spatstat v1.9-3

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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
affine.owin Apply Affine Transformation To Window
append.psp Combine Two Line Segment Patterns
Jdot Multitype J Function (i-to-any)
compatible.fv Test Whether Two Function Objects Are Compatible
as.mask Pixel Image Approximation of a Window
eval.im Evaluate Expression Involving Pixel Images
crossing.psp Crossing Points of Two Line Segment Patterns
humberside Humberside Data on Childhood Leukaemia and Lymphoma
letterR Window in Shape of Letter R
midpoints.psp Midpoints of Line Segment Pattern
cut.ppp Convert Point Pattern Marks from Numeric to Factor
eem Exponential Energy Marks
Kinhom Inhomogeneous K-function
im.object Class of Images
pairwise.family Pairwise Interaction Process Family
bdist.pixels Distance to Boundary of Window
nztrees New Zealand Trees Point Pattern
print.im Print Brief Details of an Image
Iest Estimate the I-function
area.owin Area of a Window
lengths.psp Lengths of Line Segments
rpoispp Generate Poisson Point Pattern
pairdist.ppp Pairwise distances
pcf.fv Pair Correlation Function obtained from K Function
shift.owin Apply Vector Translation To Window
crossdist Pairwise distances
pairsat.family Saturated Pairwise Interaction Point Process Family
swedishpines Swedish Pines Point Pattern
markcorr Mark Correlation Function
rsyst Systematic random point pattern
psp.object Class of Line Segment Patterns
quantile.im Sample Quantiles of Pixel Image
rmpoispp Generate Multitype Poisson Point Pattern
residuals.ppm Residuals for Fitted Point Process Model
rlabel Random Re-Labelling of Point Pattern
Strauss The Strauss Point Process Model
Kest K-function
rthin Random Thinning
split.ppp Divide Point Pattern into Sub-patterns
shift.ppp Apply Vector Translation To Point Pattern
angles.psp Orientation Angles of Line Segments
shift.im Apply Vector Translation To Pixel Image
Saturated Saturated Pairwise Interaction model
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
applynbd Apply Function to Every Neighbourhood in a Point Pattern
OrdThresh Ord's Interaction model
rpoisline Generate Poisson Random Line Process
default.dummy Generate a Default Pattern of Dummy Points
Softcore The Soft Core Point Process Model
inside.owin Test Whether Points Are Inside A Window
is.ppp Test Whether An Object Is A Point Pattern
bdist.points Distance to Boundary of Window
pairdist.psp Pairwise distances between line segments
longleaf Longleaf Pines Point Pattern
crossdist.default Pairwise distances between two different sets of points
profilepl Profile Maximum Pseudolikelihood
subset.fv Extract Subset of Function Values
data.ppm Extract Original Data from a Fitted Point Process Model
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
summary.psp Summary of a Line Segment Pattern Dataset
spatstat-deprecated Deprecated spatstat functions
distmap.psp Distance Map of Line Segment Pattern
summary.im Summarizing a Pixel Image
multiplicity.ppp Count Multiplicity of Duplicate Points
Geyer Geyer's Saturation Point Process Model
as.matrix.im Convert Pixel Image to Matrix
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
psp Create a Line Segment Pattern
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
quadratcount Quadrat counting for a point pattern
Poisson Poisson Point Process Model
pcf.ppp Pair Correlation Function of Point Pattern
MultiStrauss The Multitype Strauss Point Process Model
plot.plotppm Plot a plotppm Object Created by plot.ppm
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
quad.object Class of Quadrature Schemes
print.ppp Print Brief Details of a Point Pattern Dataset
affine Apply Affine Transformation
complement.owin Take Complement of a Window
as.psp Convert Data To Class psp
as.ppp Convert Data To Class ppp
Kdot Multitype K Function (i-to-any)
distmap Distance Map
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
centroid.owin Centroid of a window
bramblecanes Hutchings' Bramble Canes data
rNeymanScott Simulate Neyman-Scott Process
