spatstat v1.15-4

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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. 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
Gest Nearest Neighbour Distance Function G
as.data.frame.ppp Coerce Point Pattern to a Data Frame
is.multitype.ppm Test Whether A Point Process Model is Multitype
is.subset.owin Determine Whether One Window is Contained In Another
Kdot Multitype K Function (i-to-any)
lurking Lurking variable plot
allstats Calculate four standard summary functions of a point pattern.
Saturated Saturated Pairwise Interaction model
Fest Estimate the empty space function F
as.im Convert to Pixel Image
LennardJones The Lennard-Jones Potential
Poisson Poisson Point Process Model
Jcross Multitype J Function (i-to-j)
Extract.psp Extract Subset of Line Segment Pattern
Kest K-function
bdist.pixels Distance to Boundary of Window
Extract.quad Subset of Quadrature Scheme
append.psp Combine Two Line Segment Patterns
distmap Distance Map
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
Extract.fv Extract Subset of Function Values
copper Berman-Huntington points and lines data
corners Corners of a rectangle
model.images Compute Images of Constructed Covariates
lut Lookup Tables
Lest L-function
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
as.rectangle Window Frame
as.owin Convert Data To Class owin
Kinhom Inhomogeneous K-function
Jdot Multitype J Function (i-to-any)
Emark Diagnostics for random marking
plot.ppp plot a Spatial Point Pattern
dirichlet Dirichlet Tessellation of Point Pattern
spatstat-deprecated Deprecated spatstat functions
Extract.ppp Extract or Replace Subset of Point Pattern
Extract.im Extract Subset of Image
Extract.tess Extract or Replace Subset of Tessellation
crossdist Pairwise distances
as.psp Convert Data To Class psp
compatible.im Test Whether Two Pixel Images Are Compatible
is.marked.ppp Test Whether A Point Pattern is Marked
ants Harkness-Isham ants' nests data
crossdist.default Pairwise distances between two different sets of points
fitin.ppm Extract the Interaction from a Fitted Point Process Model
identify.ppp Identify Points in a Point Pattern
is.im Test Whether An Object Is A Pixel Image
OrdThresh Ord's Interaction model
markcorrint Mark Correlation Integral
density.ppp Kernel Smoothed Intensity of Point Pattern
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
eem Exponential Energy Marks
rescale.im Convert Pixel Image to Another Unit of Length
rescale.owin Convert Window to Another Unit of Length
diameter Diameter of a Window
as.ppp Convert Data To Class ppp
bounding.box.xy Convex Hull of Points
contour.im Contour plot of pixel image
Jest Estimate the J-function
Strauss The Strauss Point Process Model
plot.psp plot a Spatial Line Segment Pattern
colourmap Colour Lookup Tables
logLik.ppm Log Likelihood for Poisson Point Process Model
Replace.im Reset Values in Subset of Image
cells Biological Cells Point Pattern
hamster Aherne's hamster tumour data
Extract.fasp Extract Subset of Function Array
Hest Spherical Contact Distribution Function
ponderosa Ponderosa Pine Tree Point Pattern
rescue.rectangle Convert Window Back To Rectangle
mincontrast Method of Minimum Contrast
default.dummy Generate a Default Pattern of Dummy Points
inside.owin Test Whether Points Are Inside A Window
print.ppp Print Brief Details of a Point Pattern Dataset
opening.owin Morphological Opening of a Window
pcf Pair Correlation Function
nncross Nearest Neighbours Between Two Patterns
anova.ppm ANOVA for Fitted Point Process Models
plot.im Plot a Pixel Image
endpoints.psp Endpoints of Line Segment Pattern
project2segment Move Point To Nearest Line
rpoisline Generate Poisson Random Line Process
affine.psp Apply Affine Transformation To Line Segment Pattern
plot.quad plot a Spatial Quadrature Scheme
nndist.psp Nearest neighbour distances between line segments
is.marked.ppm Test Whether A Point Process Model is Marked
betacells Beta Ganglion Cells in Cat Retina
midpoints.psp Midpoints of Line Segment Pattern
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
pixellate Convert Point Pattern to Pixel Image
cut.im Convert Pixel Image from Numeric to Factor
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
rStrauss Perfect Simulation of the Strauss Process
rmpoispp Generate Multitype Poisson Point Pattern
Kcross Multitype K Function (Cross-type)
area.owin Area of a Window
