spatstat v1.12-9

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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
rMaternI Simulate Matern Model I
rmpoint Generate N Random Multitype Points
psp.object Class of Line Segment Patterns
rotate Rotate
redwood California Redwoods Point Pattern (Ripley's Subset)
plot.listof Plot a List of Things
ppm Fit Point Process Model to Data
raster.x Cartesian Coordinates for a Pixel Raster
plot.splitppp Plot a List of Point Patterns
rotate.owin Rotate a Window
rGaussPoisson Simulate Gauss-Poisson Process
rlinegrid Generate grid of parallel lines with random displacement
rescale Convert dataset to another unit of length
pppdist Distance Between Two Point Patterns
rescale.psp Convert Line Segment Pattern to Another Unit of Length
reduced.sample Reduced Sample Estimator using Histogram Data
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
reach Interaction Distance of a Point Process
print.ppm Print a Fitted Point Process Model
psp Create a Line Segment Pattern
quadratcount Quadrat counting for a point pattern
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
ppm.object Class of Fitted Point Process Models
ripras Estimate window from points alone
rotate.psp Rotate a Line Segment Pattern
print.owin Print Brief Details of a Spatial Window
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
rstrat Simulate Stratified Random Point Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
ppp.object Class of Point Patterns
plot.ppm plot a Fitted Point Process Model
ppp Create a Point Pattern
rotate.ppp Rotate a Point Pattern
quadscheme Generate a Quadrature Scheme from a Point Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
quad.object Class of Quadrature Schemes
rpoint Generate N Random Points
anova.ppm ANOVA for Fitted Point Process Models
plot.ppp plot a Spatial Point Pattern
plot.psp plot a Spatial Line Segment Pattern
print.psp Print Brief Details of a Line Segment Pattern Dataset
residuals.ppm Residuals for Fitted Point Process Model
is.multitype Test whether Object is Multitype
as.psp Convert Data To Class psp
affine.owin Apply Affine Transformation To Window
Kcross Multitype K Function (Cross-type)
area.owin Area of a Window
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
cut.ppp Convert Point Pattern Marks from Numeric to Factor
copper Berman-Huntington points and lines data
Gmulti Marked Nearest Neighbour Distance Function
Kest.fft K-function using FFT
Linhom L-function
pppmatching Create a Point Matching
pppmatching.object Class of Point Matchings
as.matrix.im Convert Pixel Image to Matrix
ord.family Ord Interaction Process Family
Kinhom Inhomogeneous K-function
Poisson Poisson Point Process Model
im.object Class of Images
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
spokes Spokes pattern of dummy points
coef.ppm Coefficients of Fitted Point Process Model
subset.listof Extract or Replace Subset of a List of Things
plot.fasp Plot a Function Array
Ord Generic Ord Interaction model
contour.im Contour plot of pixel image
im Create a Pixel Image Object
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
LennardJones The Lennard-Jones Potential
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
residualspaper Data and Code From JRSS Discussion Paper on Residuals
demopat Artificial Data Point Pattern
humberside Humberside Data on Childhood Leukaemia and Lymphoma
density.ppp Kernel Smoothed Intensity of Point Pattern
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
spatstat The Spatstat Package
spatstat-internal Internal spatstat functions
crossdist Pairwise distances
Gest Nearest Neighbour Distance Function G
rpoisline Generate Poisson Random Line Process
inforder.family Infinite Order Interaction Family
dilate.owin Dilate a Window
eroded.areas Areas of Morphological Erosions
Softcore The Soft Core Point Process Model
nndist.psp Nearest neighbour distances between line segments
is.ppm Test Whether An Object Is A Fitted Point Process Model
matchingdist Distance for a Point Pattern Matching
bdist.pixels Distance to Boundary of Window
data.ppm Extract Original Data from a Fitted Point Process Model
disc Circular Window
StraussHard The Strauss / Hard Core Point Process Model
Kcross.inhom Inhomogeneous Cross K Function
distmap.ppp Distance Map of Point Pattern
fitin.ppm Extract the Interaction from a Fitted Point Process Model
nndist Nearest neighbour distances
intersect.owin Intersection or Union of Two Windows
harmonic Basis for Harmonic Functions
is.ppp Test Whether An Object Is A Point Pattern
cut.im Convert Pixel Image from Numeric to Factor
nnwhich Nearest neighbour
rthin Random Thinning
DiggleGratton Diggle-Gratton model
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
plot.fv Plot Function Valuesn
mean.im Mean Pixel Value in an Image
model.images Compute Images of Constructed Covariates
is.multitype.ppp Test Whether A Point Pattern is Multitype
Iest Estimate the I-function
is.marked.ppm Test Whether A Point Process Model is Marked