spruces Spruces Point Pattern
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
diameter Diameter of a Window Frame
expand.owin Expand Window By Factor
hamster Aherne's hamster tumour data
harmonic Basis for Harmonic Functions
owin Create a Window
rescue.rectangle Convert Window Back To Rectangle
endpoints.psp Endpoints of Line Segment Pattern
nndist Nearest neighbour distances
reach Interaction Distance of a Point Process
Kest.fft K-function using FFT
anova.ppm ANOVA for Fitted Point Process Models
pcf Pair Correlation Function
plot.fv Plot Function Valuesn
subset.fasp Extract Subset of Function Array
eroded.areas Areas of Morphological Erosions
rThomas Simulate Thomas Process
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
residualspaper Data and Code From JRSS Discussion Paper on Residuals
is.im Test Whether An Object Is A Pixel Image
unmark Remove Marks from a Marked Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
unique.ppp Extract Unique Points from a Spatial Point Pattern
affine.psp Apply Affine Transformation To Line Segment Pattern
corners Corners of a rectangle
plot.owin Plot a Spatial Window
plot.splitppp Plot a List of Point Patterns
crossdist.ppp Pairwise distances between two different point patterns
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
plot.ppm plot a Fitted Point Process Model
ppp Create a Point Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
superimpose Superimpose Several Point Patterns
scanpp Read Point Pattern From Data File
nnwhich Nearest neighbour
Jmulti Marked J Function
as.owin Convert Data To Class owin
simdat Simulated Point Pattern
suffstat Sufficient Statistic of Point Process Model
demopat Artificial Data Point Pattern
Gest Nearest Neighbour Distance Function G
betacells Beta Ganglion Cells in Cat Retina
allstats Calculate four standard summary functions of a point pattern.
concatxy Concatenate x,y Coordinate Vectors
finpines Pine saplings in Finland.
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
distmap.ppp Distance Map of Point Pattern
is.owin Test Whether An Object Is A Window
fv.object Data Frames of Function Values
hist.im Histogram of Pixel Values in an Image
fasp.object Function Arrays for Spatial Patterns
is.marked Test Whether Marks Are Present
gridweights Compute Quadrature Weights Based on Grid Counts
Jest Estimate the J-function
DiggleGratton Diggle-Gratton model
print.ppm Print a Fitted Point Process Model
envelope Simulation envelopes of summary function
rshift Random Shift
intersect.owin Intersection or Union of Two Windows
kaplan.meier Kaplan-Meier Estimator using Histogram Data
runifpoint Generate N Uniform Random Points
plot.im Plot a Pixel Image
summary.ppp Summary of a Point Pattern Dataset
mincontrast Method of Minimum Contrast
rcell Simulate Baddeley-Silverman Cell Process
ppp.object Class of Point Patterns
rshift.splitppp Randomly Shift a List of Point Patterns
erode.owin Erode a Window
selfcrossing.psp Crossing Points in a Line Segment Pattern
summary.owin Summary of a Spatial Window
shift Apply Vector Translation
plot.ppp plot a Spatial Point Pattern
raster.x Cartesian Coordinates for a Pixel Raster
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rSSI Simple Sequential Inhibition
shift.psp Apply Vector Translation To Line Segment Pattern
setmarks Set or Reset the Marks in a Point Pattern
union.quad Union of Data and Dummy Points
rmh.ppm Simulate from a Fitted Point Process Model
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Kcross.inhom Inhomogeneous Cross K Function
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
bounding.box Bounding Box of a Window
Kmeasure Reduced Second Moment Measure
rotate.ppp Rotate a Point Pattern
spatstat.options Internal Options in Spatstat Package
rshift.psp Randomly Shift a Line Segment Pattern
summary.ppm Summarizing a Fitted Point Process Model
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
eval.fv Evaluate Expression Involving Functions
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
