spatstat v1.13-1

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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
bounding.box.xy Convex Hull of Points
Kinhom Inhomogeneous K-function
compatible.im Test Whether Two Pixel Images Are Compatible
Strauss The Strauss Point Process Model
Kdot.inhom Inhomogeneous Multitype K Dot Function
compatible.fv Test Whether Two Function Objects Are Compatible
Kmulti Marked K-Function
Kcross Multitype K Function (Cross-type)
Jest Estimate the J-function
Gmulti Marked Nearest Neighbour Distance Function
LennardJones The Lennard-Jones Potential
Pairwise Generic Pairwise Interaction model
gridweights Compute Quadrature Weights Based on Grid Counts
Jdot Multitype J Function (i-to-any)
DiggleGratton Diggle-Gratton model
Ord Generic Ord Interaction model
Fest Estimate the empty space function F
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
MultiStrauss The Multitype Strauss Point Process Model
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
Poisson Poisson Point Process Model
Kest K-function
affine.owin Apply Affine Transformation To Window
as.data.frame.ppp Coerce Point Pattern to a Data Frame
Kmeasure Reduced Second Moment Measure
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
envelope Simulation envelopes of summary function
demopat Artificial Data Point Pattern
Lest L-function
Kcross.inhom Inhomogeneous Cross K Function
Saturated Saturated Pairwise Interaction model
affine.ppp Apply Affine Transformation To Point Pattern
bramblecanes Hutchings' Bramble Canes data
applynbd Apply Function to Every Neighbourhood in a Point Pattern
cut.ppp Convert Point Pattern Marks from Numeric to Factor
longleaf Longleaf Pines Point Pattern
anova.ppm ANOVA for Fitted Point Process Models
Gest Nearest Neighbour Distance Function G
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
Geyer Geyer's Saturation Point Process Model
cut.im Convert Pixel Image from Numeric to Factor
area.owin Area of a Window
append.psp Combine Two Line Segment Patterns
copper Berman-Huntington points and lines data
Kdot Multitype K Function (i-to-any)
complement.owin Take Complement of a Window
distmap.psp Distance Map of Line Segment Pattern
is.marked Test Whether Marks Are Present
Jmulti Marked J Function
Linhom L-function
StraussHard The Strauss / Hard Core Point Process Model
OrdThresh Ord's Interaction model
as.owin Convert Data To Class owin
bounding.box Bounding Box of a Window or Point Pattern
affine Apply Affine Transformation
allstats Calculate four standard summary functions of a point pattern.
centroid.owin Centroid of a window
corners Corners of a rectangle
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
localK Neighbourhood density function
angles.psp Orientation Angles of Line Segments
as.mask Pixel Image Approximation of a Window
data.ppm Extract Original Data from a Fitted Point Process Model
ewcdf Weighted Empirical Cumulative Distribution Function
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
cells Biological Cells Point Pattern
as.im Convert to Pixel Image
finpines Pine saplings in Finland.
spatstat-deprecated Deprecated spatstat functions
Softcore The Soft Core Point Process Model
Iest Estimate the I-function
areadiff Difference of Disc Areas
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
spatstat The Spatstat Package
clickpoly Interactively Define a Polygon
is.marked.ppm Test Whether A Point Process Model is Marked
chorley Chorley-Ribble Cancer Data
affine.psp Apply Affine Transformation To Line Segment Pattern
dilate.owin Dilate a Window
bei Tropical rain forest trees
as.psp Convert Data To Class psp
as.matrix.im Convert Pixel Image to Matrix
plot.fv Plot Function Valuesn
concatxy Concatenate x,y Coordinate Vectors
anemones Beadlet Anemones Data
crossdist.ppp Pairwise distances between two different point patterns
contour.im Contour plot of pixel image
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
density.psp Kernel Smoothing of Line Segment Pattern
mean.im Mean Pixel Value in an Image
as.ppp Convert Data To Class ppp
density.ppp Kernel Smoothed Intensity of Point Pattern
distmap.ppp Distance Map of Point Pattern
inside.owin Test Whether Points Are Inside A Window
subset.ppp Extract or Replace Subset of Point Pattern
bdist.pixels Distance to Boundary of Window
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
BadGey Hybrid Geyer Point Process Model
distmap Distance Map
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
harmonic Basis for Harmonic Functions
ganglia Beta Ganglion Cells in Cat Retina, Old Version
clickppp Interactively Add Points
pairdist Pairwise distances
disc Circular Window
pcf.fv Pair Correlation Function obtained from K Function
Kest.fft K-function using FFT
as.rectangle Window Frame
Jcross Multitype J Function (i-to-j)
bdist.points Distance to Boundary of Window
gridcentres Rectangular grid of points
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
crossdist.psp Pairwise distances between two different line segment patterns
nndist Nearest neighbour distances
im Create a Pixel Image Object
