spatstat v1.17-4

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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
AreaInter The Area Interaction Point Process Model
Emark Diagnostics for random marking
Extract.listof Extract or Replace Subset of a List of Things
Extract.fv Extract Subset of Function Values
Extract.fasp Extract Subset of Function Array
Extract.im Extract Subset of Image
Kcross.inhom Inhomogeneous Cross K Function
DiggleGratton Diggle-Gratton model
Extract.quad Subset of Quadrature Scheme
bdist.pixels Distance to Boundary of Window
Kdot Multitype K Function (i-to-any)
Extract.psp Extract Subset of Line Segment Pattern
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
angles.psp Orientation Angles of Line Segments
Fest Estimate the empty space function F
F3est Empty Space Function of a Three-Dimensional Point Pattern
Extract.ppp Extract or Replace Subset of Point Pattern
Kdot.inhom Inhomogeneous Multitype K Dot Function
clarkevans Clark and Evans Aggregation Index
clip.infline Intersect Infinite Straight Lines with a Window
as.im Convert to Pixel Image
ants Harkness-Isham ants' nests data
affine.ppp Apply Affine Transformation To Point Pattern
concatxy Concatenate x,y Coordinate Vectors
affine.owin Apply Affine Transformation To Window
Extract.splitppp Extract or Replace Sub-Patterns
StraussHard The Strauss / Hard Core Point Process Model
anova.ppm ANOVA for Fitted Point Process Models
closing Morphological Closing
Ldot.inhom Inhomogeneous Multitype L Dot Function
Jmulti Marked J Function
as.rectangle Window Frame
Jdot Multitype J Function (i-to-any)
Kcross Multitype K Function (Cross-type)
bramblecanes Hutchings' Bramble Canes data
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
area.owin Area of a Window
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
compatible.im Test Whether Two Pixel Images Are Compatible
Jest Estimate the J-function
Softcore The Soft Core Point Process Model
LennardJones The Lennard-Jones Potential
clickpoly Interactively Define a Polygon
OrdThresh Ord's Interaction model
bounding.box Bounding Box of a Window or Point Pattern
connected Connected components of an image or window
Geyer Geyer's Saturation Point Process Model
discpartarea Area of Part of Disc
Lest L-function
K3est K-function of a Three-Dimensional Point Pattern
BadGey Hybrid Geyer Point Process Model
allstats Calculate four standard summary functions of a point pattern.
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
G3est Nearest Neighbour Distance Distribution Function of a Three-Dimensional Point Pattern
MultiStrauss The Multitype Strauss Point Process Model
Gest Nearest Neighbour Distance Function G
affine.psp Apply Affine Transformation To Line Segment Pattern
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
amacrine Hughes' Amacrine Cell Data
Gmulti Marked Nearest Neighbour Distance Function
Linhom L-function
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
Lcross.inhom Inhomogeneous Cross Type L Function
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
areaLoss Difference of Disc Areas
box3 Three-Dimensional Box
Iest Estimate the I-function
Saturated Saturated Pairwise Interaction model
Ord Generic Ord Interaction model
as.mask Pixel Image Approximation of a Window
as.owin Convert Data To Class owin
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
gridweights Compute Quadrature Weights Based on Grid Counts
default.dummy Generate a Default Pattern of Dummy Points
hamster Aherne's hamster tumour data
Kmulti Marked K-Function
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
anemones Beadlet Anemones Data
Kinhom Inhomogeneous K-function
affine Apply Affine Transformation
as.tess Convert Data To Tessellation
convexhull.xy Convex Hull of Points
deltametric Delta Metric
Hest Spherical Contact Distribution Function
Extract.tess Extract or Replace Subset of Tessellation
border Border Region of a Window
cells Biological Cells Point Pattern
areaGain Difference of Disc Areas
as.data.frame.ppp Coerce Point Pattern to a Data Frame
Kmeasure Reduced Second Moment Measure
