spatstat v1.9-4

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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
Jdot Multitype J Function (i-to-any)
Fest Estimate the empty space function F
corners Corners of a rectangle
anova.ppm ANOVA for Fitted Point Process Models
LennardJones The Lennard-Jones Potential
Softcore The Soft Core Point Process Model
DiggleGratton Diggle-Gratton model
Iest Estimate the I-function
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
ants Harkness-Isham ants' nests data
betacells Beta Ganglion Cells in Cat Retina
Jest Estimate the J-function
allstats Calculate four standard summary functions of a point pattern.
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
Saturated Saturated Pairwise Interaction model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
Kcross Multitype K Function (Cross-type)
Pairwise Generic Pairwise Interaction model
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
angles.psp Orientation Angles of Line Segments
im Create a Pixel Image Object
crossdist.ppp Pairwise distances between two different point patterns
Kest K-function
affine.ppp Apply Affine Transformation To Point Pattern
copper Berman-Huntington points and lines data
Geyer Geyer's Saturation Point Process Model
OrdThresh Ord's Interaction model
affine.psp Apply Affine Transformation To Line Segment Pattern
bdist.points Distance to Boundary of Window
expand.owin Expand Window By Factor
bounding.box Bounding Box of a Window
fv.object Data Frames of Function Values
as.im Convert to Pixel Image
erode.owin Erode a Window
Kmeasure Reduced Second Moment Measure
demopat Artificial Data Point Pattern
plot.im Plot a Pixel Image
rMaternII Simulate Matern Model II
owin Create a Window
endpoints.psp Endpoints of Line Segment Pattern
append.psp Combine Two Line Segment Patterns
as.matrix.im Convert Pixel Image to Matrix
quadscheme Generate a Quadrature Scheme from a Point Pattern
humberside Humberside Data on Childhood Leukaemia and Lymphoma
eval.fv Evaluate Expression Involving Functions
pairwise.family Pairwise Interaction Process Family
is.subset.owin Determine Whether One Window is Contained In Another
centroid.owin Centroid of a window
hist.im Histogram of Pixel Values in an Image
plot.owin Plot a Spatial Window
Poisson Poisson Point Process Model
letterR Window in Shape of Letter R
owin.object Class owin
rThomas Simulate Thomas Process
chorley Chorley-Ribble Cancer Data
pairdist.default Pairwise distances
predict.ppm Prediction from a Fitted Point Process Model
cells Biological Cells Point Pattern
ripras Estimate window from points alone
shift.ppp Apply Vector Translation To Point Pattern
quantile.im Sample Quantiles of Pixel Image
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
envelope Simulation envelopes of summary function
multiplicity.ppp Count Multiplicity of Duplicate Points
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
spatstat The Spatstat Package
data.ppm Extract Original Data from a Fitted Point Process Model
crossdist Pairwise distances
rpoint Generate N Random Points
gridcentres Rectangular grid of points
MultiStrauss The Multitype Strauss Point Process Model
pcf Pair Correlation Function
simdat Simulated Point Pattern
plot.plotppm Plot a plotppm Object Created by plot.ppm
print.ppp Print Brief Details of a Point Pattern Dataset
density.ppp Kernel Smoothed Intensity of Point Pattern
harmonic Basis for Harmonic Functions
pppdist Optimal Match Between Two Point Patterns
print.owin Print Brief Details of a Spatial Window
square Square Window
spatstat-deprecated Deprecated spatstat functions
complement.owin Take Complement of a Window
density.psp Kernel Smoothing of Line Segment Pattern
rotate.owin Rotate a Window
eval.im Evaluate Expression Involving Pixel Images
Gest Nearest Neighbour Distance Function G
Kinhom Inhomogeneous K-function
rotate.psp Rotate a Line Segment Pattern
pairdist.ppp Pairwise distances
selfcrossing.psp Crossing Points in a Line Segment Pattern
kaplan.meier Kaplan-Meier Estimator using Histogram Data
lengths.psp Lengths of Line Segments
rotate.ppp Rotate a Point Pattern
