spatstat v1.11-1

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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 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
applynbd Apply Function to Every Neighbourhood in a Point Pattern
complement.owin Take Complement of a Window
Kmeasure Reduced Second Moment Measure
erode.owin Erode a Window
crossdist Pairwise distances
spatstat The Spatstat Package
Kmulti Marked K-Function
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
as.ppp Convert Data To Class ppp
density.psp Kernel Smoothing of Line Segment Pattern
cells Biological Cells Point Pattern
Kcross.inhom Inhomogeneous Cross K Function
gridcentres Rectangular grid of points
identify.ppp Identify Points in a Point Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
Kcross Multitype K Function (Cross-type)
Geyer Geyer's Saturation Point Process Model
Kest.fft K-function using FFT
cut.ppp Convert Point Pattern Marks from Numeric to Factor
mean.im Mean Pixel Value in an Image
distmap.ppp Distance Map of Point Pattern
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
Kinhom Inhomogeneous K-function
concatxy Concatenate x,y Coordinate Vectors
MultiStrauss The Multitype Strauss Point Process Model
humberside Humberside Data on Childhood Leukaemia and Lymphoma
is.owin Test Whether An Object Is A Window
Gmulti Marked Nearest Neighbour Distance Function
disc Circular Window
pcf.fv Pair Correlation Function obtained from K Function
mincontrast Method of Minimum Contrast
density.ppp Kernel Smoothed Intensity of Point Pattern
pairdist.default Pairwise distances
Strauss The Strauss Point Process Model
envelope Simulation envelopes of summary function
print.owin Print Brief Details of a Spatial Window
Jmulti Marked J Function
Fest Estimate the empty space function F
chorley Chorley-Ribble Cancer Data
rStrauss Perfect Simulation of the Strauss Process
as.matrix.im Convert Pixel Image to Matrix
is.multitype.ppp Test Whether A Point Pattern is Multitype
Softcore The Soft Core Point Process Model
pcf Pair Correlation Function
endpoints.psp Endpoints of Line Segment Pattern
as.mask Pixel Image Approximation of a Window
gridweights Compute Quadrature Weights Based on Grid Counts
rescale.ppp Convert Point Pattern to Another Unit of Length
finpines Pine saplings in Finland.
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
OrdThresh Ord's Interaction model
print.ppp Print Brief Details of a Point Pattern Dataset
harmonic Basis for Harmonic Functions
clickppp Interactively Add Points
bramblecanes Hutchings' Bramble Canes data
im Create a Pixel Image Object
ants Harkness-Isham ants' nests data
Iest Estimate the I-function
affine.owin Apply Affine Transformation To Window
as.psp Convert Data To Class psp
Jest Estimate the J-function
distmap Distance Map
bdist.pixels Distance to Boundary of Window
StraussHard The Strauss / Hard Core Point Process Model
hist.im Histogram of Pixel Values in an Image
amacrine Hughes' Amacrine Cell Data
rescale.owin Convert Window to Another Unit of Length
pairsat.family Saturated Pairwise Interaction Point Process Family
inside.owin Test Whether Points Are Inside A Window
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
distmap.psp Distance Map of Line Segment Pattern
betacells Beta Ganglion Cells in Cat Retina
bei Tropical rain forest trees
is.marked.ppp Test Whether A Point Pattern is Marked
pcf.fasp Pair Correlation Function obtained from array of K functions
kaplan.meier Kaplan-Meier Estimator using Histogram Data
pairdist.psp Pairwise distances between line segments
ppm Fit Point Process Model to Data
is.marked.ppm Test Whether A Point Process Model is Marked
rescale.psp Convert Line Segment Pattern to Another Unit of Length
Poisson Poisson Point Process Model
longleaf Longleaf Pines Point Pattern
demopat Artificial Data Point Pattern
plot.ppm plot a Fitted Point Process Model
crossdist.default Pairwise distances between two different sets of points
rshift.ppp Randomly Shift a Point Pattern
subset.fasp Extract Subset of Function Array
rcell Simulate Baddeley-Silverman Cell Process
