spatstat v1.9-1

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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, 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
Geyer Geyer's Saturation Point Process Model
betacells Beta Ganglion Cells in Cat Retina
as.mask Pixel Image Approximation of a Window
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
crossdist.psp Pairwise distances between two different line segment patterns
density.psp Kernel Smoothing of Line Segment Pattern
default.dummy Generate a Default Pattern of Dummy Points
spatstat-deprecated Deprecated spatstat functions
diameter Diameter of a Window Frame
spatstat-internal Internal spatstat functions
eval.im Evaluate Expression Involving Pixel Images
harmonic Basis for Harmonic Functions
is.owin Test Whether An Object Is A Window
longleaf Longleaf Pines Point Pattern
ppm.object Class of Fitted Point Process Models
anova.ppm ANOVA for Fitted Point Process Models
Saturated Saturated Pairwise Interaction model
nndist Nearest neighbour distances
envelope Simulation envelopes of summary function
rlabel Random Re-Labelling of Point Pattern
distmap.owin Distance Map of Window
as.im Convert to Pixel Image
as.matrix.im Convert Pixel Image to Matrix
compatible.fv Test Whether Two Function Objects Are Compatible
plot.fv Plot Function Valuesn
mincontrast Method of Minimum Contrast
hamster Aherne's hamster tumour data
nnwhich Nearest neighbour
plot.quad plot a Spatial Quadrature Scheme
thomas.estK Fit the Thomas Point Process by Minimum Contrast
crossdist.default Pairwise distances between two different sets of points
print.owin Print Brief Details of a Spatial Window
OrdThresh Ord's Interaction model
Pairwise Generic Pairwise Interaction model
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
fv.object Data Frames of Function Values
fasp.object Function Arrays for Spatial Patterns
print.ppm Print a Fitted Point Process Model
rshift.ppp Randomly Shift a Point Pattern
plot.owin Plot a Spatial Window
ganglia Beta Ganglion Cells in Cat Retina, Old Version
kaplan.meier Kaplan-Meier Estimator using Histogram Data
rmpoispp Generate Multitype Poisson Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
subset.fv Extract Subset of Function Values
ppp.object Class of Point Patterns
setcov Set Covariance of a Window
mean.im Mean Pixel Value in an Image
owin Create a Window
rstrat Stratified random point pattern
shift.psp Apply Vector Translation To Line Segment Pattern
pcf.fasp Pair Correlation Function obtained from array of K functions
summary.ppm Summarizing a Fitted Point Process Model
predict.ppm Prediction from a Fitted Point Process Model
summary.owin Summary of a Spatial Window
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
Kcross Multitype K Function (Cross-type)
Softcore The Soft Core Point Process Model
reach Interaction Distance of a Point Process
ants Harkness-Isham ants' nests data
shift.owin Apply Vector Translation To Window
affine.psp Apply Affine Transformation To Line Segment Pattern
is.ppp Test Whether An Object Is A Point Pattern
pairwise.family Pairwise Interaction Process Family
reduced.sample Reduced Sample Estimator using Histogram Data
Kest K-function
unmark Remove Marks from a Marked Point Pattern
Kmulti Marked K-Function
Jest Estimate the J-function
Jdot Multitype J Function (i-to-any)
Ord Generic Ord Interaction model
affine Apply Affine Transformation
as.psp Convert Data To Class psp
as.ppp Convert Data To Class ppp
amacrine Hughes' Amacrine Cell Data
area.owin Area of a Window
endpoints.psp Endpoints of Line Segment Pattern
complement.owin Take Complement of a Window
data.ppm Extract Original Data from a Fitted Point Process Model
nztrees New Zealand Trees Point Pattern
coef.ppm Coefficients of Fitted Point Process Model
eval.fv Evaluate Expression Involving Functions
erode.owin Erode a Window
Fest Estimate the empty space function F
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
Kest.fft K-function using FFT
bounding.box Bounding Box of a Window
lurking Lurking variable plot
dilate.owin Dilate a Window
rMaternII Simulate Matern Model II
midpoints.psp Midpoints of Line Segment Pattern
