spatstat v1.9-2

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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, 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
betacells Beta Ganglion Cells in Cat Retina
as.rectangle Window Frame
append.psp Combine Two Line Segment Patterns
midpoints.psp Midpoints of Line Segment Pattern
Saturated Saturated Pairwise Interaction model
corners Corners of a rectangle
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
Gmulti Marked Nearest Neighbour Distance Function
pairwise.family Pairwise Interaction Process Family
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
eem Exponential Energy Marks
is.marked.ppp Test Whether A Point Pattern is Marked
centroid.owin Centroid of a window
rmpoispp Generate Multitype Poisson Point Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
cut.ppp Convert Point Pattern Marks from Numeric to Factor
distmap.ppp Distance Map of Point Pattern
markcorr Mark Correlation Function
Iest Estimate the I-function
pcf.fasp Pair Correlation Function obtained from array of K functions
Strauss The Strauss Point Process Model
Kdot Multitype K Function (i-to-any)
eval.fv Evaluate Expression Involving Functions
kaplan.meier Kaplan-Meier Estimator using Histogram Data
raster.x Cartesian Coordinates for a Pixel Raster
predict.ppm Prediction from a Fitted Point Process Model
shift.psp Apply Vector Translation To Line Segment Pattern
ppm.object Class of Fitted Point Process Models
owin Create a Window
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rotate.psp Rotate a Line Segment Pattern
Gest Nearest Neighbour Distance Function G
as.mask Pixel Image Approximation of a Window
rshift Random Shift
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
copper Berman-Huntington points and lines data
suffstat Sufficient Statistic of Point Process Model
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
angles.psp Orientation Angles of Line Segments
mean.im Mean Pixel Value in an Image
plot.plotppm Plot a plotppm Object Created by plot.ppm
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
Jest Estimate the J-function
as.im Convert to Pixel Image
bdist.points Distance to Boundary of Window
complement.owin Take Complement of a Window
is.subset.owin Determine Whether One Window is Contained In Another
crossing.psp Crossing Points of Two Line Segment Patterns
print.owin Print Brief Details of a Spatial Window
diameter Diameter of a Window Frame
ppp.object Class of Point Patterns
rlabel Random Re-Labelling of Point Pattern
Ord Generic Ord Interaction model
setmarks Set or Reset the Marks in a Point Pattern
compatible.fv Test Whether Two Function Objects Are Compatible
rotate.owin Rotate a Window
cells Biological Cells Point Pattern
longleaf Longleaf Pines Point Pattern
runifpoint Generate N Uniform Random Points
erode.owin Erode a Window
Kest K-function
finpines Pine saplings in Finland.
spatstat The Spatstat Package
applynbd Apply Function to Every Neighbourhood in a Point Pattern
crossdist Pairwise distances
density.psp Kernel Smoothing of Line Segment Pattern
cut.im Convert Pixel Image from Numeric to Factor
profilepl Profile Maximum Pseudolikelihood
distmap.psp Distance Map of Line Segment Pattern
pairdist.psp Pairwise distances between line segments
levelset Level Set of a Pixel Image
rMaternII Simulate Matern Model II
reach Interaction Distance of a Point Process
update.ppm Update a Fitted Point Process Model
Fest Estimate the empty space function F
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
LennardJones The Lennard-Jones Potential
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
psp Create a Line Segment Pattern
rstrat Stratified random point pattern
residualspaper Data and Code From JRSS Discussion Paper on Residuals
DiggleGratton Diggle-Gratton model
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Pairwise Generic Pairwise Interaction model
Kmeasure Reduced Second Moment Measure
expand.owin Expand Window By Factor
Poisson Poisson Point Process Model
dilate.owin Dilate a Window
mincontrast Method of Minimum Contrast
area.owin Area of a Window
is.im Test Whether An Object Is A Pixel Image
print.im Print Brief Details of an Image
pairsat.family Saturated Pairwise Interaction Point Process Family
print.quad Print a Quadrature Scheme
as.psp Convert Data To Class psp
crossdist.ppp Pairwise distances between two different point patterns
rSSI Simple Sequential Inhibition
rMaternI Simulate Matern Model I
union.quad Union of Data and Dummy Points
plot.fasp Plot a Function Array
swedishpines Swedish Pines Point Pattern
redwood California Redwoods Point Pattern (Ripley's Subset)
summary.quad Summarizing a Quadrature Scheme
fv.object Data Frames of Function Values
Jcross Multitype J Function (i-to-j)
harmonic Basis for Harmonic Functions
gridweights Compute Quadrature Weights Based on Grid Counts
subset.fv Extract Subset of Function Values
ripras Estimate window from points alone
StraussHard The Strauss / Hard Core Point Process Model
im Create a Pixel Image Object
nndist Nearest neighbour distances
reduced.sample Reduced Sample Estimator using Histogram Data
OrdThresh Ord's Interaction model
demopat Artificial Data Point Pattern
quad.object Class of Quadrature Schemes
compatible.im Test Whether Two Pixel Images Are Compatible
pairdist.default Pairwise distances
rshift.psp Randomly Shift a Line Segment Pattern
setcov Set Covariance of a Window
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
envelope Simulation envelopes of summary function
ppp Create a Point Pattern
ppm Fit Point Process Model to Data
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
spruces Spruces Point Pattern
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
density.ppp Kernel Smoothed Intensity of Point Pattern
rpoint Generate N Random Points
Geyer Geyer's Saturation Point Process Model
unique.ppp Extract Unique Points from a Spatial Point Pattern
Jdot Multitype J Function (i-to-any)
data.ppm Extract Original Data from a Fitted Point Process Model
Kdot.inhom Inhomogeneous Multitype K Dot Function
subset.im Extract Subset of Image
Kcross Multitype K Function (Cross-type)
MultiStrauss The Multitype Strauss Point Process Model
rThomas Simulate Thomas Process
Kinhom Inhomogeneous K-function
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
eroded.areas Areas of Morphological Erosions
as.matrix.im Convert Pixel Image to Matrix
plot.ppm plot a Fitted Point Process Model
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
Kmulti Marked K-Function
bramblecanes Hutchings' Bramble Canes data
subset.fasp Extract Subset of Function Array
affine.psp Apply Affine Transformation To Line Segment Pattern
as.owin Convert Data To Class owin
pairdist Pairwise distances
lurking Lurking variable plot
affine Apply Affine Transformation
plot.ppp plot a Spatial Point Pattern
crossdist.default Pairwise distances between two different sets of points
pcf Pair Correlation Function
concatxy Concatenate x,y Coordinate Vectors
print.psp Print Brief Details of a Line Segment Pattern Dataset
coef.ppm Coefficients of Fitted Point Process Model
crossdist.psp Pairwise distances between two different line segment patterns
spatstat-deprecated Deprecated spatstat functions
hamster Aherne's hamster tumour data
subset.psp Extract Subset of Line Segment Pattern
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
shift.im Apply Vector Translation To Pixel Image
rNeymanScott Simulate Neyman-Scott Process
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
affine.owin Apply Affine Transformation To Window
plot.psp plot a Spatial Line Segment Pattern
lengths.psp Lengths of Line Segments
rpoisline Generate Poisson Random Line Process
summary.ppm Summarizing a Fitted Point Process Model
anova.ppm ANOVA for Fitted Point Process Models
allstats Calculate four standard summary functions of a point pattern.
