spatstat v1.12-8

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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
fasp.object Function Arrays for Spatial Patterns
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
plot.hyperframe Plot Entries in a Hyperframe
distmap Distance Map
is.multitype.ppm Test Whether A Point Process Model is Multitype
rotate.psp Rotate a Line Segment Pattern
eroded.areas Areas of Morphological Erosions
is.im Test Whether An Object Is A Pixel Image
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
profilepl Profile Maximum Pseudolikelihood
demopat Artificial Data Point Pattern
matchingdist Distance for a Point Pattern Matching
pairdist.default Pairwise distances
spatstat-deprecated Deprecated spatstat functions
hyperframe Hyper Data Frame
plot.owin Plot a Spatial Window
redwoodfull California Redwoods Point Pattern (Entire Dataset)
inforder.family Infinite Order Interaction Family
summary.ppm Summarizing a Fitted Point Process Model
intersect.owin Intersection or Union of Two Windows
lansing Lansing Woods Point Pattern
nncross Nearest Neighbour in Another Point Pattern
finpines Pine saplings in Finland.
unmark Remove Marks from a Marked Point Pattern
dilate.owin Dilate a Window
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
hist.im Histogram of Pixel Values in an Image
identify.ppp Identify Points in a Point Pattern
distmap.ppp Distance Map of Point Pattern
plot.im Plot a Pixel Image
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
nbfires Point Patterns of New Brunswick Forest Fires
superimpose Superimpose Several Point Patterns
spatstat-internal Internal spatstat functions
default.dummy Generate a Default Pattern of Dummy Points
kaplan.meier Kaplan-Meier Estimator using Histogram Data
logLik.ppm Log Likelihood for Poisson Point Process Model
rThomas Simulate Thomas Process
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
expand.owin Expand Window By Factor
crossdist Pairwise distances
rmh.ppm Simulate from a Fitted Point Process Model
complement.owin Take Complement of a Window
suffstat Sufficient Statistic of Point Process Model
subset.psp Extract Subset of Line Segment Pattern
persp.im Perspective Plot of Pixel Image
ppp.object Class of Point Patterns
interp.im Interpolate a Pixel Image
gridweights Compute Quadrature Weights Based on Grid Counts
plot.splitppp Plot a List of Point Patterns
rmpoispp Generate Multitype Poisson Point Pattern
rGaussPoisson Simulate Gauss-Poisson Process
owin.object Class owin
compatible.fv Test Whether Two Function Objects Are Compatible
subset.ppp Extract or Replace Subset of Point Pattern
rpoisline Generate Poisson Random Line Process
update.ppm Update a Fitted Point Process Model
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
fitin.ppm Extract the Interaction from a Fitted Point Process Model
pairwise.family Pairwise Interaction Process Family
nztrees New Zealand Trees Point Pattern
owin Create a Window
crossdist.psp Pairwise distances between two different line segment patterns
pppmatching Create a Point Matching
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
raster.x Cartesian Coordinates for a Pixel Raster
eval.fv Evaluate Expression Involving Functions
mincontrast Method of Minimum Contrast
multiplicity.ppp Count Multiplicity of Duplicate Points
psp Create a Line Segment Pattern
rMaternII Simulate Matern Model II
hamster Aherne's hamster tumour data
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
nnwhich Nearest neighbour
cut.im Convert Pixel Image from Numeric to Factor
lurking Lurking variable plot
corners Corners of a rectangle
unique.ppp Extract Unique Points from a Spatial Point Pattern
is.owin Test Whether An Object Is A Window
is.marked.ppm Test Whether A Point Process Model is Marked
print.owin Print Brief Details of a Spatial Window
redwood California Redwoods Point Pattern (Ripley's Subset)
rshift Random Shift
eval.im Evaluate Expression Involving Pixel Images
subsetget.im Reset Values in Subset of Image
ganglia Beta Ganglion Cells in Cat Retina, Old Version
fv.object Data Frames of Function Values
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
eem Exponential Energy Marks
contour.im Contour plot of pixel image
is.ppp Test Whether An Object Is A Point Pattern
predict.ppm Prediction from a Fitted Point Process Model
plot.ppm plot a Fitted Point Process Model
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
ppm.object Class of Fitted Point Process Models
density.ppp Kernel Smoothed Intensity of Point Pattern
residuals.ppm Residuals for Fitted Point Process Model
ewcdf Weighted Empirical Cumulative Distribution Function
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
gridcentres Rectangular grid of points
pppdist Distance Between Two Point Patterns
print.psp Print Brief Details of a Line Segment Pattern Dataset
markcorr Mark Correlation Function
rstrat Simulate Stratified Random Point Pattern
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