plot.plotppm Plot a plotppm Object Created by plot.ppm
rMatClust Simulate Matern Cluster Process
rmpoint Generate N Random Multitype Points
markcorr Mark Correlation Function
quad.object Class of Quadrature Schemes
rthin Random Thinning
pairsat.family Saturated Pairwise Interaction Point Process Family
identify.ppp Identify Points in a Point Pattern
simdat Simulated Point Pattern
pairdist.ppp Pairwise distances
quadscheme Generate a Quadrature Scheme from a Point Pattern
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
lengths.psp Lengths of Line Segments
rpoint Generate N Random Points
nearest.raster.point Find Pixel Nearest to a Given Point
is.im Test Whether An Object Is A Pixel Image
rshift.splitppp Randomly Shift a List of Point Patterns
subset.ppp Extract or Replace Subset of Point Pattern
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
residualspaper Data and Code From JRSS Discussion Paper on Residuals
setmarks Set or Reset the Marks in a Point Pattern
Poisson Poisson Point Process Model
allstats Calculate four standard summary functions of a point pattern.
Jmulti Marked J Function
centroid.owin Centroid of a window
concatxy Concatenate x,y Coordinate Vectors
bramblecanes Hutchings' Bramble Canes data
superimpose Superimpose Several Point Patterns
Gest Nearest Neighbour Distance Function G
Kmeasure Reduced Second Moment Measure
compatible.im Test Whether Two Pixel Images Are Compatible
affine.owin Apply Affine Transformation To Window
chorley Chorley-Ribble Cancer Data
distmap.ppp Distance Map of Point Pattern
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
inside.owin Test Whether Points Are Inside A Window
cut.ppp Convert Point Pattern Marks from Numeric to Factor
is.marked.ppm Test Whether A Point Process Model is Marked
square Square Window
rshift Random Shift
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
pairdist Pairwise distances
rotate.ppp Rotate a Point Pattern
plot.im Plot a Pixel Image
eroded.areas Areas of Morphological Erosions
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
ppm Fit Point Process Model to Data
suffstat Sufficient Statistic of Point Process Model
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
print.ppp Print Brief Details of a Point Pattern Dataset
rmh.ppm Simulate from a Fitted Point Process Model
raster.x Cartesian Coordinates for a Pixel Raster
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
DiggleGratton Diggle-Gratton model
Jcross Multitype J Function (i-to-j)
StraussHard The Strauss / Hard Core Point Process Model
Gmulti Marked Nearest Neighbour Distance Function
bdist.points Distance to Boundary of Window
Kcross.inhom Inhomogeneous Cross K Function
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
is.marked Test Whether Marks Are Present
crossing.psp Crossing Points of Two Line Segment Patterns
spatstat The Spatstat Package
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
cut.im Convert Pixel Image from Numeric to Factor
affine.ppp Apply Affine Transformation To Point Pattern
as.rectangle Window Frame
LennardJones The Lennard-Jones Potential
distmap.psp Distance Map of Line Segment Pattern
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
bdist.pixels Distance to Boundary of Window
angles.psp Orientation Angles of Line Segments
distmap Distance Map
gridweights Compute Quadrature Weights Based on Grid Counts
hist.im Histogram of Pixel Values in an Image
as.owin Convert Data To Class owin
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
rNeymanScott Simulate Neyman-Scott Process
Iest Estimate the I-function
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
applynbd Apply Function to Every Neighbourhood in a Point Pattern
levelset Level Set of a Pixel Image
Kinhom Inhomogeneous K-function
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
letterR Window in Shape of Letter R
psp.object Class of Line Segment Patterns
pcf.fv Pair Correlation Function obtained from K Function
humberside Humberside Data on Childhood Leukaemia and Lymphoma
multiplicity.ppp Count Multiplicity of Duplicate Points
rotate Rotate
subset.fasp Extract Subset of Function Array
intersect.owin Intersection or Union of Two Windows
finpines Pine saplings in Finland.