lansing Lansing Woods Point Pattern
midpoints.psp Midpoints of Line Segment Pattern
ripras Estimate window from points alone
psp Create a Line Segment Pattern
data.ppm Extract Original Data from a Fitted Point Process Model
subset.ppp Extract or Replace Subset of Point Pattern
residualspaper Data and Code From JRSS Discussion Paper on Residuals
summary.quad Summarizing a Quadrature Scheme
plot.quad plot a Spatial Quadrature Scheme
runifpoint Generate N Uniform Random Points
is.ppm Test Whether An Object Is A Fitted Point Process Model
markcorr Mark Correlation Function
im.object Class of Images
nearest.raster.point Find Pixel Nearest to a Given Point
plot.plotppm Plot a plotppm Object Created by plot.ppm
Jcross Multitype J Function (i-to-j)
pppdist Optimal Match Between Two Point Patterns
runifdisc Generate N Uniform Random Points in a Disc
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
eval.im Evaluate Expression Involving Pixel Images
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
summary.splitppp Summary of a Split Point Pattern
ppp.object Class of Point Patterns
Pairwise Generic Pairwise Interaction model
intersect.owin Intersection or Union of Two Windows
crossdist.ppp Pairwise distances between two different point patterns
subset.im Extract Subset of Image
rshift Random Shift
rescale Convert dataset to another unit of length
fasp.object Function Arrays for Spatial Patterns
redwoodfull California Redwoods Point Pattern (Entire Dataset)
hamster Aherne's hamster tumour data
summary.owin Summary of a Spatial Window
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
is.marked Test Whether Marks Are Present
is.ppp Test Whether An Object Is A Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
nztrees New Zealand Trees Point Pattern
print.psp Print Brief Details of a Line Segment Pattern Dataset
ord.family Ord Interaction Process Family
angles.psp Orientation Angles of Line Segments
shift.im Apply Vector Translation To Pixel Image
rshift.psp Randomly Shift a Line Segment Pattern
rstrat Simulate Stratified Random Point Pattern
print.quad Print a Quadrature Scheme
levelset Level Set of a Pixel Image
shift.ppp Apply Vector Translation To Point Pattern
subset.splitppp Extract or Replace Sub-Patterns
shift Apply Vector Translation
unique.ppp Extract Unique Points from a Spatial Point Pattern
trim.rectangle Cut margins from rectangle
superimpose Superimpose Several Point Patterns
rsyst Simulate systematic random point pattern
fv.object Data Frames of Function Values
affine Apply Affine Transformation
letterR Window in Shape of Letter R
nbfires Point Patterns of New Brunswick Forest Fires
update.ppm Update a Fitted Point Process Model
Ord Generic Ord Interaction model
rmpoispp Generate Multitype Poisson Point Pattern
DiggleGratton Diggle-Gratton model
spatstat-internal Internal spatstat functions
centroid.owin Centroid of a window
spatstat.options Internal Options in Spatstat Package
is.multitype.ppm Test Whether A Point Process Model is Multitype
summary.ppm Summarizing a Fitted Point Process Model
plot.fasp Plot a Function Array
square Square Window
bounding.box Bounding Box of a Window
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
plot.owin Plot a Spatial Window
LennardJones The Lennard-Jones Potential
nndist Nearest neighbour distances
as.rectangle Window Frame
crossing.psp Crossing Points of Two Line Segment Patterns
compatible.fv Test Whether Two Function Objects Are Compatible
units Name for Unit of Length
nncross Nearest Neighbour in Another Point Pattern
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
ppm.object Class of Fitted Point Process Models
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
ppp Create a Point Pattern
corners Corners of a rectangle
copper Berman-Huntington points and lines data
print.im Print Brief Details of an Image
fitted.ppm Fitted Conditional Intensity for Point Process Model
Kest K-function
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
allstats Calculate four standard summary functions of a point pattern.