bdist.tiles Distance to Boundary of Window
dirichlet Dirichlet Tessellation of Point Pattern
diameter.box3 Geometrical Calculations for Three-Dimensional Box
distmap.ppp Distance Map of Point Pattern
Poisson Poisson Point Process Model
bounding.box.xy Convex Hull of Points
crossdist.psp Pairwise distances between two different line segment patterns
bdist.points Distance to Boundary of Window
chorley Chorley-Ribble Cancer Data
centroid.owin Centroid of a window
erosion Morphological Erosion
complement.owin Take Complement of a Window
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
Lcross Multitype L-function (cross-type)
Pairwise Generic Pairwise Interaction model
spatstat-deprecated Deprecated spatstat functions
methods.ppx Methods for Multidimensional Space-Time Point Patterns
Ldot Multitype L-function (i-to-any)
Kest K-function
dilated.areas Areas of Morphological Dilations
coef.ppm Coefficients of Fitted Point Process Model
cut.im Convert Pixel Image from Numeric to Factor
as.box3 Convert Data to Three-Dimensional Box
eval.fasp Evaluate Expression Involving Function Arrays
density.ppp Kernel Smoothed Intensity of Point Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
Jcross Multitype J Function (i-to-j)
fitted.ppm Fitted Conditional Intensity for Point Process Model
ganglia Beta Ganglion Cells in Cat Retina, Old Version
is.convex Test Whether a Window is Convex
corners Corners of a rectangle
disc Circular Window
envelope Simulation envelopes of summary function
betacells Beta Ganglion Cells in Cat Retina
fasp.object Function Arrays for Spatial Patterns
as.hyperframe Convert Data to Hyperframe
gpc2owin Convert Polygonal Region into Different Format
Replace.im Reset Values in Subset of Image
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
Kest.fft K-function using FFT
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
finpines Pine saplings in Finland.
distfun Distance Map as a Function
append.psp Combine Two Line Segment Patterns
coords Extract Coordinates of a Spatial or Spatiotemporal Point Pattern
midpoints.psp Midpoints of Line Segment Pattern
interp.im Interpolate a Pixel Image
mean.im Mean, Median and Range of Pixel Values in an Image
lut Lookup Tables
im.object Class of Images
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
as.ppp Convert Data To Class ppp
is.marked Test Whether Marks Are Present
crossdist.default Pairwise distances between two different sets of points
japanesepines Japanese Pines Point Pattern
pcfcross Multitype pair correlation function (cross-type)
is.ppm Test Whether An Object Is A Fitted Point Process Model
is.owin Test Whether An Object Is A Window
contour.im Contour plot of pixel image
dilation Morphological Dilation
lurking Lurking variable plot
letterR Window in Shape of Letter R
pixellate Convert Spatial Object to Pixel Image
endpoints.psp Endpoints of Line Segment Pattern
as.polygonal Convert a Window to a Polygonal Window
eroded.areas Areas of Morphological Erosions
nndist Nearest neighbour distances
as.hyperframe.ppx Extract coordinates and marks of multidimensional point pattern
markvario Mark Variogram
persp.im Perspective Plot of Pixel Image
opening Morphological Opening
model.matrix.ppm Extract Design Matrix from Point Process Model
rMosaicField Mosaic Random Field
nnwhich Nearest neighbour
blur Apply Gaussian Blur to a Pixel Image
eval.fv Evaluate Expression Involving Functions
Strauss The Strauss Point Process Model
incircle Find Largest Circle Inside Window
runifpoint3 Generate N Uniform Random Points in Three Dimensions
compatible.fv Test Whether Two Function Objects Are Compatible
markcorr Mark Correlation Function
colourmap Colour Lookup Tables
fryplot Fry Plot of Point Pattern
crossdist.ppp Pairwise distances between two different point patterns
convexhull Convex Hull
hyperframe Hyper Data Frame
logLik.ppm Log Likelihood for Poisson Point Process Model
as.psp Convert Data To Class psp
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
spatstat-internal Internal spatstat functions
psp.object Class of Line Segment Patterns
inforder.family Infinite Order Interaction Family