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
subset.fasp Extract Subset of Function Array
applynbd Apply Function to Every Neighbourhood in a Point Pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
levelset Level Set of a Pixel Image
identify.ppp Identify Points in a Point Pattern
is.owin Test Whether An Object Is A Window
bdist.pixels Distance to Boundary of Window
rshift Random Shift
nztrees New Zealand Trees Point Pattern
pairdist Pairwise distances
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
as.psp Convert Data To Class psp
affine.owin Apply Affine Transformation To Window
pcf.ppp Pair Correlation Function of Point Pattern
is.ppm Test Whether An Object Is A Fitted Point Process Model
rthin Random Thinning
markcorr Mark Correlation Function
shift.psp Apply Vector Translation To Line Segment Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
rstrat Simulate Stratified Random Point Pattern
crossdist.psp Pairwise distances between two different line segment patterns
mean.im Mean Pixel Value in an Image
print.im Print Brief Details of an Image
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
shift.owin Apply Vector Translation To Window
rmh.ppm Simulate from a Fitted Point Process Model
cut.ppp Convert Point Pattern Marks from Numeric to Factor
area.owin Area of a Window
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
as.ppp Convert Data To Class ppp
eem Exponential Energy Marks
is.marked Test Whether Marks Are Present
cut.im Convert Pixel Image from Numeric to Factor
ganglia Beta Ganglion Cells in Cat Retina, Old Version
intersect.owin Intersection or Union of Two Windows
hamster Aherne's hamster tumour data
is.marked.ppp Test Whether A Point Pattern is Marked
Gmulti Marked Nearest Neighbour Distance Function
Kdot Multitype K Function (i-to-any)
ord.family Ord Interaction Process Family
Kest.fft K-function using FFT
pairdist.psp Pairwise distances between line segments
Ord Generic Ord Interaction model
amacrine Hughes' Amacrine Cell Data
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
as.mask Pixel Image Approximation of a Window
plot.psp plot a Spatial Line Segment Pattern
psp Create a Line Segment Pattern
nndist Nearest neighbour distances
as.rectangle Window Frame
ppp Create a Point Pattern
bramblecanes Hutchings' Bramble Canes data
quadratcount Quadrat counting for a point pattern
residuals.ppm Residuals for Fitted Point Process Model
unique.ppp Extract Unique Points from a Spatial Point Pattern
rNeymanScott Simulate Neyman-Scott Process
summary.im Summarizing a Pixel Image
setcov Set Covariance of a Window
rcell Simulate Baddeley-Silverman Cell Process
nnwhich Nearest neighbour
crossdist.default Pairwise distances between two different sets of points
finpines Pine saplings in Finland.
is.ppp Test Whether An Object Is A Point Pattern
ppp.object Class of Point Patterns
nearest.raster.point Find Pixel Nearest to a Given Point
rpoisline Generate Poisson Random Line Process
rMatClust Simulate Matern Cluster Process
mincontrast Method of Minimum Contrast
spatstat.options Internal Options in Spatstat Package
shift Apply Vector Translation
subset.ppp Extract or Replace Subset of Point Pattern
rpoispp Generate Poisson Point Pattern
crossing.psp Crossing Points of Two Line Segment Patterns
fasp.object Function Arrays for Spatial Patterns
is.im Test Whether An Object Is A Pixel Image
thomas.estK Fit the Thomas Point Process by Minimum Contrast
coef.ppm Coefficients of Fitted Point Process Model
concatxy Concatenate x,y Coordinate Vectors
gridweights Compute Quadrature Weights Based on Grid Counts
distmap Distance Map
ppm Fit Point Process Model to Data
rMaternI Simulate Matern Model I
superimpose Superimpose Several Point Patterns
reduced.sample Reduced Sample Estimator using Histogram Data
summary.quad Summarizing a Quadrature Scheme
midpoints.psp Midpoints of Line Segment Pattern
union.quad Union of Data and Dummy Points
setmarks Set or Reset the Marks in a Point Pattern
persp.im Perspective Plot of Pixel Image
summary.psp Summary of a Line Segment Pattern Dataset
redwood California Redwoods Point Pattern (Ripley's Subset)
runifpoint Generate N Uniform Random Points
