spatstat v1.10-1

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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, 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
Kmeasure Reduced Second Moment Measure
append.psp Combine Two Line Segment Patterns
Ord Generic Ord Interaction model
Jmulti Marked J Function
anova.ppm ANOVA for Fitted Point Process Models
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
eem Exponential Energy Marks
diameter Diameter of a Window Frame
hamster Aherne's hamster tumour data
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
is.ppm Test Whether An Object Is A Fitted Point Process Model
pairdist.psp Pairwise distances between line segments
compatible.im Test Whether Two Pixel Images Are Compatible
is.owin Test Whether An Object Is A Window
humberside Humberside Data on Childhood Leukaemia and Lymphoma
pairsat.family Saturated Pairwise Interaction Point Process Family
cut.im Convert Pixel Image from Numeric to Factor
dilate.owin Dilate a Window
profilepl Profile Maximum Pseudolikelihood
crossdist.default Pairwise distances between two different sets of points
affine.psp Apply Affine Transformation To Line Segment Pattern
distmap Distance Map
psp Create a Line Segment Pattern
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
pcf Pair Correlation Function
owin Create a Window
rSSI Simulate Simple Sequential Inhibition
rmpoispp Generate Multitype Poisson Point Pattern
is.marked Test Whether Marks Are Present
markcorr Mark Correlation Function
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
erode.owin Erode a Window
pairdist.ppp Pairwise distances
rshift.splitppp Randomly Shift a List of Point Patterns
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
ripras Estimate window from points alone
spatstat The Spatstat Package
shift.im Apply Vector Translation To Pixel Image
rmpoint Generate N Random Multitype Points
suffstat Sufficient Statistic of Point Process Model
ppm.object Class of Fitted Point Process Models
rNeymanScott Simulate Neyman-Scott Process
rcell Simulate Baddeley-Silverman Cell Process
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
raster.x Cartesian Coordinates for a Pixel Raster
spatstat.options Internal Options in Spatstat Package
Kcross.inhom Inhomogeneous Cross K Function
Jest Estimate the J-function
rmh.ppm Simulate from a Fitted Point Process Model
split.ppp Divide Point Pattern into Sub-patterns
rstrat Simulate Stratified Random Point Pattern
eroded.areas Areas of Morphological Erosions
lengths.psp Lengths of Line Segments
print.ppm Print a Fitted Point Process Model
OrdThresh Ord's Interaction model
Kmulti Marked K-Function
pppdist Optimal Match Between Two Point Patterns
affine Apply Affine Transformation
LennardJones The Lennard-Jones Potential
ppp Create a Point Pattern
rMaternII Simulate Matern Model II
StraussHard The Strauss / Hard Core Point Process Model
redwoodfull California Redwoods Point Pattern (Entire Dataset)
ants Harkness-Isham ants' nests data
allstats Calculate four standard summary functions of a point pattern.
density.ppp Kernel Smoothed Intensity of Point Pattern
centroid.owin Centroid of a window
corners Corners of a rectangle
Kest.fft K-function using FFT
applynbd Apply Function to Every Neighbourhood in a Point Pattern
bei Tropical rain forest trees
angles.psp Orientation Angles of Line Segments
bramblecanes Hutchings' Bramble Canes data
distmap.ppp Distance Map of Point Pattern
Jcross Multitype J Function (i-to-j)
intersect.owin Intersection or Union of Two Windows
Fest Estimate the empty space function F
betacells Beta Ganglion Cells in Cat Retina
as.mask Pixel Image Approximation of a Window
coef.ppm Coefficients of Fitted Point Process Model
pcf.fv Pair Correlation Function obtained from K Function
cells Biological Cells Point Pattern
im.object Class of Images
plot.ppm plot a Fitted Point Process Model
density.psp Kernel Smoothing of Line Segment Pattern
quadscheme Generate a Quadrature Scheme from a Point Pattern
concatxy Concatenate x,y Coordinate Vectors
distmap.owin Distance Map of Window
is.marked.ppp Test Whether A Point Pattern is Marked
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
ord.family Ord Interaction Process Family
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
Strauss The Strauss Point Process Model
finpines Pine saplings in Finland.