pcf.ppp Pair Correlation Function of Point Pattern
redwood California Redwoods Point Pattern (Ripley's Subset)
corners Corners of a rectangle
append.psp Combine Two Line Segment Patterns
Strauss The Strauss Point Process Model
is.subset.owin Determine Whether One Window is Contained In Another
is.marked.ppp Test Whether A Point Pattern is Marked
rpoisline Generate Poisson Random Line Process
ord.family Ord Interaction Process Family
MultiStrauss The Multitype Strauss Point Process Model
cells Biological Cells Point Pattern
expand.owin Expand Window By Factor
Kdot Multitype K Function (i-to-any)
shift.ppp Apply Vector Translation To Point Pattern
quantile.im Sample Quantiles of Pixel Image
plot.ppm plot a Fitted Point Process Model
rSSI Simple Sequential Inhibition
Kdot.inhom Inhomogeneous Multitype K Dot Function
rotate.owin Rotate a Window
im.object Class of Images
lansing Lansing Woods Point Pattern
density.ppp Kernel Smoothed Intensity of Point Pattern
crossdist.ppp Pairwise distances between two different point patterns
japanesepines Japanese Pines Point Pattern
gridcentres Rectangular grid of points
is.ppm Test Whether An Object Is A Fitted Point Process Model
print.im Print Brief Details of an Image
rescue.rectangle Convert Window Back To Rectangle
plot.ppp plot a Spatial Point Pattern
plot.psp plot a Spatial Line Segment Pattern
plot.splitppp Plot a List of Point Patterns
subset.im Extract Subset of Image
rpoispp Generate Poisson Point Pattern
pairdist.default Pairwise distances
owin.object Class owin
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
shift Apply Vector Translation
spokes Spokes pattern of dummy points
shift.im Apply Vector Translation To Pixel Image
split.ppp Divide Point Pattern into Sub-patterns
psp Create a Line Segment Pattern
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
pcf Pair Correlation Function
copper Berman-Huntington points and lines data
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
summary.psp Summary of a Line Segment Pattern Dataset
runifpoint Generate N Uniform Random Points
rThomas Simulate Thomas Process
ppp Create a Point Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
print.quad Print a Quadrature Scheme
fitted.ppm Fitted Conditional Intensity for Point Process Model
redwoodfull California Redwoods Point Pattern (Entire Dataset)
ripras Estimate window from points alone
im Create a Pixel Image Object
rMaternI Simulate Matern Model I
crossdist Pairwise distances
scanpp Read Point Pattern From Data File
union.quad Union of Data and Dummy Points
unique.ppp Extract Unique Points from a Spatial Point Pattern
demopat Artificial Data Point Pattern
subset.psp Extract Subset of Line Segment Pattern
print.psp Print Brief Details of a Line Segment Pattern Dataset
spruces Spruces Point Pattern
pairdist.psp Pairwise distances between line segments
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
quadratcount Quadrat counting for a point pattern
rshift.psp Randomly Shift a Line Segment Pattern
rcell Simulate Baddeley-Silverman Cell Process
plot.fasp Plot a Function Array
residuals.ppm Residuals for Fitted Point Process Model
eem Exponential Energy Marks
swedishpines Swedish Pines Point Pattern
summary.ppp Summary of a Point Pattern Dataset
rotate.psp Rotate a Line Segment Pattern
summary.quad Summarizing a Quadrature Scheme
spatstat.options Internal Options in Spatstat Package
update.ppm Update a Fitted Point Process Model
rsyst Systematic random point pattern
summary.im Summarizing a Pixel Image
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Date 26 May 2006
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Fri May 26 12:14:51 2006; adrian

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