spatstat v1.12-7

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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
crossdist.default Pairwise distances between two different sets of points
eval.fv Evaluate Expression Involving Functions
Kdot Multitype K Function (i-to-any)
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
Kcross Multitype K Function (Cross-type)
rcell Simulate Baddeley-Silverman Cell Process
Saturated Saturated Pairwise Interaction model
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
as.im Convert to Pixel Image
Kdot.inhom Inhomogeneous Multitype K Dot Function
StraussHard The Strauss / Hard Core Point Process Model
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
as.mask Pixel Image Approximation of a Window
corners Corners of a rectangle
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
anemones Beadlet Anemones Data
Jcross Multitype J Function (i-to-j)
Linhom L-function
plot.ppm plot a Fitted Point Process Model
Gest Nearest Neighbour Distance Function G
Fest Estimate the empty space function F
AreaInter The Area Interaction Point Process Model
Geyer Geyer's Saturation Point Process Model
inside.owin Test Whether Points Are Inside A Window
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
rpoisline Generate Poisson Random Line Process
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
ants Harkness-Isham ants' nests data
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
distmap.psp Distance Map of Line Segment Pattern
plot.owin Plot a Spatial Window
plot.hyperframe Plot Entries in a Hyperframe
as.matrix.im Convert Pixel Image to Matrix
concatxy Concatenate x,y Coordinate Vectors
Kinhom Inhomogeneous K-function
cells Biological Cells Point Pattern
pairdist.ppp Pairwise distances
copper Berman-Huntington points and lines data
rMaternI Simulate Matern Model I
betacells Beta Ganglion Cells in Cat Retina
areadiff Difference of Disc Areas
markcorr Mark Correlation Function
ewcdf Weighted Empirical Cumulative Distribution Function
redwoodfull California Redwoods Point Pattern (Entire Dataset)
eroded.areas Areas of Morphological Erosions
cut.ppp Convert Point Pattern Marks from Numeric to Factor
nbfires Point Patterns of New Brunswick Forest Fires
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
quadscheme Generate a Quadrature Scheme from a Point Pattern
coef.ppm Coefficients of Fitted Point Process Model
mean.im Mean Pixel Value in an Image
as.owin Convert Data To Class owin
affine.owin Apply Affine Transformation To Window
redwood California Redwoods Point Pattern (Ripley's Subset)
LennardJones The Lennard-Jones Potential
as.psp Convert Data To Class psp
lansing Lansing Woods Point Pattern
bounding.box.xy Convex Hull of Points
centroid.owin Centroid of a window
gridweights Compute Quadrature Weights Based on Grid Counts
Kmeasure Reduced Second Moment Measure
amacrine Hughes' Amacrine Cell Data
Jdot Multitype J Function (i-to-any)
lurking Lurking variable plot
simdat Simulated Point Pattern
density.psp Kernel Smoothing of Line Segment Pattern
harmonic Basis for Harmonic Functions
pcf.fasp Pair Correlation Function obtained from array of K functions
crossdist Pairwise distances
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
plot.fasp Plot a Function Array
kaplan.meier Kaplan-Meier Estimator using Histogram Data
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
compatible.fv Test Whether Two Function Objects Are Compatible
psp.object Class of Line Segment Patterns
nztrees New Zealand Trees Point Pattern
intersect.owin Intersection or Union of Two Windows
is.owin Test Whether An Object Is A Window
print.owin Print Brief Details of a Spatial Window
rSSI Simulate Simple Sequential Inhibition
pairwise.family Pairwise Interaction Process Family
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
spatstat-internal Internal spatstat functions
pairsat.family Saturated Pairwise Interaction Point Process Family
ppm.object Class of Fitted Point Process Models
print.im Print Brief Details of an Image
im.object Class of Images
rsyst Simulate systematic random point pattern
area.owin Area of a Window
multiplicity.ppp Count Multiplicity of Duplicate Points
ripras Estimate window from points alone
eem Exponential Energy Marks
pppmatching Create a Point Matching
hist.im Histogram of Pixel Values in an Image
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
Jest Estimate the J-function
owin Create a Window
rlabel Random Re-Labelling of Point Pattern
reach Interaction Distance of a Point Process
crossdist.psp Pairwise distances between two different line segment patterns
Poisson Poisson Point Process Model
rGaussPoisson Simulate Gauss-Poisson Process
bei Tropical rain forest trees
Iest Estimate the I-function
dilate.owin Dilate a Window
rStrauss Perfect Simulation of the Strauss Process
quadratcount Quadrat counting for a point pattern
rpoispp Generate Poisson Point Pattern
lengths.psp Lengths of Line Segments
print.ppm Print a Fitted Point Process Model
quantile.im Sample Quantiles of Pixel Image
Lest L-function
summary.listof Summary of a List of Things
eval.im Evaluate Expression Involving Pixel Images
plot.fv Plot Function Valuesn
rmh.ppm Simulate from a Fitted Point Process Model
summary.im Summarizing a Pixel Image
fasp.object Function Arrays for Spatial Patterns
summary.ppp Summary of a Point Pattern Dataset
plot.listof Plot a List of Things
