spatstat v1.9-5

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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
Fest Estimate the empty space function F
Jest Estimate the J-function
Kmulti Marked K-Function
MultiStrauss The Multitype Strauss Point Process Model
bei Tropical rain forest trees
contour.im Contour plot of pixel image
hamster Aherne's hamster tumour data
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
plot.fv Plot Function Valuesn
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
Saturated Saturated Pairwise Interaction model
pairdist Pairwise distances
ppp.object Class of Point Patterns
pcf.fv Pair Correlation Function obtained from K Function
spatstat The Spatstat Package
print.psp Print Brief Details of a Line Segment Pattern Dataset
bramblecanes Hutchings' Bramble Canes data
reduced.sample Reduced Sample Estimator using Histogram Data
cells Biological Cells Point Pattern
rpoint Generate N Random Points
im.object Class of Images
bdist.pixels Distance to Boundary of Window
identify.ppp Identify Points in a Point Pattern
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
crossdist.default Pairwise distances between two different sets of points
rstrat Simulate Stratified Random Point Pattern
Kdot Multitype K Function (i-to-any)
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
nztrees New Zealand Trees Point Pattern
Poisson Poisson Point Process Model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
coef.ppm Coefficients of Fitted Point Process Model
im Create a Pixel Image Object
Jcross Multitype J Function (i-to-j)
dilate.owin Dilate a Window
pcf.ppp Pair Correlation Function of Point Pattern
mean.im Mean Pixel Value in an Image
angles.psp Orientation Angles of Line Segments
plot.im Plot a Pixel Image
rNeymanScott Simulate Neyman-Scott Process
is.im Test Whether An Object Is A Pixel Image
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
rpoisline Generate Poisson Random Line Process
amacrine Hughes' Amacrine Cell Data
unmark Remove Marks from a Marked Point Pattern
mincontrast Method of Minimum Contrast
split.ppp Divide Point Pattern into Sub-patterns
complement.owin Take Complement of a Window
Pairwise Generic Pairwise Interaction model
ppm.object Class of Fitted Point Process Models
rSSI Simulate Simple Sequential Inhibition
cut.ppp Convert Point Pattern Marks from Numeric to Factor
owin Create a Window
as.owin Convert Data To Class owin
pairwise.family Pairwise Interaction Process Family
clickppp Interactively Add Points
psp.object Class of Line Segment Patterns
concatxy Concatenate x,y Coordinate Vectors
fv.object Data Frames of Function Values
crossdist.psp Pairwise distances between two different line segment patterns
cut.im Convert Pixel Image from Numeric to Factor
pairdist.psp Pairwise distances between line segments
reach Interaction Distance of a Point Process
pairsat.family Saturated Pairwise Interaction Point Process Family
print.ppp Print Brief Details of a Point Pattern Dataset
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
midpoints.psp Midpoints of Line Segment Pattern
nnwhich Nearest neighbour
shift.ppp Apply Vector Translation To Point Pattern
plot.splitppp Plot a List of Point Patterns
rotate Rotate
rthin Random Thinning
OrdThresh Ord's Interaction model
union.quad Union of Data and Dummy Points
eval.fv Evaluate Expression Involving Functions
corners Corners of a rectangle
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
spatstat-deprecated Deprecated spatstat functions
inside.owin Test Whether Points Are Inside A Window
distmap.psp Distance Map of Line Segment Pattern
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
distmap.ppp Distance Map of Point Pattern
eval.im Evaluate Expression Involving Pixel Images