summary.ppm Summarizing a Fitted Point Process Model
rshift.psp Randomly Shift a Line Segment Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
shift.im Apply Vector Translation To Pixel Image
subset.fv Extract Subset of Function Values
split.ppp Divide Point Pattern into Sub-patterns
Jcross Multitype J Function (i-to-j)
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
unmark Remove Marks from a Marked Point Pattern
distmap.owin Distance Map of Window
im.object Class of Images
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
print.ppm Print a Fitted Point Process Model
psp.object Class of Line Segment Patterns
rStrauss Perfect Simulation of the Strauss Process
print.quad Print a Quadrature Scheme
scanpp Read Point Pattern From Data File
suffstat Sufficient Statistic of Point Process Model
spruces Spruces Point Pattern
rsyst Simulate systematic random point pattern
update.ppm Update a Fitted Point Process Model
subset.psp Extract Subset of Line Segment Pattern
Kmulti Marked K-Function
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
StraussHard The Strauss / Hard Core Point Process Model
inside.owin Test Whether Points Are Inside A Window
lurking Lurking variable plot
plot.fv Plot Function Valuesn
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
residualspaper Data and Code From JRSS Discussion Paper on Residuals
eroded.areas Areas of Morphological Erosions
Jmulti Marked J Function
fitted.ppm Fitted Conditional Intensity for Point Process Model
is.marked.ppm Test Whether A Point Process Model is Marked
nncross Nearest Neighbour in Another Point Pattern
plot.quad plot a Spatial Quadrature Scheme
plot.ppp plot a Spatial Point Pattern
profilepl Profile Maximum Pseudolikelihood
quad.object Class of Quadrature Schemes
rmpoint Generate N Random Multitype Points
lansing Lansing Woods Point Pattern
spokes Spokes pattern of dummy points
rescue.rectangle Convert Window Back To Rectangle
affine Apply Affine Transformation
as.owin Convert Data To Class owin
default.dummy Generate a Default Pattern of Dummy Points
clickppp Interactively Add Points
compatible.fv Test Whether Two Function Objects Are Compatible
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
dilate.owin Dilate a Window
bei Tropical rain forest trees
diameter Diameter of a Window Frame
print.psp Print Brief Details of a Line Segment Pattern Dataset
distmap.ppp Distance Map of Point Pattern
Kcross.inhom Inhomogeneous Cross K Function
Kdot.inhom Inhomogeneous Multitype K Dot Function
Strauss The Strauss Point Process Model
summary.ppp Summary of a Point Pattern Dataset
rshift.splitppp Randomly Shift a List of Point Patterns
ppm.object Class of Fitted Point Process Models
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rSSI Simulate Simple Sequential Inhibition
plot.fasp Plot a Function Array
pairsat.family Saturated Pairwise Interaction Point Process Family
pcf.fv Pair Correlation Function obtained from K Function
plot.ppm plot a Fitted Point Process Model
japanesepines Japanese Pines Point Pattern
raster.x Cartesian Coordinates for a Pixel Raster
spatstat-internal Internal spatstat functions
longleaf Longleaf Pines Point Pattern
rshift.ppp Randomly Shift a Point Pattern
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
distmap.psp Distance Map of Line Segment Pattern
rmpoispp Generate Multitype Poisson Point Pattern
plot.splitppp Plot a List of Point Patterns
swedishpines Swedish Pines Point Pattern
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
rlabel Random Re-Labelling of Point Pattern
summary.owin Summary of a Spatial Window
subset.im Extract Subset of Image
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
redwoodfull California Redwoods Point Pattern (Entire Dataset)
rotate Rotate
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
pcf.fasp Pair Correlation Function obtained from array of K functions
reach Interaction Distance of a Point Process
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Date 3 August 2006
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Thu Aug 3 14:31:58 2006; adrian

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