shift.ppp Apply Vector Translation To Point Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
multiplicity.ppp Count Multiplicity of Duplicate Points
rcell Simulate Baddeley-Silverman Cell Process
residuals.ppm Residuals for Fitted Point Process Model
identify.ppp Identify Points in a Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
Kest.fft K-function using FFT
gridcentres Rectangular grid of points
distmap.owin Distance Map of Window
endpoints.psp Endpoints of Line Segment Pattern
inside.owin Test Whether Points Are Inside A Window
is.ppp Test Whether An Object Is A Point Pattern
square Square Window
is.marked Test Whether Marks Are Present
is.ppm Test Whether An Object Is A Fitted Point Process Model
intersect.owin Intersection or Union of Two Windows
default.dummy Generate a Default Pattern of Dummy Points
summary.im Summarizing a Pixel Image
plot.im Plot a Pixel Image
japanesepines Japanese Pines Point Pattern
Kcross.inhom Inhomogeneous Cross K Function
simdat Simulated Point Pattern
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
pairdist.ppp Pairwise distances
spokes Spokes pattern of dummy points
as.ppp Convert Data To Class ppp
plot.quad plot a Spatial Quadrature Scheme
bounding.box Bounding Box of a Window
quadratcount Quadrat counting for a point pattern
summary.owin Summary of a Spatial Window
owin.object Class owin
im.object Class of Images
spatstat-internal Internal spatstat functions
nztrees New Zealand Trees Point Pattern
rotate Rotate
lansing Lansing Woods Point Pattern
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
letterR Window in Shape of Letter R
chorley Chorley-Ribble Cancer Data
unmark Remove Marks from a Marked Point Pattern
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
rshift.ppp Randomly Shift a Point Pattern
plot.owin Plot a Spatial Window
rpoispp Generate Poisson Point Pattern
nnwhich Nearest neighbour
superimpose Superimpose Several Point Patterns
eval.im Evaluate Expression Involving Pixel Images
rmh.ppm Simulate from a Fitted Point Process Model
Jmulti Marked J Function
is.owin Test Whether An Object Is A Window
plot.splitppp Plot a List of Point Patterns
ganglia Beta Ganglion Cells in Cat Retina, Old Version
rmpoint Generate N Random Multitype Points
shift Apply Vector Translation
shift.owin Apply Vector Translation To Window
split.ppp Divide Point Pattern into Sub-patterns
amacrine Hughes' Amacrine Cell Data
distmap Distance Map
rMatClust Simulate Matern Cluster Process
rshift.splitppp Randomly Shift a List of Point Patterns
hist.im Histogram of Pixel Values in an Image
rthin Random Thinning
spatstat.options Internal Options in Spatstat Package
rsyst Systematic random point pattern
subset.ppp Extract or Replace Subset of Point Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
persp.im Perspective Plot of Pixel Image
plot.fv Plot Function Valuesn
pcf.fv Pair Correlation Function obtained from K Function
pcf.ppp Pair Correlation Function of Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
print.ppp Print Brief Details of a Point Pattern Dataset
Softcore The Soft Core Point Process Model
scanpp Read Point Pattern From Data File
quadscheme Generate a Quadrature Scheme from a Point Pattern
quantile.im Sample Quantiles of Pixel Image
affine.ppp Apply Affine Transformation To Point Pattern
ants Harkness-Isham ants' nests data
rescue.rectangle Convert Window Back To Rectangle
bdist.pixels Distance to Boundary of Window
fitted.ppm Fitted Conditional Intensity for Point Process Model
rotate.ppp Rotate a Point Pattern
fasp.object Function Arrays for Spatial Patterns
humberside Humberside Data on Childhood Leukaemia and Lymphoma
is.marked.ppm Test Whether A Point Process Model is Marked
ord.family Ord Interaction Process Family
print.ppm Print a Fitted Point Process Model
psp.object Class of Line Segment Patterns
summary.ppp Summary of a Point Pattern Dataset
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Date 5 June 2006
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Mon Jun 5 11:53:50 2006; adrian

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