shift.owin Apply Vector Translation To Window
Ord Generic Ord Interaction model
suffstat Sufficient Statistic of Point Process Model
intersect.owin Intersection or Union of Two Windows
Kinhom Inhomogeneous K-function
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
multiplicity.ppp Count Multiplicity of Duplicate Points
subset.ppp Extract or Replace Subset of Point Pattern
ants Harkness-Isham ants' nests data
is.marked Test Whether Marks Are Present
harmonic Basis for Harmonic Functions
pairdist.default Pairwise distances
StraussHard The Strauss / Hard Core Point Process Model
persp.im Perspective Plot of Pixel Image
plot.fasp Plot a Function Array
pcf Pair Correlation Function
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
Geyer Geyer's Saturation Point Process Model
nearest.raster.point Find Pixel Nearest to a Given Point
plot.psp plot a Spatial Line Segment Pattern
LennardJones The Lennard-Jones Potential
Kdot.inhom Inhomogeneous Multitype K Dot Function
plot.quad plot a Spatial Quadrature Scheme
area.owin Area of a Window
anova.ppm ANOVA for Fitted Point Process Models
plot.ppm plot a Fitted Point Process Model
pairdist.ppp Pairwise distances
eem Exponential Energy Marks
crossdist.ppp Pairwise distances between two different point patterns
summary.quad Summarizing a Quadrature Scheme
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
demopat Artificial Data Point Pattern
print.owin Print Brief Details of a Spatial Window
rMaternI Simulate Matern Model I
rcell Simulate Baddeley-Silverman Cell Process
profilepl Profile Maximum Pseudolikelihood
spatstat.options Internal Options in Spatstat Package
rMatClust Simulate Matern Cluster Process
rmh.ppm Simulate from a Fitted Point Process Model
rlabel Random Re-Labelling of Point Pattern
rpoispp Generate Poisson Point Pattern
kaplan.meier Kaplan-Meier Estimator using Histogram Data
lengths.psp Lengths of Line Segments
shift.im Apply Vector Translation To Pixel Image
Strauss The Strauss Point Process Model
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
subset.fv Extract Subset of Function Values
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
spokes Spokes pattern of dummy points
fitted.ppm Fitted Conditional Intensity for Point Process Model
eroded.areas Areas of Morphological Erosions
is.marked.ppp Test Whether A Point Pattern is Marked
spatstat-internal Internal spatstat functions
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
pcf.fasp Pair Correlation Function obtained from array of K functions
residuals.ppm Residuals for Fitted Point Process Model
rmpoispp Generate Multitype Poisson Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
nncross Nearest Neighbour in Another Point Pattern
plot.owin Plot a Spatial Window
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
quad.object Class of Quadrature Schemes
bounding.box Bounding Box of a Window
summary.psp Summary of a Line Segment Pattern Dataset
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
chorley Chorley-Ribble Cancer Data
compatible.im Test Whether Two Pixel Images Are Compatible
copper Berman-Huntington points and lines data
envelope Simulation envelopes of summary function
ganglia Beta Ganglion Cells in Cat Retina, Old Version
is.ppp Test Whether An Object Is A Point Pattern
superimpose Superimpose Several Point Patterns
plot.plotppm Plot a plotppm Object Created by plot.ppm
ppm Fit Point Process Model to Data
print.quad Print a Quadrature Scheme
gridweights Compute Quadrature Weights Based on Grid Counts
is.marked.ppm Test Whether A Point Process Model is Marked
rescue.rectangle Convert Window Back To Rectangle
ripras Estimate window from points alone
allstats Calculate four standard summary functions of a point pattern.