rshift.ppp Randomly Shift a Point Pattern
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
interp.im Interpolate a Pixel Image
summary.psp Summary of a Line Segment Pattern Dataset
subset.fv Extract Subset of Function Values
spatstat.options Internal Options in Spatstat Package
distmap.owin Distance Map of Window
split.ppp Divide Point Pattern into Sub-patterns
ppp.object Class of Point Patterns
OrdThresh Ord's Interaction model
summary.quad Summarizing a Quadrature Scheme
default.dummy Generate a Default Pattern of Dummy Points
rmpoispp Generate Multitype Poisson Point Pattern
convexhull.xy Convex Hull of Points
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
density.ppp Kernel Smoothed Intensity of Point Pattern
expand.owin Expand Window By Factor
bdist.points Distance to Boundary of Window
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
thomas.estK Fit the Thomas Point Process by Minimum Contrast
ganglia Beta Ganglion Cells in Cat Retina, Old Version
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
inforder.family Infinite Order Interaction Family
rlinegrid Generate grid of parallel lines with random displacement
pcf Pair Correlation Function
ponderosa Ponderosa Pine Tree Point Pattern
rMaternII Simulate Matern Model II
setcov Set Covariance of a Window
is.ppp Test Whether An Object Is A Point Pattern
superimpose Superimpose Several Point Patterns
mincontrast Method of Minimum Contrast
is.marked.ppm Test Whether A Point Process Model is Marked
hyperframe Hyper Data Frame
affine.ppp Apply Affine Transformation To Point Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
humberside Humberside Data on Childhood Leukaemia and Lymphoma
rescale.psp Convert Line Segment Pattern to Another Unit of Length
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
hamster Aherne's hamster tumour data
rshift.psp Randomly Shift a Line Segment Pattern
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
residuals.ppm Residuals for Fitted Point Process Model
DiggleGratton Diggle-Gratton model
selfcrossing.psp Crossing Points in a Line Segment Pattern
pppmatching.object Class of Point Matchings
demopat Artificial Data Point Pattern
letterR Window in Shape of Letter R
localK Neighbourhood density function
shift.ppp Apply Vector Translation To Point Pattern
psp Create a Line Segment Pattern
complement.owin Take Complement of a Window
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
distmap.ppp Distance Map of Point Pattern
bdist.pixels Distance to Boundary of Window
is.multitype.ppp Test Whether A Point Pattern is Multitype
ppp Create a Point Pattern
rotate Rotate
union.quad Union of Data and Dummy Points
pppdist Distance Between Two Point Patterns
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
spatstat The Spatstat Package
progressreport Print Progress Reports
clickppp Interactively Add Points
is.marked Test Whether Marks Are Present
applynbd Apply Function to Every Neighbourhood in a Point Pattern
rNeymanScott Simulate Neyman-Scott Process
longleaf Longleaf Pines Point Pattern
nndist.psp Nearest neighbour distances between line segments
is.im Test Whether An Object Is A Pixel Image
affine Apply Affine Transformation
quad.object Class of Quadrature Schemes
erode.owin Erode a Window
rescale.owin Convert Window to Another Unit of Length
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
Ord Generic Ord Interaction model
rescue.rectangle Convert Window Back To Rectangle
as.data.frame.ppp Coerce Point Pattern to a Data Frame
plot.ppp plot a Spatial Point Pattern
angles.psp Orientation Angles of Line Segments
rshift Random Shift
contour.im Contour plot of pixel image
subset.im Extract Subset of Image
crossing.psp Crossing Points of Two Line Segment Patterns
as.ppp Convert Data To Class ppp
predict.ppm Prediction from a Fitted Point Process Model
swedishpines Swedish Pines Point Pattern
MultiStrauss The Multitype Strauss Point Process Model
print.psp Print Brief Details of a Line Segment Pattern Dataset
trim.rectangle Cut margins from rectangle
rotate.owin Rotate a Window
japanesepines Japanese Pines Point Pattern
summary.splitppp Summary of a Split Point Pattern
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
is.ppm Test Whether An Object Is A Fitted Point Process Model
plot.im Plot a Pixel Image
plot.splitppp Plot a List of Point Patterns
fitin.ppm Extract the Interaction from a Fitted Point Process Model
shift Apply Vector Translation
unmark Remove Marks from a Marked Point Pattern
endpoints.psp Endpoints of Line Segment Pattern
shift.owin Apply Vector Translation To Window
anova.ppm ANOVA for Fitted Point Process Models
vertices Vertices of a Window
setmarks Set or Reset the Marks in a Point Pattern
unitname Name for Unit of Length
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
subset.fasp Extract Subset of Function Array
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
clickpoly Interactively Define a Polygon
crossdist.ppp Pairwise distances between two different point patterns
Kest.fft K-function using FFT
matchingdist Distance for a Point Pattern Matching
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
rotate.psp Rotate a Line Segment Pattern
print.quad Print a Quadrature Scheme
rthin Random Thinning
shift.im Apply Vector Translation To Pixel Image
subset.ppp Extract or Replace Subset of Point Pattern
allstats Calculate four standard summary functions of a point pattern.