runifpoint Generate N Uniform Random Points
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
crossdist.psp Pairwise distances between two different line segment patterns
as.ppp Convert Data To Class ppp
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
betacells Beta Ganglion Cells in Cat Retina
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
midpoints.psp Midpoints of Line Segment Pattern
is.marked.ppp Test Whether A Point Pattern is Marked
pairwise.family Pairwise Interaction Process Family
rThomas Simulate Thomas Process
plot.owin Plot a Spatial Window
angles.psp Orientation Angles of Line Segments
rSSI Simulate Simple Sequential Inhibition
clickpoly Interactively Define a Polygon
as.im Convert to Pixel Image
default.dummy Generate a Default Pattern of Dummy Points
nncross Nearest Neighbour in Another Point Pattern
endpoints.psp Endpoints of Line Segment Pattern
erode.owin Erode a Window
progressreport Print Progress Reports
pairdist.default Pairwise distances
distmap.psp Distance Map of Line Segment Pattern
plot.hyperframe Plot Entries in a Hyperframe
Lest L-function
Pairwise Generic Pairwise Interaction model
Jmulti Marked J Function
localK Neighbourhood density function
Jcross Multitype J Function (i-to-j)
Strauss The Strauss Point Process Model
summary.im Summarizing a Pixel Image
as.data.frame.ppp Coerce Point Pattern to a Data Frame
subset.fasp Extract Subset of Function Array
MultiStrauss The Multitype Strauss Point Process Model
chorley Chorley-Ribble Cancer Data
Jdot Multitype J Function (i-to-any)
superimpose Superimpose Several Point Patterns
pcf.fasp Pair Correlation Function obtained from array of K functions
shift.im Apply Vector Translation To Pixel Image
crossdist.ppp Pairwise distances between two different point patterns
corners Corners of a rectangle
inside.owin Test Whether Points Are Inside A Window
expand.owin Expand Window By Factor
split.ppp Divide Point Pattern into Sub-patterns
subset.psp Extract Subset of Line Segment Pattern
distmap.owin Distance Map of Window
amacrine Hughes' Amacrine Cell Data
rshift.ppp Randomly Shift a Point Pattern
nztrees New Zealand Trees Point Pattern
owin Create a Window
cells Biological Cells Point Pattern
union.quad Union of Data and Dummy Points
is.owin Test Whether An Object Is A Window
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
OrdThresh Ord's Interaction model
crossdist.default Pairwise distances between two different sets of points
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
is.marked Test Whether Marks Are Present
setmarks Set or Reset the Marks in a Point Pattern
square Square Window
update.ppm Update a Fitted Point Process Model
pcf.ppp Pair Correlation Function of Point Pattern
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
multiplicity.ppp Count Multiplicity of Duplicate Points
AreaInter The Area Interaction Point Process Model
areadiff Difference of Disc Areas
summary.owin Summary of a Spatial Window
summary.psp Summary of a Line Segment Pattern Dataset
summary.ppm Summarizing a Fitted Point Process Model
mincontrast Method of Minimum Contrast
Kmeasure Reduced Second Moment Measure
clarkevans Clark and Evans Aggregation Index
bounding.box.xy Convex Hull of Points
as.rectangle Window Frame
simdat Simulated Point Pattern
crossing.psp Crossing Points of Two Line Segment Patterns
summary.listof Summary of a List of Things
unique.ppp Extract Unique Points from a Spatial Point Pattern
fitted.ppm Fitted Conditional Intensity for Point Process Model
affine.psp Apply Affine Transformation To Line Segment Pattern
Jest Estimate the J-function
rStrauss Perfect Simulation of the Strauss Process
concatxy Concatenate x,y Coordinate Vectors
pairdist Pairwise distances
affine.ppp Apply Affine Transformation To Point Pattern
centroid.owin Centroid of a window
identify.ppp Identify Points in a Point Pattern
density.psp Kernel Smoothing of Line Segment Pattern
spruces Spruces Point Pattern
subset.ppp Extract or Replace Subset of Point Pattern
hyperframe Hyper Data Frame
setcov Set Covariance of a Window
hamster Aherne's hamster tumour data
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
lansing Lansing Woods Point Pattern
lurking Lurking variable plot
ponderosa Ponderosa Pine Tree Point Pattern
pairdist.ppp Pairwise distances
nbfires Point Patterns of New Brunswick Forest Fires
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
subset.im Extract Subset of Image
hist.im Histogram of Pixel Values in an Image
ganglia Beta Ganglion Cells in Cat Retina, Old Version
bramblecanes Hutchings' Bramble Canes data
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
unitname Name for Unit of Length
shift.owin Apply Vector Translation To Window
profilepl Profile Maximum Pseudolikelihood
suffstat Sufficient Statistic of Point Process Model
runifdisc Generate N Uniform Random Points in a Disc
longleaf Longleaf Pines Point Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
fasp.object Function Arrays for Spatial Patterns