discretise Safely Convert Point Pattern Window to Binary Mask
selfcrossing.psp Crossing Points in a Line Segment Pattern
runifdisc Generate N Uniform Random Points in a Disc
crossdist.ppp Pairwise distances between two different point patterns
rcell Simulate Baddeley-Silverman Cell Process
pcf.fv Pair Correlation Function obtained from K Function
shift.im Apply Vector Translation To Pixel Image
nearest.raster.point Find Pixel Nearest to a Given Point
localK Neighbourhood density function
levelset Level Set of a Pixel Image
midpoints.psp Midpoints of Line Segment Pattern
concatxy Concatenate x,y Coordinate Vectors
is.multitype.ppp Test Whether A Point Pattern is Multitype
distmap.owin Distance Map of Window
diameter Diameter of a Window
residualspaper Data and Code From JRSS Discussion Paper on Residuals
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
quadratcount Quadrat counting for a point pattern
plot.ppp plot a Spatial Point Pattern
simdat Simulated Point Pattern
reduced.sample Reduced Sample Estimator using Histogram Data
im.object Class of Images
crossing.psp Crossing Points of Two Line Segment Patterns
mean.im Mean Pixel Value in an Image
convexhull.xy Convex Hull of Points
pairdist Pairwise distances
pairdist.psp Pairwise distances between line segments
letterR Window in Shape of Letter R
rotate.ppp Rotate a Point Pattern
summary.im Summarizing a Pixel Image
distmap.psp Distance Map of Line Segment Pattern
rshift.splitppp Randomly Shift a List of Point Patterns
pcf.fasp Pair Correlation Function obtained from array of K functions
japanesepines Japanese Pines Point Pattern
is.marked.ppp Test Whether A Point Pattern is Marked
setcov Set Covariance of a Window
print.im Print Brief Details of an Image
is.ppm Test Whether An Object Is A Fitted Point Process Model
plot.fasp Plot a Function Array
rescue.rectangle Convert Window Back To Rectangle
is.subset.owin Determine Whether One Window is Contained In Another
rescale.ppp Convert Point Pattern to Another Unit of Length
plot.quad plot a Spatial Quadrature Scheme
rmpoint Generate N Random Multitype Points
endpoints.psp Endpoints of Line Segment Pattern
rotate.owin Rotate a Window
print.quad Print a Quadrature Scheme
summary.ppp Summary of a Point Pattern Dataset
rpoispp Generate Poisson Point Pattern
pairdist.ppp Pairwise distances
spruces Spruces Point Pattern
quad.object Class of Quadrature Schemes
data.ppm Extract Original Data from a Fitted Point Process Model
rescale Convert dataset to another unit of length
shift.owin Apply Vector Translation To Window
ppp Create a Point Pattern
rlabel Random Re-Labelling of Point Pattern
harmonic Basis for Harmonic Functions
print.ppm Print a Fitted Point Process Model
erode.owin Erode a Window
scanpp Read Point Pattern From Data File
is.multitype Test whether Object is Multitype
rescale.owin Convert Window to Another Unit of Length
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
rMaternI Simulate Matern Model I
inside.owin Test Whether Points Are Inside A Window
pppmatching.object Class of Point Matchings
rNeymanScott Simulate Neyman-Scott Process
print.ppp Print Brief Details of a Point Pattern Dataset
envelope Simulation envelopes of summary function
rthin Random Thinning
subset.fasp Extract Subset of Function Array
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
copper Berman-Huntington points and lines data
subset.splitppp Extract or Replace Sub-Patterns
nndist.psp Nearest neighbour distances between line segments
runifpoint Generate N Uniform Random Points
thomas.estK Fit the Thomas Point Process by Minimum Contrast
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
shift.psp Apply Vector Translation To Line Segment Pattern
rsyst Simulate systematic random point pattern
quantile.im Sample Quantiles of Pixel Image
fitted.ppm Fitted Conditional Intensity for Point Process Model
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
nndist Nearest neighbour distances
rpoint Generate N Random Points
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
plot.listof Plot a List of Things
unitname Name for Unit of Length
subset.im Extract Subset of Image
psp.object Class of Line Segment Patterns
rshift.psp Randomly Shift a Line Segment Pattern
as.owin Convert Data To Class owin
rshift.ppp Randomly Shift a Point Pattern
OrdThresh Ord's Interaction model
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rMatClust Simulate Matern Cluster Process
crossdist.default Pairwise distances between two different sets of points
rSSI Simulate Simple Sequential Inhibition
ord.family Ord Interaction Process Family
shift Apply Vector Translation
trim.rectangle Cut margins from rectangle
Softcore The Soft Core Point Process Model
progressreport Print Progress Reports
smooth.ppp Spatial smoothing of observations at irregular points
Kdot.inhom Inhomogeneous Multitype K Dot Function
vertices Vertices of a Window
applynbd Apply Function to Every Neighbourhood in a Point Pattern
subset.listof Extract or Replace Subset of a List of Things