bounding.box Bounding Box of a Window or Point Pattern
scanpp Read Point Pattern From Data File
is.subset.owin Determine Whether One Window is Contained In Another
discretise Safely Convert Point Pattern Window to Binary Mask
Jmulti Marked J Function
suffstat Sufficient Statistic of Point Process Model
rThomas Simulate Thomas Process
fitted.ppm Fitted Conditional Intensity for Point Process Model
unique.ppp Extract Unique Points from a Spatial Point Pattern
finpines Pine saplings in Finland.
rmpoint Generate N Random Multitype Points
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
subset.splitppp Extract or Replace Sub-Patterns
persp.im Perspective Plot of Pixel Image
rshift.splitppp Randomly Shift a List of Point Patterns
Pairwise Generic Pairwise Interaction model
spruces Spruces Point Pattern
cut.im Convert Pixel Image from Numeric to Factor
spatstat-deprecated Deprecated spatstat functions
Gmulti Marked Nearest Neighbour Distance Function
append.psp Combine Two Line Segment Patterns
is.marked.ppp Test Whether A Point Pattern is Marked
residualspaper Data and Code From JRSS Discussion Paper on Residuals
rpoint Generate N Random Points
plot.psp plot a Spatial Line Segment Pattern
plot.plotppm Plot a plotppm Object Created by plot.ppm
profilepl Profile Maximum Pseudolikelihood
data.ppm Extract Original Data from a Fitted Point Process Model
diameter Diameter of a Window
Softcore The Soft Core Point Process Model
Strauss The Strauss Point Process Model
update.ppm Update a Fitted Point Process Model
fv.object Data Frames of Function Values
bramblecanes Hutchings' Bramble Canes data
chorley Chorley-Ribble Cancer Data
subset.psp Extract Subset of Line Segment Pattern
print.ppp Print Brief Details of a Point Pattern Dataset
as.rectangle Window Frame
subsetget.im Reset Values in Subset of Image
distmap Distance Map
owin.object Class owin
nearest.raster.point Find Pixel Nearest to a Given Point
raster.x Cartesian Coordinates for a Pixel Raster
nnwhich Nearest neighbour
envelope Simulation envelopes of summary function
summary.owin Summary of a Spatial Window
rstrat Simulate Stratified Random Point Pattern
rMatClust Simulate Matern Cluster Process
rescale.ppp Convert Point Pattern to Another Unit of Length
shift.psp Apply Vector Translation To Line Segment Pattern
subset.listof Extract or Replace Subset of a List of Things
spokes Spokes pattern of dummy points
nncross Nearest Neighbour in Another Point Pattern
Kest K-function
clarkevans Clark and Evans Aggregation Index
logLik.ppm Log Likelihood for Poisson Point Process Model
pcf.ppp Pair Correlation Function of Point Pattern
nndist Nearest neighbour distances
pairdist.psp Pairwise distances between line segments
midpoints.psp Midpoints of Line Segment Pattern
is.multitype Test whether Object is Multitype
pcf.fv Pair Correlation Function obtained from K Function
pairdist Pairwise distances
plot.quad plot a Spatial Quadrature Scheme
ppm Fit Point Process Model to Data
affine.psp Apply Affine Transformation To Line Segment Pattern
smooth.ppp Spatial smoothing of observations at irregular points
runifpoint Generate N Uniform Random Points
summary.ppm Summarizing a Fitted Point Process Model
rescale Convert dataset to another unit of length
runifdisc Generate N Uniform Random Points in a Disc
square Square Window
rotate.ppp Rotate a Point Pattern
Kcross.inhom Inhomogeneous Cross K Function
Kmulti Marked K-Function
disc Circular Window
im Create a Pixel Image Object
identify.ppp Identify Points in a Point Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
levelset Level Set of a Pixel Image
ord.family Ord Interaction Process Family
pairdist.default Pairwise distances
reduced.sample Reduced Sample Estimator using Histogram Data
gridcentres Rectangular grid of points
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Date 11 February 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Tue Feb 12 00:14:29 2008; adrian

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