crossing.psp Crossing Points of Two Line Segment Patterns
predict.ppm Prediction from a Fitted Point Process Model
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
inforder.family Infinite Order Interaction Family
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
is.multitype Test whether Object is Multitype
AreaInter The Area Interaction Point Process Model
coef.ppm Coefficients of Fitted Point Process Model
ants Harkness-Isham ants' nests data
mincontrast Method of Minimum Contrast
amacrine Hughes' Amacrine Cell Data
hamster Aherne's hamster tumour data
distmap.owin Distance Map of Window
fasp.object Function Arrays for Spatial Patterns
fv.object Data Frames of Function Values
rSSI Simulate Simple Sequential Inhibition
eem Exponential Energy Marks
pcf Pair Correlation Function
markcorr Mark Correlation Function
hist.im Histogram of Pixel Values in an Image
diameter Diameter of a Window
fitin.ppm Extract the Interaction from a Fitted Point Process Model
owin Create a Window
crossdist Pairwise distances
default.dummy Generate a Default Pattern of Dummy Points
lurking Lurking variable plot
is.marked.ppp Test Whether A Point Pattern is Marked
subsetget.im Reset Values in Subset of Image
erode.owin Erode a Window
betacells Beta Ganglion Cells in Cat Retina
convexhull.xy Convex Hull of Points
clarkevans Clark and Evans Aggregation Index
is.multitype.ppm Test Whether A Point Process Model is Multitype
nbfires Point Patterns of New Brunswick Forest Fires
is.ppm Test Whether An Object Is A Fitted Point Process Model
rotate.ppp Rotate a Point Pattern
letterR Window in Shape of Letter R
is.im Test Whether An Object Is A Pixel Image
trim.rectangle Cut margins from rectangle
is.ppp Test Whether An Object Is A Point Pattern
reduced.sample Reduced Sample Estimator using Histogram Data
multiplicity.ppp Count Multiplicity of Duplicate Points
ripras Estimate window from points alone
print.ppp Print Brief Details of a Point Pattern Dataset
lansing Lansing Woods Point Pattern
hyperframe Hyper Data Frame
japanesepines Japanese Pines Point Pattern
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
midpoints.psp Midpoints of Line Segment Pattern
pppmatching Create a Point Matching
nztrees New Zealand Trees Point Pattern
kaplan.meier Kaplan-Meier Estimator using Histogram Data
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
nearest.raster.point Find Pixel Nearest to a Given Point
pcf.fasp Pair Correlation Function obtained from array of K functions
endpoints.psp Endpoints of Line Segment Pattern
identify.ppp Identify Points in a Point Pattern
fitted.ppm Fitted Conditional Intensity for Point Process Model
pairwise.family Pairwise Interaction Process Family
logLik.ppm Log Likelihood for Poisson Point Process Model
levelset Level Set of a Pixel Image
nncross Nearest Neighbour in Another Point Pattern
is.multitype.ppp Test Whether A Point Pattern is Multitype
ord.family Ord Interaction Process Family
matchingdist Distance for a Point Pattern Matching
plot.owin Plot a Spatial Window
progressreport Print Progress Reports
pairdist.psp Pairwise distances between line segments
crossdist.default Pairwise distances between two different sets of points
spatstat-internal Internal spatstat functions
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
print.im Print Brief Details of an Image
owin.object Class owin
ppm Fit Point Process Model to Data
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
eroded.areas Areas of Morphological Erosions
discretise Safely Convert Point Pattern Window to Binary Mask
rescue.rectangle Convert Window Back To Rectangle
im.object Class of Images
pppdist Distance Between Two Point Patterns
rStrauss Perfect Simulation of the Strauss Process
rsyst Simulate systematic random point pattern
rThomas Simulate Thomas Process
is.subset.owin Determine Whether One Window is Contained In Another
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
unmark Remove Marks from a Marked Point Pattern
ppp Create a Point Pattern
runifdisc Generate N Uniform Random Points in a Disc
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
rescale.owin Convert Window to Another Unit of Length
intersect.owin Intersection or Union of Two Windows
eval.fv Evaluate Expression Involving Functions
humberside Humberside Data on Childhood Leukaemia and Lymphoma
nndist.psp Nearest neighbour distances between line segments
expand.owin Expand Window By Factor
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
rshift.ppp Randomly Shift a Point Pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
nnwhich Nearest neighbour
lengths.psp Lengths of Line Segments
pairdist.ppp Pairwise distances
quantile.im Sample Quantiles of Pixel Image
eval.im Evaluate Expression Involving Pixel Images
is.owin Test Whether An Object Is A Window
pcf.ppp Pair Correlation Function of Point Pattern
plot.im Plot a Pixel Image
model.matrix.ppm Extract Design Matrix from Point Process Model
plot.fasp Plot a Function Array
quad.object Class of Quadrature Schemes
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