Fest Estimate the empty space function F
DiggleGratton Diggle-Gratton model
Poisson Poisson Point Process Model
spokes Spokes pattern of dummy points
summary.owin Summary of a Spatial Window
quadscheme Generate a Quadrature Scheme from a Point Pattern
Geyer Geyer's Saturation Point Process Model
coef.ppm Coefficients of Fitted Point Process Model
as.ppp Convert Data To Class ppp
Lest L-function
subset.fv Extract Subset of Function Values
betacells Beta Ganglion Cells in Cat Retina
as.psp Convert Data To Class psp
AreaInter The Area Interaction Point Process Model
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Ord Generic Ord Interaction model
bounding.box.xy Convex Hull of Points
anemones Beadlet Anemones Data
affine Apply Affine Transformation
pcf.ppp Pair Correlation Function of Point Pattern
split.ppp Divide Point Pattern into Sub-patterns
as.data.frame.ppp Coerce Point Pattern to a Data Frame
bramblecanes Hutchings' Bramble Canes data
clickpoly Interactively Define a Polygon
summary.quad Summarizing a Quadrature Scheme
Jest Estimate the J-function
angles.psp Orientation Angles of Line Segments
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Gmulti Marked Nearest Neighbour Distance Function
anova.ppm ANOVA for Fitted Point Process Models
MultiStrauss The Multitype Strauss Point Process Model
affine.ppp Apply Affine Transformation To Point Pattern
as.im Convert to Pixel Image
Linhom L-function
append.psp Combine Two Line Segment Patterns
LennardJones The Lennard-Jones Potential
Kmulti Marked K-Function
bounding.box Bounding Box of a Window or Point Pattern
ppm Fit Point Process Model to Data
setmarks Set or Reset the Marks in a Point Pattern
Kmeasure Reduced Second Moment Measure
areadiff Difference of Disc Areas
affine.owin Apply Affine Transformation To Window
Jcross Multitype J Function (i-to-j)
as.mask Pixel Image Approximation of a Window
Kdot Multitype K Function (i-to-any)
centroid.owin Centroid of a window
amacrine Hughes' Amacrine Cell Data
cells Biological Cells Point Pattern
area.owin Area of a Window
swedishpines Swedish Pines Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
Gest Nearest Neighbour Distance Function G
Kcross Multitype K Function (Cross-type)
StraussHard The Strauss / Hard Core Point Process Model
Pairwise Generic Pairwise Interaction model
union.quad Union of Data and Dummy Points
as.matrix.im Convert Pixel Image to Matrix
Kest K-function
chorley Chorley-Ribble Cancer Data
Kest.fft K-function using FFT
as.rectangle Window Frame
allstats Calculate four standard summary functions of a point pattern.
bdist.points Distance to Boundary of Window
Kcross.inhom Inhomogeneous Cross K Function
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
clarkevans Clark and Evans Aggregation Index
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
bei Tropical rain forest trees
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
Strauss The Strauss Point Process Model
Kinhom Inhomogeneous K-function
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
density.psp Kernel Smoothing of Line Segment Pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
disc Circular Window
ponderosa Ponderosa Pine Tree Point Pattern
longleaf Longleaf Pines Point Pattern
im Create a Pixel Image Object
plot.psp plot a Spatial Line Segment Pattern
is.marked Test Whether Marks Are Present
plot.fv Plot Function Valuesn
reach Interaction Distance of a Point Process
rlinegrid Generate grid of parallel lines with random displacement
ripras Estimate window from points alone
humberside Humberside Data on Childhood Leukaemia and Lymphoma
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
rescale.psp Convert Line Segment Pattern to Another Unit of Length
Saturated Saturated Pairwise Interaction model
Jmulti Marked J Function
Iest Estimate the I-function
pairsat.family Saturated Pairwise Interaction Point Process Family
summary.listof Summary of a List of Things
square Square Window
rStrauss Perfect Simulation of the Strauss Process
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
summary.splitppp Summary of a Split Point Pattern
Jdot Multitype J Function (i-to-any)
ants Harkness-Isham ants' nests data
bdist.pixels Distance to Boundary of Window
clickppp Interactively Add Points
compatible.im Test Whether Two Pixel Images Are Compatible
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
cut.ppp Convert Point Pattern Marks from Numeric to Factor
plot.plotppm Plot a plotppm Object Created by plot.ppm
lengths.psp Lengths of Line Segments
pcf Pair Correlation Function
spatstat.options Internal Options in Spatstat Package
shift.ppp Apply Vector Translation To Point Pattern
rotate Rotate
spatstat The Spatstat Package
affine.psp Apply Affine Transformation To Line Segment Pattern
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Date 26 February 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Tue Feb 26 22:19:55 2008; adrian

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