pairdist.ppp Pairwise distances
pairdist Pairwise distances
simplify.owin Approximate a Polygon by a Simpler Polygon
plot.owin Plot a Spatial Window
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
print.im Print Brief Details of an Image
simdat Simulated Point Pattern
eval.im Evaluate Expression Involving Pixel Images
applynbd Apply Function to Every Neighbourhood in a Point Pattern
erode.owin Erode a Window
rMatClust Simulate Matern Cluster Process
is.multitype.ppp Test Whether A Point Pattern is Multitype
concatxy Concatenate x,y Coordinate Vectors
as.matrix.im Convert Pixel Image to Matrix
centroid.owin Centroid of a window
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
pairwise.family Pairwise Interaction Process Family
nearestsegment Find Line Segment Nearest to Each Point
residuals.ppm Residuals for Fitted Point Process Model
unique.ppp Extract Unique Points from a Spatial Point Pattern
rMaternII Simulate Matern Model II
bdist.points Distance to Boundary of Window
summary.quad Summarizing a Quadrature Scheme
AreaInter The Area Interaction Point Process Model
rMaternI Simulate Matern Model I
rsyst Simulate systematic random point pattern
raster.x Cartesian Coordinates for a Pixel Raster
Extract.splitppp Extract or Replace Sub-Patterns
inforder.family Infinite Order Interaction Family
rotate Rotate
chorley Chorley-Ribble Cancer Data
angles.psp Orientation Angles of Line Segments
unitname Name for Unit of Length
coef.ppm Coefficients of Fitted Point Process Model
bounding.box Bounding Box of a Window or Point Pattern
affine.owin Apply Affine Transformation To Window
Kdot.inhom Inhomogeneous Multitype K Dot Function
ppp.object Class of Point Patterns
hist.im Histogram of Pixel Values in an Image
rotate.ppp Rotate a Point Pattern
rMosaicSet Mosaic Random Set
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
pairdist.psp Pairwise distances between line segments
data.ppm Extract Original Data from a Fitted Point Process Model
reduced.sample Reduced Sample Estimator using Histogram Data
closing.owin Morphological Closing of a Window
anemones Beadlet Anemones Data
eval.fv Evaluate Expression Involving Functions
quadratresample Resample a Point Pattern by Resampling Quadrats
redwoodfull California Redwoods Point Pattern (Entire Dataset)
BadGey Hybrid Geyer Point Process Model
intersect.owin Intersection or Union of Two Windows
nbfires Point Patterns of New Brunswick Forest Fires
rescale Convert dataset to another unit of length
pcf.fv Pair Correlation Function obtained from K Function
rMosaicField Mosaic Random Field
complement.owin Take Complement of a Window
crossing.psp Crossing Points of Two Line Segment Patterns
clickpoly Interactively Define a Polygon
Jmulti Marked J Function
is.marked Test Whether Marks Are Present
distmap.owin Distance Map of Window
shift.ppp Apply Vector Translation To Point Pattern
hyperframe Hyper Data Frame
with.fv Evaluate an Expression in a Function Table
levelset Level Set of a Pixel Image
rstrat Simulate Stratified Random Point Pattern
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
plot.ppm plot a Fitted Point Process Model
rescale.ppp Convert Point Pattern to Another Unit of Length
Gmulti Marked Nearest Neighbour Distance Function
distmap.ppp Distance Map of Point Pattern
Kmulti Marked K-Function
nncorr Nearest-Neighbour Correlation Indices of Marked Point Pattern
split.im Divide Image Into Sub-images
rotate.psp Rotate a Line Segment Pattern
rotate.owin Rotate a Window
clip.infline Intersect Infinite Straight Lines with a Window
summary.listof Summary of a List of Things
Kmeasure Reduced Second Moment Measure
pppmatching Create a Point Matching
mean.im Mean, Median and Range of Pixel Values in an Image
crossdist.psp Pairwise distances between two different line segment patterns
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
nztrees New Zealand Trees Point Pattern
affine Apply Affine Transformation
rmh.ppm Simulate from a Fitted Point Process Model
Ldot Multitype L-function (i-to-any)
heather Diggle's Heather Data
smooth.ppp Spatial smoothing of observations at irregular points
square Square Window
bei Tropical rain forest trees
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
is.ppp Test Whether An Object Is A Point Pattern
bramblecanes Hutchings' Bramble Canes data
japanesepines Japanese Pines Point Pattern
finpines Pine saplings in Finland.