Jdot Multitype J Function (i-to-any)
affine.ppp Apply Affine Transformation To Point Pattern
rmpoint Generate N Random Multitype Points
as.mask Pixel Image Approximation of a Window
diameter Diameter of a Window Frame
centroid.owin Centroid of a window
compatible.fv Test Whether Two Function Objects Are Compatible
is.owin Test Whether An Object Is A Window
summary.im Summarizing a Pixel Image
levelset Level Set of a Pixel Image
endpoints.psp Endpoints of Line Segment Pattern
markcorr Mark Correlation Function
is.subset.owin Determine Whether One Window is Contained In Another
distmap.owin Distance Map of Window
ord.family Ord Interaction Process Family
quantile.im Sample Quantiles of Pixel Image
quadscheme Generate a Quadrature Scheme from a Point Pattern
rshift.psp Randomly Shift a Line Segment Pattern
raster.x Cartesian Coordinates for a Pixel Raster
rshift Random Shift
selfcrossing.psp Crossing Points in a Line Segment Pattern
spruces Spruces Point Pattern
square Square Window
subset.psp Extract Subset of Line Segment Pattern
Iest Estimate the I-function
DiggleGratton Diggle-Gratton model
is.ppm Test Whether An Object Is A Fitted Point Process Model
lansing Lansing Woods Point Pattern
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rMaternII Simulate Matern Model II
rotate.psp Rotate a Line Segment Pattern
shift Apply Vector Translation
rshift.splitppp Randomly Shift a List of Point Patterns
Gest Nearest Neighbour Distance Function G
bdist.points Distance to Boundary of Window
crossing.psp Crossing Points of Two Line Segment Patterns
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
hist.im Histogram of Pixel Values in an Image
residualspaper Data and Code From JRSS Discussion Paper on Residuals
swedishpines Swedish Pines Point Pattern
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
Kmeasure Reduced Second Moment Measure
as.im Convert to Pixel Image
as.rectangle Window Frame
erode.owin Erode a Window
Jmulti Marked J Function
gridcentres Rectangular grid of points
affine.psp Apply Affine Transformation To Line Segment Pattern
affine.owin Apply Affine Transformation To Window
affine Apply Affine Transformation
applynbd Apply Function to Every Neighbourhood in a Point Pattern
letterR Window in Shape of Letter R
finpines Pine saplings in Finland.
fasp.object Function Arrays for Spatial Patterns
crossdist Pairwise distances
longleaf Longleaf Pines Point Pattern
rotate.owin Rotate a Window
data.ppm Extract Original Data from a Fitted Point Process Model
distmap Distance Map
density.psp Kernel Smoothing of Line Segment Pattern
as.psp Convert Data To Class psp
Softcore The Soft Core Point Process Model
plot.ppp plot a Spatial Point Pattern
append.psp Combine Two Line Segment Patterns
expand.owin Expand Window By Factor
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
scanpp Read Point Pattern From Data File
print.ppm Print a Fitted Point Process Model
nndist Nearest neighbour distances
setcov Set Covariance of a Window
density.ppp Kernel Smoothed Intensity of Point Pattern
rsyst Simulate systematic random point pattern
quadratcount Quadrat counting for a point pattern
rStrauss Perfect Simulation of the Strauss Process
as.matrix.im Convert Pixel Image to Matrix
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
humberside Humberside Data on Childhood Leukaemia and Lymphoma
japanesepines Japanese Pines Point Pattern
rshift.ppp Randomly Shift a Point Pattern
Kest K-function
as.ppp Convert Data To Class ppp
print.im Print Brief Details of an Image
setmarks Set or Reset the Marks in a Point Pattern
psp Create a Line Segment Pattern
owin.object Class owin
rotate.ppp Rotate a Point Pattern
pppdist Optimal Match Between Two Point Patterns
Kcross Multitype K Function (Cross-type)
betacells Beta Ganglion Cells in Cat Retina
unique.ppp Extract Unique Points from a Spatial Point Pattern
default.dummy Generate a Default Pattern of Dummy Points
rThomas Simulate Thomas Process
ppp Create a Point Pattern
runifpoint Generate N Uniform Random Points
redwood California Redwoods Point Pattern (Ripley's Subset)
simdat Simulated Point Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
shift.psp Apply Vector Translation To Line Segment Pattern
summary.ppp Summary of a Point Pattern Dataset
Kcross.inhom Inhomogeneous Cross K Function
Kest.fft K-function using FFT
lurking Lurking variable plot
summary.owin Summary of a Spatial Window
update.ppm Update a Fitted Point Process Model
subset.fasp Extract Subset of Function Array
subset.im Extract Subset of Image
redwoodfull California Redwoods Point Pattern (Entire Dataset)
predict.ppm Prediction from a Fitted Point Process Model
summary.ppm Summarizing a Fitted Point Process Model
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Date 22 August 2006
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Tue Aug 22 10:23:25 2006; adrian

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