model.images Compute Images of Constructed Covariates
cut.ppp Classify Points in a Point Pattern
plot.hyperframe Plot Entries in a Hyperframe
nndist.psp Nearest neighbour distances between line segments
chop.tess Subdivide a Window or Tessellation using a Set of Lines
nncross Nearest Neighbours Between Two Patterns
gridcentres Rectangular grid of points
ewcdf Weighted Empirical Cumulative Distribution Function
rotate.psp Rotate a Line Segment Pattern
infline Infinite Straight Lines
as.matrix.im Convert Pixel Image to Matrix
compatible.fasp Test Whether Two Function Arrays Are Compatible
demopat Artificial Data Point Pattern
crossdist Pairwise distances
humberside Humberside Data on Childhood Leukaemia and Lymphoma
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
intersect.tess Intersection of Two Tessellations
pairwise.family Pairwise Interaction Process Family
applynbd Apply Function to Every Neighbourhood in a Point Pattern
data.ppm Extract Original Data from a Fitted Point Process Model
is.subset.owin Determine Whether One Window is Contained In Another
eem Exponential Energy Marks
distmap.owin Distance Map of Window
im Create a Pixel Image Object
methods.box3 Methods for Three-Dimensional Box
is.marked.ppp Test Whether A Point Pattern is Marked
lengths.psp Lengths of Line Segments
reach Interaction Distance of a Point Process
bermantest Berman's Tests for Point Process Model
plot.colourmap Plot a Colour Map
plot.pp3 Plot a three-dimensional point pattern
clickppp Interactively Add Points
bei Tropical rain forest trees
pairdist Pairwise distances
bronzefilter Bronze gradient filter data
by.im Apply Function to Image Broken Down by Factor
pcf.ppp Pair Correlation Function of Point Pattern
nztrees New Zealand Trees Point Pattern
crossing.psp Crossing Points of Two Line Segment Patterns
is.im Test Whether An Object Is A Pixel Image
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
owin.object Class owin
delaunay Delaunay Triangulation of Point Pattern
quad.object Class of Quadrature Schemes
nbfires Point Patterns of New Brunswick Forest Fires
nearest.raster.point Find Pixel Nearest to a Given Point
lansing Lansing Woods Point Pattern
nearestsegment Find Line Segment Nearest to Each Point
is.empty Test Whether An Object Is Empty
discretise Safely Convert Point Pattern Window to Binary Mask
eval.im Evaluate Expression Involving Pixel Images
diameter Diameter of a Window
is.multitype.ppp Test Whether A Point Pattern is Multitype
quadratresample Resample a Point Pattern by Resampling Quadrats
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
ripras Estimate window from points alone
rmpoispp Generate Multitype Poisson Point Pattern
distmap Distance Map
shift.im Apply Vector Translation To Pixel Image
kaplan.meier Kaplan-Meier Estimator using Histogram Data
murchison Murchison gold deposits
unitname Name for Unit of Length
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
shapley Galaxies in the Shapley Supercluster
plot.quad plot a Spatial Quadrature Scheme
copper Berman-Huntington points and lines data
ppm.object Class of Fitted Point Process Models
pixellate.owin Convert Window to Pixel Image
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
pointsOnLines Place Points Evenly Along Specified Lines
heather Diggle's Heather Data
reduced.sample Reduced Sample Estimator using Histogram Data
markcorrint Mark Correlation Integral
setmarks Set or Reset the Marks in a Point Pattern
harmonic Basis for Harmonic Functions
methods.pp3 Methods for three-dimensional point patterns
fitin.ppm Extract the Interaction from a Fitted Point Process Model
plot.fasp Plot a Function Array
density.psp Kernel Smoothing of Line Segment Pattern
pcf.fv Pair Correlation Function obtained from K Function
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
plot.im Plot a Pixel Image
union.quad Union of Data and Dummy Points
intersect.owin Intersection, Union or Set Subtraction of Two Windows
localK Neighbourhood density function
ord.family Ord Interaction Process Family
rMaternII Simulate Matern Model II
miplot Morishita Index Plot
pppdist Distance Between Two Point Patterns