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
plot.quad plot a Spatial Quadrature Scheme
summary.quad Summarizing a Quadrature Scheme
applynbd Apply Function to Every Neighbourhood in a Point Pattern
affine Apply Affine Transformation
gridcentres Rectangular grid of points
unmark Remove Marks from a Marked Point Pattern
levelset Level Set of a Pixel Image
as.owin Convert Data To Class owin
vertices Vertices of a Window
rsyst Simulate systematic random point pattern
rescale.ppp Convert Point Pattern to Another Unit of Length
trim.rectangle Cut margins from rectangle
ewcdf Weighted Empirical Cumulative Distribution Function
is.multitype.ppm Test Whether A Point Process Model is Multitype
eem Exponential Energy Marks
Kmulti Marked K-Function
pcf Pair Correlation Function
rshift.splitppp Randomly Shift a List of Point Patterns
discretise Safely Convert Point Pattern Window to Binary Mask
letterR Window in Shape of Letter R
complement.owin Take Complement of a Window
clickppp Interactively Add Points
print.im Print Brief Details of an Image
pcf.fv Pair Correlation Function obtained from K Function
convexhull.xy Convex Hull of Points
spatstat.options Internal Options in Spatstat Package
owin.object Class owin
compatible.im Test Whether Two Pixel Images Are Compatible
ants Harkness-Isham ants' nests data
japanesepines Japanese Pines Point Pattern
eval.im Evaluate Expression Involving Pixel Images
logLik.ppm Log Likelihood for Poisson Point Process Model
finpines Pine saplings in Finland.
diameter Diameter of a Window
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
plot.plotppm Plot a plotppm Object Created by plot.ppm
model.matrix.ppm Extract Design Matrix from Point Process Model
summary.splitppp Summary of a Split Point Pattern
subset.splitppp Extract or Replace Sub-Patterns
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
anemones Beadlet Anemones Data
envelope Simulation envelopes of summary function
as.mask Pixel Image Approximation of a Window
rmpoispp Generate Multitype Poisson Point Pattern
summary.ppp Summary of a Point Pattern Dataset
eval.fv Evaluate Expression Involving Functions
plot.im Plot a Pixel Image
thomas.estK Fit the Thomas Point Process by Minimum Contrast
kaplan.meier Kaplan-Meier Estimator using Histogram Data
distmap Distance Map
shift.psp Apply Vector Translation To Line Segment Pattern
shift Apply Vector Translation
lengths.psp Lengths of Line Segments
rshift.psp Randomly Shift a Line Segment Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
fv.object Data Frames of Function Values
predict.ppm Prediction from a Fitted Point Process Model
rcell Simulate Baddeley-Silverman Cell Process
Kdot Multitype K Function (i-to-any)
append.psp Combine Two Line Segment Patterns
Saturated Saturated Pairwise Interaction model
compatible.fv Test Whether Two Function Objects Are Compatible
interp.im Interpolate a Pixel Image
pairsat.family Saturated Pairwise Interaction Point Process Family
is.im Test Whether An Object Is A Pixel Image
rMatClust Simulate Matern Cluster Process
scanpp Read Point Pattern From Data File
rshift Random Shift
spatstat-deprecated Deprecated spatstat functions
smooth.ppp Spatial smoothing of observations at irregular points
markcorr Mark Correlation Function
rpoispp Generate Poisson Point Pattern
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
swedishpines Swedish Pines Point Pattern
rMaternII Simulate Matern Model II
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
quantile.im Sample Quantiles of Pixel Image
bei Tropical rain forest trees
Geyer Geyer's Saturation Point Process Model
Kdot.inhom Inhomogeneous Multitype K Dot Function
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
pairdist.psp Pairwise distances between line segments
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
persp.im Perspective Plot of Pixel Image
subsetget.im Reset Values in Subset of Image
rNeymanScott Simulate Neyman-Scott Process
rescue.rectangle Convert Window Back To Rectangle
subset.fv Extract Subset of Function Values
gridweights Compute Quadrature Weights Based on Grid Counts
shift.ppp Apply Vector Translation To Point Pattern
print.quad Print a Quadrature Scheme
rescale.owin Convert Window to Another Unit of Length
rlabel Random Re-Labelling of Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
Kest K-function
bdist.points Distance to Boundary of Window
bounding.box Bounding Box of a Window or Point Pattern
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
is.subset.owin Determine Whether One Window is Contained In Another
allstats Calculate four standard summary functions of a point pattern.
rmh.ppm Simulate from a Fitted Point Process Model
Fest Estimate the empty space function F
print.ppp Print Brief Details of a Point Pattern Dataset
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Date 18 March 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Tue Mar 18 19:05:24 2008; adrian

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