im.object Class of Images
trim.rectangle Cut margins from rectangle
blur Apply Gaussian Blur to a Pixel Image
print.psp Print Brief Details of a Line Segment Pattern Dataset
Ord Generic Ord Interaction model
Kcross.inhom Inhomogeneous Cross K Function
areadiff Difference of Disc Areas
eroded.areas Areas of Morphological Erosions
is.ppm Test Whether An Object Is A Fitted Point Process Model
Lcross Multitype L-function (cross-type)
intersect.tess Intersection of Two Tessellations
rshift.splitppp Randomly Shift a List of Point Patterns
is.multitype Test whether Object is Multitype
tiles Extract List of Tiles in a Tessellation
predict.kppm Prediction from a Fitted Cluster Point Process Model
density.psp Kernel Smoothing of Line Segment Pattern
Softcore The Soft Core Point Process Model
demopat Artificial Data Point Pattern
plot.colourmap Plot a Colour Map
plot.listof Plot a List of Things
plot.fasp Plot a Function Array
compatible.fv Test Whether Two Function Objects Are Compatible
cut.ppp Classify Points in a Point Pattern
spatstat.options Internal Options in Spatstat Package
simulate.kppm Simulate a fitted cluster point process model.
expand.owin Expand Window By Factor
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
shift Apply Vector Translation
ganglia Beta Ganglion Cells in Cat Retina, Old Version
print.quad Print a Quadrature Scheme
Kest.fft K-function using FFT
profilepl Profile Maximum Pseudolikelihood
spatstat The Spatstat Package
runifdisc Generate N Uniform Random Points in a Disc
lansing Lansing Woods Point Pattern
rpoispp Generate Poisson Point Pattern
delaunay Delaunay Triangulation of Point Pattern
kaplan.meier Kaplan-Meier Estimator using Histogram Data
incircle Find Largest Circle Inside Window
Geyer Geyer's Saturation Point Process Model
update.kppm Update a Fitted Cluster Point Process Model
infline Infinite Straight Lines
markcorr Mark Correlation Function
rshift Random Shift
disc Circular Window
fasp.object Function Arrays for Spatial Patterns
crossdist.ppp Pairwise distances between two different point patterns
progressreport Print Progress Reports
compatible.fasp Test Whether Two Function Arrays Are Compatible
DiggleGratton Diggle-Gratton model
nnwhich Nearest neighbour
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
runifpoint Generate N Uniform Random Points
vertices Vertices of a Window
suffstat Sufficient Statistic of Point Process Model
gridcentres Rectangular grid of points
chop.tess Subdivide a Window or Tessellation using a Set of Lines
clickppp Interactively Add Points
Linhom L-function
superimposePSP Superimpose Several Line Segment Patterns
spokes Spokes pattern of dummy points
convexhull.xy Convex Hull of Points
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
ppm Fit Point Process Model to Data
shift.im Apply Vector Translation To Pixel Image
plot.fv Plot Function Valuesn
Pairwise Generic Pairwise Interaction model
pairsat.family Saturated Pairwise Interaction Point Process Family
urkiola Urkiola Woods Point Pattern
psp.object Class of Line Segment Patterns
Extract.listof Extract or Replace Subset of a List of Things
ord.family Ord Interaction Process Family
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
clarkevans Clark and Evans Aggregation Index
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
as.mask Pixel Image Approximation of a Window
StraussHard The Strauss / Hard Core Point Process Model
pppmatching.object Class of Point Matchings
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
shift.owin Apply Vector Translation To Window
humberside Humberside Data on Childhood Leukaemia and Lymphoma
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
amacrine Hughes' Amacrine Cell Data
rpoislinetess Poisson Line Tessellation
MultiStrauss The Multitype Strauss Point Process Model
by.im Apply Function to Image Broken Down by Factor
miplot Morishita Index Plot
lengths.psp Lengths of Line Segments
matchingdist Distance for a Point Pattern Matching
envelope Simulation envelopes of summary function
multiplicity.ppp Count Multiplicity of Duplicate Points
quantile.im Sample Quantiles of Pixel Image
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
nearest.raster.point Find Pixel Nearest to a Given Point
quad.object Class of Quadrature Schemes
letterR Window in Shape of Letter R
setmarks Set or Reset the Marks in a Point Pattern
dilate.owin Dilate a Window
longleaf Longleaf Pines Point Pattern
as.tess Convert Data To Tessellation
plot.plotppm Plot a plotppm Object Created by plot.ppm
summary.im Summarizing a Pixel Image
summary.ppm Summarizing a Fitted Point Process Model