plot.kppm Plot a fitted cluster point process
mincontrast Method of Minimum Contrast
plot.splitppp Plot a List of Point Patterns
plot.owin Plot a Spatial Window
plot.plotppm Plot a plotppm Object Created by plot.ppm
pairdist.ppp Pairwise distances
rotate Rotate
print.im Print Brief Details of an Image
rshift.ppp Randomly Shift a Point Pattern
profilepl Profile Maximum Pseudolikelihood
progressreport Print Progress Reports
hist.im Histogram of Pixel Values in an Image
unique.ppp Extract Unique Points from a Spatial Point Pattern
is.multitype Test whether Object is Multitype
istat Point and Click Interface for Exploratory Analysis of Point Pattern
integral.im Integral of a Pixel Image
pixellate.ppp Convert Point Pattern to Pixel Image
pcf Pair Correlation Function
pcfcross.inhom Inhomogeneous Multitype Pair Correlation Function (Cross-Type)
plot.bermantest Plot Result of Berman Test
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
shift.ppp Apply Vector Translation To Point Pattern
iplot Point and Click Interface for Displaying a Point Pattern
rescale.im Convert Pixel Image to Another Unit of Length
longleaf Longleaf Pines Point Pattern
ppp.object Class of Point Patterns
plot.kstest Plot a Spatial Kolmogorov-Smirnov Test
fv.object Data Frames of Function Values
print.ppp Print Brief Details of a Point Pattern Dataset
suffstat Sufficient Statistic of Point Process Model
print.quad Print a Quadrature Scheme
spatstat.options Internal Options in Spatstat Package
levelset Level Set of a Pixel Image
predict.ppm Prediction from a Fitted Point Process Model
markconnect Mark Connection Function
pp3 Three Dimensional Point Pattern
pppmatching Create a Point Matching
is.ppp Test Whether An Object Is A Point Pattern
rSSI Simulate Simple Sequential Inhibition
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
pairsat.family Saturated Pairwise Interaction Point Process Family
identify.ppp Identify Points in a Point Pattern
psp Create a Line Segment Pattern
smooth.ppp Spatial smoothing of observations at irregular points
vertices Vertices of a Window
setcov Set Covariance of a Window
summary.owin Summary of a Spatial Window
quadratcount Quadrat counting for a point pattern
quadscheme Generate a Quadrature Scheme from a Point Pattern
kppm Fit cluster point process model
pcfdot Multitype pair correlation function (i-to-any)
urkiola Urkiola Woods Point Pattern
inside.owin Test Whether Points Are Inside A Window
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
plot.listof Plot a List of Things
rThomas Simulate Thomas Process
spruces Spruces Point Pattern
superimposePSP Superimpose Several Line Segment Patterns
residuals.ppm Residuals for Fitted Point Process Model
unmark Remove Marks
rMosaicSet Mosaic Random Set
is.marked.ppm Test Whether A Point Process Model is Marked
owin Create a Window
pairdist.psp Pairwise distances between line segments
distmap.psp Distance Map of Line Segment Pattern
swedishpines Swedish Pines Point Pattern
pcf.fasp Pair Correlation Function obtained from array of K functions
runifpointOnLines Generate N Uniform Random Points On Line Segments
rescale.psp Convert Line Segment Pattern to Another Unit of Length
multiplicity.ppp Count Multiplicity of Duplicate Points
pixelquad Quadrature Scheme Based on Pixel Grid
expand.owin Expand Window By Factor
plot.tess Plot a tessellation
rlabel Random Re-Labelling of Point Pattern
ppp Create a Point Pattern
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
plot.psp plot a Spatial Line Segment Pattern
rMaternI Simulate Matern Model I
simdat Simulated Point Pattern
simplify.owin Approximate a Polygon by a Simpler Polygon
ppx Multidimensional Space-Time Point Pattern
ponderosa Ponderosa Pine Tree Point Pattern
rpoisline Generate Poisson Random Line Process
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
rpoislinetess Poisson Line Tessellation
pcfinhom Inhomogeneous Pair Correlation Function
predict.kppm Prediction from a Fitted Cluster Point Process Model
perimeter Perimeter Length of Window
rjitter Random Perturbation of a Point Pattern