plot.quad plot a Spatial Quadrature Scheme
rMaternII Simulate Matern Model II
print.ppm Print a Fitted Point Process Model
plot.hyperframe Plot Entries in a Hyperframe
shift.psp Apply Vector Translation To Line Segment Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
stieltjes Compute Integral of Function Against Cumulative Distribution
rstrat Simulate Stratified Random Point Pattern
subset.splitppp Extract or Replace Sub-Patterns
rmh.ppm Simulate from a Fitted Point Process Model
pairsat.family Saturated Pairwise Interaction Point Process Family
plot.ppp plot a Spatial Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
residualspaper Data and Code From JRSS Discussion Paper on Residuals
ppp.object Class of Point Patterns
quadratcount Quadrat counting for a point pattern
print.psp Print Brief Details of a Line Segment Pattern Dataset
swedishpines Swedish Pines Point Pattern
smooth.ppp Spatial smoothing of observations at irregular points
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
update.ppm Update a Fitted Point Process Model
pairdist.default Pairwise distances
rGaussPoisson Simulate Gauss-Poisson Process
plot.psp plot a Spatial Line Segment Pattern
rlabel Random Re-Labelling of Point Pattern
psp.object Class of Line Segment Patterns
pppmatching.object Class of Point Matchings
plot.listof Plot a List of Things
plot.plotppm Plot a plotppm Object Created by plot.ppm
shift.ppp Apply Vector Translation To Point Pattern
summary.owin Summary of a Spatial Window
print.quad Print a Quadrature Scheme
rthin Random Thinning
rotate Rotate
unitname Name for Unit of Length
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rMaternI Simulate Matern Model I
print.owin Print Brief Details of a Spatial Window
ponderosa Ponderosa Pine Tree Point Pattern
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
spokes Spokes pattern of dummy points
rMatClust Simulate Matern Cluster Process
reach Interaction Distance of a Point Process
summary.im Summarizing a Pixel Image
residuals.ppm Residuals for Fitted Point Process Model
rotate.owin Rotate a Window
rcell Simulate Baddeley-Silverman Cell Process
rshift Random Shift
rshift.psp Randomly Shift a Line Segment Pattern
ppm.object Class of Fitted Point Process Models
subset.im Extract Subset of Image
subset.fasp Extract Subset of Function Array
spatstat.options Internal Options in Spatstat Package
persp.im Perspective Plot of Pixel Image
rNeymanScott Simulate Neyman-Scott Process
scanpp Read Point Pattern From Data File
rmpoispp Generate Multitype Poisson Point Pattern
redwood California Redwoods Point Pattern (Ripley's Subset)
plot.splitppp Plot a List of Point Patterns
model.images Compute Images of Constructed Covariates
shift Apply Vector Translation
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
quadscheme Generate a Quadrature Scheme from a Point Pattern
rescale.ppp Convert Point Pattern to Another Unit of Length
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
rpoisline Generate Poisson Random Line Process
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
plot.ppm plot a Fitted Point Process Model
rshift.splitppp Randomly Shift a List of Point Patterns
union.quad Union of Data and Dummy Points
interp.im Interpolate a Pixel Image
rlinegrid Generate grid of parallel lines with random displacement
unique.ppp Extract Unique Points from a Spatial Point Pattern
simdat Simulated Point Pattern
rescale.psp Convert Line Segment Pattern to Another Unit of Length
setmarks Set or Reset the Marks in a Point Pattern
setcov Set Covariance of a Window
rpoint Generate N Random Points
psp Create a Line Segment Pattern
subset.psp Extract Subset of Line Segment Pattern
profilepl Profile Maximum Pseudolikelihood
rpoispp Generate Poisson Point Pattern
square Square Window
suffstat Sufficient Statistic of Point Process Model
rescale Convert dataset to another unit of length
subset.listof Extract or Replace Subset of a List of Things
rotate.psp Rotate a Line Segment Pattern
superimpose Superimpose Several Point Patterns
shift.im Apply Vector Translation To Pixel Image
thomas.estK Fit the Thomas Point Process by Minimum Contrast
runifpoint Generate N Uniform Random Points
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
vertices Vertices of a Window
rmpoint Generate N Random Multitype Points
shift.owin Apply Vector Translation To Window
summary.listof Summary of a List of Things
redwoodfull California Redwoods Point Pattern (Entire Dataset)
raster.x Cartesian Coordinates for a Pixel Raster
summary.psp Summary of a Line Segment Pattern Dataset
spruces Spruces Point Pattern
summary.quad Summarizing a Quadrature Scheme
split.ppp Divide Point Pattern into Sub-patterns
summary.ppp Summary of a Point Pattern Dataset
subset.fv Extract Subset of Function Values
summary.ppm Summarizing a Fitted Point Process Model
summary.splitppp Summary of a Split Point Pattern
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Date 23 April 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Thu Apr 24 21:43:35 2008; adrian

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