psp.object Class of Line Segment Patterns
area.owin Area of a Window
owin.object Class owin
reduced.sample Reduced Sample Estimator using Histogram Data
rotate.psp Rotate a Line Segment Pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
diameter Diameter of a Window
summary.psp Summary of a Line Segment Pattern Dataset
rpoint Generate N Random Points
rotate.ppp Rotate a Point Pattern
persp.im Perspective Plot of Pixel Image
spruces Spruces Point Pattern
plot.fv Plot Function Valuesn
thomas.estK Fit the Thomas Point Process by Minimum Contrast
plot.ppp plot a Spatial Point Pattern
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
japanesepines Japanese Pines Point Pattern
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
residuals.ppm Residuals for Fitted Point Process Model
rlabel Random Re-Labelling of Point Pattern
reach Interaction Distance of a Point Process
rpoisline Generate Poisson Random Line Process
raster.x Cartesian Coordinates for a Pixel Raster
Saturated Saturated Pairwise Interaction model
rmpoint Generate N Random Multitype Points
rpoispp Generate Poisson Point Pattern
as.im Convert to Pixel Image
default.dummy Generate a Default Pattern of Dummy Points
suffstat Sufficient Statistic of Point Process Model
bdist.points Distance to Boundary of Window
expand.owin Expand Window By Factor
lurking Lurking variable plot
is.subset.owin Determine Whether One Window is Contained In Another
predict.ppm Prediction from a Fitted Point Process Model
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
redwood California Redwoods Point Pattern (Ripley's Subset)
summary.listof Summary of a List of Things
contour.im Contour plot of pixel image
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
is.im Test Whether An Object Is A Pixel Image
is.multitype Test whether Object is Multitype
pairdist Pairwise distances
owin Create a Window
plot.splitppp Plot a List of Point Patterns
quadratcount Quadrat counting for a point pattern
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rotate Rotate
scanpp Read Point Pattern From Data File
subset.fv Extract Subset of Function Values
vertices Vertices of a Window
Jdot Multitype J Function (i-to-any)
eroded.areas Areas of Morphological Erosions
ganglia Beta Ganglion Cells in Cat Retina, Old Version
lengths.psp Lengths of Line Segments
pairwise.family Pairwise Interaction Process Family
rSSI Simulate Simple Sequential Inhibition
print.ppm Print a Fitted Point Process Model
rotate.owin Rotate a Window
shift.owin Apply Vector Translation To Window
setmarks Set or Reset the Marks in a Point Pattern
affine.psp Apply Affine Transformation To Line Segment Pattern
affine.ppp Apply Affine Transformation To Point Pattern
Kdot.inhom Inhomogeneous Multitype K Dot Function
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
crossdist.psp Pairwise distances between two different line segment patterns
Kdot Multitype K Function (i-to-any)
cut.im Convert Pixel Image from Numeric to Factor
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
eem Exponential Energy Marks
anova.ppm ANOVA for Fitted Point Process Models
distmap.owin Distance Map of Window
as.owin Convert Data To Class owin
multiplicity.ppp Count Multiplicity of Duplicate Points
dilate.owin Dilate a Window
rMatClust Simulate Matern Cluster Process
rshift.splitppp Randomly Shift a List of Point Patterns
rescue.rectangle Convert Window Back To Rectangle
subset.psp Extract Subset of Line Segment Pattern
swedishpines Swedish Pines Point Pattern
setcov Set Covariance of a Window
quantile.im Sample Quantiles of Pixel Image
rMaternII Simulate Matern Model II
rthin Random Thinning
subset.listof Extract or Replace Subset of a List of Things
Gest Nearest Neighbour Distance Function G
append.psp Combine Two Line Segment Patterns
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
spatstat-deprecated Deprecated spatstat functions
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
nnwhich Nearest neighbour
plot.psp plot a Spatial Line Segment Pattern
plot.listof Plot a List of Things
rNeymanScott Simulate Neyman-Scott Process
quadscheme Generate a Quadrature Scheme from a Point Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
shift.psp Apply Vector Translation To Line Segment Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
summary.ppp Summary of a Point Pattern Dataset
unmark Remove Marks from a Marked Point Pattern
union.quad Union of Data and Dummy Points
rmh.ppm Simulate from a Fitted Point Process Model
coef.ppm Coefficients of Fitted Point Process Model
eval.fv Evaluate Expression Involving Functions
pairdist.ppp Pairwise distances
plot.im Plot a Pixel Image
pcf.ppp Pair Correlation Function of Point Pattern
profilepl Profile Maximum Pseudolikelihood
quad.object Class of Quadrature Schemes
rThomas Simulate Thomas Process
rMaternI Simulate Matern Model I
progressreport Print Progress Reports
spokes Spokes pattern of dummy points
split.ppp Divide Point Pattern into Sub-patterns
summary.im Summarizing a Pixel Image
simdat Simulated Point Pattern
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Date 01 February 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Thu Feb 1 11:09:56 2007; adrian

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