woods Point Pattern
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
quadratcount Quadrat counting for a point pattern
rescue.rectangle Convert Window Back To Rectangle
plot.hyperframe Plot Entries in a Hyperframe
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
plot.splitppp Plot a List of Point Patterns
fitted.ppm Fitted Conditional Intensity for Point Process Model
ganglia Beta Ganglion Cells in Cat Retina, Old Version
rGaussPoisson Simulate Gauss-Poisson Process
rmpoint Generate N Random Multitype Points
heather Diggle's Heather Data
rpoint Generate N Random Points
square Square Window
rmpoispp Generate Multitype Poisson Point Pattern
runifpointOnLines Generate N Uniform Random Points On Line Segments
kaplan.meier Kaplan-Meier Estimator using Histogram Data
is.owin Test Whether An Object Is A Window
logLik.ppm Log Likelihood for Poisson Point Process Model
mean.im Mean, Median and Range of Pixel Values in an Image
shift Apply Vector Translation
shapley Galaxies in the Shapley Supercluster
predict.kppm Prediction from a Fitted Cluster Point Process Model
suffstat Sufficient Statistic of Point Process Model
plot.quad plot a Spatial Quadrature Scheme
pixellate.ppp Convert Point Pattern to Pixel Image
murchison Murchison gold deposits
unique.ppp Extract Unique Points from a Spatial Point Pattern
pcf.fv Pair Correlation Function obtained from K Function
pointsOnLines Place Points Evenly Along Specified Lines
print.psp Print Brief Details of a Line Segment Pattern Dataset
rstrat Simulate Stratified Random Point Pattern
spatstat.options Internal Options in Spatstat Package
pairdist.default Pairwise distances
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rcell Simulate Baddeley-Silverman Cell Process
rlinegrid Generate grid of parallel lines with random displacement
nnwhich Nearest neighbour
pppmatching Create a Point Matching
summary.splitppp Summary of a Split Point Pattern
rshift Random Shift
summary.owin Summary of a Spatial Window
profilepl Profile Maximum Pseudolikelihood
summary.ppm Summarizing a Fitted Point Process Model
setcov Set Covariance of a Window
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
pcf.fasp Pair Correlation Function obtained from array of K functions
reach Interaction Distance of a Point Process
pppmatching.object Class of Point Matchings
runifdisc Generate N Uniform Random Points in a Disc
pairwise.family Pairwise Interaction Process Family
rMatClust Simulate Matern Cluster Process
ppx Multidimensional Space-Time Point Pattern
rpoispp Generate Poisson Point Pattern
rpoislinetess Poisson Line Tessellation
pcf.ppp Pair Correlation Function of Point Pattern
rMosaicSet Mosaic Random Set
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
ppp Create a Point Pattern
superimpose Superimpose Several Point Patterns
residualspaper Data and Code From JRSS Discussion Paper on Residuals
pixellate Convert Spatial Object to Pixel Image
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
unitname Name for Unit of Length
rSSI Simulate Simple Sequential Inhibition
rmh.ppm Simulate from a Fitted Point Process Model
OrdThresh Ord's Interaction model
ord.family Ord Interaction Process Family
psp Create a Line Segment Pattern
pixelquad Quadrature Scheme Based on Pixel Grid
plot.colourmap Plot a Colour Map
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
plot.ppm plot a Fitted Point Process Model
rshift.ppp Randomly Shift a Point Pattern
scanpp Read Point Pattern From Data File
summary.psp Summary of a Line Segment Pattern Dataset
rjitter Random Perturbation of a Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
rshift.splitppp Randomly Shift a List of Point Patterns
rthin Random Thinning
rThomas Simulate Thomas Process
as.mask Pixel Image Approximation of a Window
rotate Rotate
simulate.ppm Simulate a Fitted Gibbs Point Process Model
ppm Fit Point Process Model to Data
as.psp Convert Data To Class psp
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
spatstat-package The Spatstat Package
connected Connected components of an image or window
rMaternI Simulate Matern Model I
spokes Spokes pattern of dummy points
reduced.sample Reduced Sample Estimator using Histogram Data
with.fv Evaluate an Expression in a Function Table
vertices Vertices of a Window
shift.psp Apply Vector Translation To Line Segment Pattern
rlabel Random Re-Labelling of Point Pattern
update.kppm Update a Fitted Cluster Point Process Model
with.hyperframe Evaluate an Expression in Each Row of a Hyperframe
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
trim.rectangle Cut margins from rectangle
rpoispp3 Generate Poisson Point Pattern in Three Dimensions
crossdist.psp Pairwise distances between two different line segment patterns
simulate.kppm Simulate a Fitted Cluster Point Process Model
simdat Simulated Point Pattern
split.ppp Divide Point Pattern into Sub-patterns
summary.quad Summarizing a Quadrature Scheme
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
diameter.box3 Geometrical Calculations for Three-Dimensional Box
runifpoint Generate N Uniform Random Points
model.images Compute Images of Constructed Covariates
superimposePSP Superimpose Several Line Segment Patterns
lurking Lurking variable plot
nndist Nearest neighbour distances
nndist.psp Nearest neighbour distances between line segments
plot.pp3 Plot a three-dimensional point pattern
pppdist Distance Between Two Point Patterns
print.owin Print Brief Details of a Spatial Window
quadratresample Resample a Point Pattern by Resampling Quadrats
rescale.im Convert Pixel Image to Another Unit of Length
ripras Estimate window from points alone
rotate.psp Rotate a Line Segment Pattern
Extract.fasp Extract Subset of Function Array
Ord Generic Ord Interaction model
runifpoint3 Generate N Uniform Random Points in Three Dimensions
setmarks Set or Reset the Marks in a Point Pattern
unmark Remove Marks
Kest K-function
allstats Calculate four standard summary functions of a point pattern.
affine.owin Apply Affine Transformation To Window
bdist.tiles Distance to Boundary of Window
centroid.owin Centroid of a window
deltametric Delta Metric
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
is.marked.ppp Test Whether A Point Pattern is Marked
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
pixellate.owin Convert Window to Pixel Image
plot.tess Plot a tessellation
print.ppp Print Brief Details of a Point Pattern Dataset
rMosaicField Mosaic Random Field
rescale.owin Convert Window to Another Unit of Length
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
split.im Divide Image Into Sub-images
summary.ppp Summary of a Point Pattern Dataset
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Date 10 november 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2009-11-10 21:02:06 UTC; adrian
Repository CRAN
Date/Publication 2009-11-10 10:15:26

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