stieltjes Compute Integral of Function Against Cumulative Distribution
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
rshift Random Shift
superimpose Superimpose Several Point Patterns
split.ppp Divide Point Pattern into Sub-patterns
split.im Divide Image Into Sub-images
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
matchingdist Distance for a Point Pattern Matching
pppmatching.object Class of Point Matchings
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rNeymanScott Simulate Neyman-Scott Process
rescale.ppp Convert Point Pattern to Another Unit of Length
plot.fv Plot Function Values
raster.x Cartesian Coordinates for a Pixel Raster
rotate.ppp Rotate a Point Pattern
pcfdot.inhom Inhomogeneous Multitype Pair Correlation Function (Type-i-To-Any-Type)
rStrauss Perfect Simulation of the Strauss Process
print.ppm Print a Fitted Point Process Model
rpoispp3 Generate Poisson Point Pattern in Three Dimensions
print.owin Print Brief Details of a Spatial Window
redwood California Redwoods Point Pattern (Ripley's Subset)
ppm Fit Point Process Model to Data
print.psp Print Brief Details of a Line Segment Pattern Dataset
rthin Random Thinning
rescue.rectangle Convert Window Back To Rectangle
rescale Convert dataset to another unit of length
quantile.im Sample Quantiles of Pixel Image
rlinegrid Generate grid of parallel lines with random displacement
tess Create a Tessellation
rGaussPoisson Simulate Gauss-Poisson Process
summary.ppp Summary of a Point Pattern Dataset
rcell Simulate Baddeley-Silverman Cell Process
rsyst Simulate systematic random point pattern
rescale.owin Convert Window to Another Unit of Length
residualspaper Data and Code From JRSS Discussion Paper on Residuals
rotate.owin Rotate a Window
square Square Window
project2segment Move Point To Nearest Line
rmh.ppm Simulate from a Fitted Point Process Model
scanpp Read Point Pattern From Data File
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
summary.ppm Summarizing a Fitted Point Process Model
redwoodfull California Redwoods Point Pattern (Entire Dataset)
shift.owin Apply Vector Translation To Window
selfcrossing.psp Crossing Points in a Line Segment Pattern
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
spokes Spokes pattern of dummy points
pairdist.default Pairwise distances
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
shift.psp Apply Vector Translation To Line Segment Pattern
spatstat-package The Spatstat Package
summary.splitppp Summary of a Split Point Pattern
rmpoint Generate N Random Multitype Points
rshift.splitppp Randomly Shift a List of Point Patterns
summary.listof Summary of a List of Things
runifdisc Generate N Uniform Random Points in a Disc
simulate.kppm Simulate a Fitted Cluster Point Process Model
shift Apply Vector Translation
plot.ppm plot a Fitted Point Process Model
summary.im Summarizing a Pixel Image
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
plot.ppp plot a Spatial Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
rstrat Simulate Stratified Random Point Pattern
summary.quad Summarizing a Quadrature Scheme
update.kppm Update a Fitted Cluster Point Process Model
simulate.ppm Simulate a Fitted Gibbs Point Process Model
tiles Extract List of Tiles in a Tessellation
rMatClust Simulate Matern Cluster Process
rpoint Generate N Random Points
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
quadrats Divide Region into Quadrats
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
runifpoint Generate N Uniform Random Points
rpoispp Generate Poisson Point Pattern
rshift.psp Randomly Shift a Line Segment Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
with.hyperframe Evaluate an Expression in Each Row of a Hyperframe
trim.rectangle Cut margins from rectangle
with.fv Evaluate an Expression in a Function Table
whist Weighted Histogram
update.ppm Update a Fitted Point Process Model
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Date 15 december 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2009-12-17 06:52:14 UTC; adrian
Repository CRAN
Date/Publication 2009-12-17 17:17:51

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