plot.tess Plot a tessellation
markconnect Mark Connection Function
markvario Mark Variogram
is.owin Test Whether An Object Is A Window
reach Interaction Distance of a Point Process
pointsOnLines Place Points Evenly Along Specified Lines
discretise Safely Convert Point Pattern Window to Binary Mask
tess Create a Tessellation
fitted.ppm Fitted Conditional Intensity for Point Process Model
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
eval.fasp Evaluate Expression Involving Function Arrays
owin Create a Window
plot.splitppp Plot a List of Point Patterns
update.ppm Update a Fitted Point Process Model
predict.ppm Prediction from a Fitted Point Process Model
owin.object Class owin
fv.object Data Frames of Function Values
interp.im Interpolate a Pixel Image
distmap.psp Distance Map of Line Segment Pattern
quadscheme Generate a Quadrature Scheme from a Point Pattern
spatstat-internal Internal spatstat functions
superimpose Superimpose Several Point Patterns
redwood California Redwoods Point Pattern (Ripley's Subset)
rNeymanScott Simulate Neyman-Scott Process
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
unmark Remove Marks
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
rlinegrid Generate grid of parallel lines with random displacement
ppm.object Class of Fitted Point Process Models
fryplot Fry Plot of Point Pattern
rpoint Generate N Random Points
model.matrix.ppm Extract Design Matrix from Point Process Model
harmonic Basis for Harmonic Functions
union.quad Union of Data and Dummy Points
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
pairdist.default Pairwise distances
stieltjes Compute Integral of Function Against Cumulative Distribution
ppp Create a Point Pattern
quadratcount Quadrat counting for a point pattern
psp Create a Line Segment Pattern
gridweights Compute Quadrature Weights Based on Grid Counts
kppm Fit cluster point process model
quadrats Divide Region into Quadrats
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
pcfcross Multitype pair correlation function
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
scanpp Read Point Pattern From Data File
ewcdf Weighted Empirical Cumulative Distribution Function
rmpoint Generate N Random Multitype Points
summary.ppp Summary of a Point Pattern Dataset
localK Neighbourhood density function
murchison Murchison gold deposits
rThomas Simulate Thomas Process
rlabel Random Re-Labelling of Point Pattern
rshift.ppp Randomly Shift a Point Pattern
print.ppm Print a Fitted Point Process Model
pcf.fasp Pair Correlation Function obtained from array of K functions
affine.ppp Apply Affine Transformation To Point Pattern
plot.kppm Plot a fitted cluster point process
rcell Simulate Baddeley-Silverman Cell Process
pixelquad Quadrature Scheme Based on Pixel Grid
connected Connected components of an image or window
summary.psp Summary of a Line Segment Pattern Dataset
rjitter Random Perturbation of a Point Pattern
split.ppp Divide Point Pattern into Sub-patterns
rSSI Simulate Simple Sequential Inhibition
setcov Set Covariance of a Window
nndist Nearest neighbour distances
Iest Estimate the I-function
persp.im Perspective Plot of Pixel Image
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
thomas.estK Fit the Thomas Point Process by Minimum Contrast
rGaussPoisson Simulate Gauss-Poisson Process
pcf.ppp Pair Correlation Function of Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
shift.psp Apply Vector Translation To Line Segment Pattern
runifpointOnLines Generate N Uniform Random Points On Line Segments
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
ripras Estimate window from points alone
swedishpines Swedish Pines Point Pattern
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
im Create a Pixel Image Object
spruces Spruces Point Pattern
rthin Random Thinning
gpc2owin Convert Polygonal Region into Different Format
rescale.psp Convert Line Segment Pattern to Another Unit of Length
shapley Galaxies in the Shapley Supercluster
summary.owin Summary of a Spatial Window
summary.splitppp Summary of a Split Point Pattern
print.owin Print Brief Details of a Spatial Window
rshift.psp Randomly Shift a Line Segment Pattern
pppdist Distance Between Two Point Patterns
plot.hyperframe Plot Entries in a Hyperframe
residualspaper Data and Code From JRSS Discussion Paper on Residuals
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Date 11 June 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged 2009-06-13 04:22:17 UTC; adrian
Repository CRAN
Date/Publication 2009-06-16 13:11:44

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