pairdist.default Pairwise distances
plot.psp plot a Spatial Line Segment Pattern
print.owin Print Brief Details of a Spatial Window
print.psp Print Brief Details of a Line Segment Pattern Dataset
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
rotate Rotate
Kcross Multitype K Function (Cross-type)
copper Berman-Huntington points and lines data
density.ppp Kernel Smoothed Intensity of Point Pattern
is.ppm Test Whether An Object Is A Fitted Point Process Model
japanesepines Japanese Pines Point Pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
nearest.raster.point Find Pixel Nearest to a Given Point
plot.fasp Plot a Function Array
lurking Lurking variable plot
print.quad Print a Quadrature Scheme
predict.ppm Prediction from a Fitted Point Process Model
ants Harkness-Isham ants' nests data
compatible.im Test Whether Two Pixel Images Are Compatible
identify.ppp Identify Points in a Point Pattern
lansing Lansing Woods Point Pattern
quadscheme Generate a Quadrature Scheme from a Point Pattern
ripras Estimate window from points alone
rshift.ppp Randomly Shift a Point Pattern
rstrat Stratified random point pattern
summary.quad Summarizing a Quadrature Scheme
pairdist Pairwise distances
levelset Level Set of a Pixel Image
redwood California Redwoods Point Pattern (Ripley's Subset)
owin.object Class owin
square Square Window
rotate.psp Rotate a Line Segment Pattern
subset.ppp Extract or Replace Subset of Point Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
StraussHard The Strauss / Hard Core Point Process Model
amacrine Hughes' Amacrine Cell Data
density.psp Kernel Smoothing of Line Segment Pattern
as.rectangle Window Frame
coef.ppm Coefficients of Fitted Point Process Model
spatstat-internal Internal spatstat functions
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
distmap.owin Distance Map of Window
ord.family Ord Interaction Process Family
Fest Estimate the empty space function F
Kdot.inhom Inhomogeneous Multitype K Dot Function
setcov Set Covariance of a Window
Kmulti Marked K-Function
Pairwise Generic Pairwise Interaction model
chorley Chorley-Ribble Cancer Data
as.im Convert to Pixel Image
cells Biological Cells Point Pattern
Jcross Multitype J Function (i-to-j)
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
LennardJones The Lennard-Jones Potential
crossdist.psp Pairwise distances between two different line segment patterns
redwoodfull California Redwoods Point Pattern (Entire Dataset)
is.marked.ppp Test Whether A Point Pattern is Marked
mean.im Mean Pixel Value in an Image
is.marked.ppm Test Whether A Point Process Model is Marked
spatstat The Spatstat Package
fitted.ppm Fitted Conditional Intensity for Point Process Model
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
im Create a Pixel Image Object
gridcentres Rectangular grid of points
rMaternII Simulate Matern Model II
is.subset.owin Determine Whether One Window is Contained In Another
plot.quad plot a Spatial Quadrature Scheme
reduced.sample Reduced Sample Estimator using Histogram Data
rotate.owin Rotate a Window
ppm Fit Point Process Model to Data
ppm.object Class of Fitted Point Process Models
rmpoint Generate N Random Multitype Points
spokes Spokes pattern of dummy points
rpoint Generate N Random Points
rMatClust Simulate Matern Cluster Process
subset.psp Extract Subset of Line Segment Pattern
rMaternI Simulate Matern Model I
dilate.owin Dilate a Window
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
pcf.fasp Pair Correlation Function obtained from array of K functions
affine.ppp Apply Affine Transformation To Point Pattern
persp.im Perspective Plot of Pixel Image
ganglia Beta Ganglion Cells in Cat Retina, Old Version
subset.im Extract Subset of Image
Ord Generic Ord Interaction model
cut.im Convert Pixel Image from Numeric to Factor
update.ppm Update a Fitted Point Process Model
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Date 20 June 2006
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Wed Jun 21 12:37:31 2006; adrian

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