crossdist.psp Pairwise distances between two different line segment patterns
data.ppm Extract Original Data from a Fitted Point Process Model
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
rthin Random Thinning
hist.im Histogram of Pixel Values in an Image
is.multitype.ppm Test Whether A Point Process Model is Multitype
plot.splitppp Plot a List of Point Patterns
multiplicity.ppp Count Multiplicity of Duplicate Points
longleaf Longleaf Pines Point Pattern
japanesepines Japanese Pines Point Pattern
pcf.fasp Pair Correlation Function obtained from array of K functions
print.quad Print a Quadrature Scheme
MultiStrauss The Multitype Strauss Point Process Model
gridcentres Rectangular grid of points
is.multitype Test whether Object is Multitype
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
nearest.raster.point Find Pixel Nearest to a Given Point
chorley Chorley-Ribble Cancer Data
nndist Nearest neighbour distances
nnwhich Nearest neighbour
rotate.ppp Rotate a Point Pattern
complement.owin Take Complement of a Window
print.owin Print Brief Details of a Spatial Window
quadratcount Quadrat counting for a point pattern
residuals.ppm Residuals for Fitted Point Process Model
DiggleGratton Diggle-Gratton model
residualspaper Data and Code From JRSS Discussion Paper on Residuals
Kest K-function
scanpp Read Point Pattern From Data File
rotate.owin Rotate a Window
default.dummy Generate a Default Pattern of Dummy Points
rsyst Simulate systematic random point pattern
shift.psp Apply Vector Translation To Line Segment Pattern
rpoint Generate N Random Points
shift.owin Apply Vector Translation To Window
plot.plotppm Plot a plotppm Object Created by plot.ppm
predict.ppm Prediction from a Fitted Point Process Model
spatstat-deprecated Deprecated spatstat functions
disc Circular Window
print.im Print Brief Details of an Image
setcov Set Covariance of a Window
rStrauss Perfect Simulation of the Strauss Process
ganglia Beta Ganglion Cells in Cat Retina, Old Version
rescue.rectangle Convert Window Back To Rectangle
shift.ppp Apply Vector Translation To Point Pattern
square Square Window
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
superimpose Superimpose Several Point Patterns
Softcore The Soft Core Point Process Model
contour.im Contour plot of pixel image
spruces Spruces Point Pattern
is.ppp Test Whether An Object Is A Point Pattern
swedishpines Swedish Pines Point Pattern
pairdist Pairwise distances
plot.fv Plot Function Valuesn
plot.quad plot a Spatial Quadrature Scheme
Geyer Geyer's Saturation Point Process Model
Gmulti Marked Nearest Neighbour Distance Function
Kcross Multitype K Function (Cross-type)
Kdot.inhom Inhomogeneous Multitype K Dot Function
Poisson Poisson Point Process Model
Kinhom Inhomogeneous K-function
rshift Random Shift
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
area.owin Area of a Window
as.rectangle Window Frame
as.psp Convert Data To Class psp
as.im Convert to Pixel Image
summary.ppp Summary of a Point Pattern Dataset
compatible.fv Test Whether Two Function Objects Are Compatible
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
spokes Spokes pattern of dummy points
lurking Lurking variable plot
runifpoint Generate N Uniform Random Points
reach Interaction Distance of a Point Process
fv.object Data Frames of Function Values
plot.im Plot a Pixel Image
levelset Level Set of a Pixel Image
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
mincontrast Method of Minimum Contrast
redwood California Redwoods Point Pattern (Ripley's Subset)
plot.psp plot a Spatial Line Segment Pattern
nncross Nearest Neighbour in Another Point Pattern
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
Saturated Saturated Pairwise Interaction model
plot.fasp Plot a Function Array
bounding.box Bounding Box of a Window
crossdist Pairwise distances
plot.listof Plot a List of Things
crossdist.ppp Pairwise distances between two different point patterns
endpoints.psp Endpoints of Line Segment Pattern
trim.rectangle Cut margins from rectangle
unmark Remove Marks from a Marked Point Pattern
eval.im Evaluate Expression Involving Pixel Images
kaplan.meier Kaplan-Meier Estimator using Histogram Data
rMaternI Simulate Matern Model I
pairdist.default Pairwise distances
print.ppp Print Brief Details of a Point Pattern Dataset
quantile.im Sample Quantiles of Pixel Image
rlabel Random Re-Labelling of Point Pattern
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
setmarks Set or Reset the Marks in a Point Pattern
union.quad Union of Data and Dummy Points
Iest Estimate the I-function
as.matrix.im Convert Pixel Image to Matrix
affine.ppp Apply Affine Transformation To Point Pattern
copper Berman-Huntington points and lines data
bdist.points Distance to Boundary of Window
inside.owin Test Whether Points Are Inside A Window
is.subset.owin Determine Whether One Window is Contained In Another
mean.im Mean Pixel Value in an Image
subset.im Extract Subset of Image
as.ppp Convert Data To Class ppp
summary.psp Summary of a Line Segment Pattern Dataset
owin.object Class owin
is.marked.ppm Test Whether A Point Process Model is Marked
distmap.psp Distance Map of Line Segment Pattern
pcf.ppp Pair Correlation Function of Point Pattern
ppm Fit Point Process Model to Data
letterR Window in Shape of Letter R
psp.object Class of Line Segment Patterns
is.multitype.ppp Test Whether A Point Pattern is Multitype
midpoints.psp Midpoints of Line Segment Pattern
ppp.object Class of Point Patterns
rMatClust Simulate Matern Cluster Process
is.im Test Whether An Object Is A Pixel Image
rshift.psp Randomly Shift a Line Segment Pattern
runifdisc Generate N Uniform Random Points in a Disc
eval.fv Evaluate Expression Involving Functions
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
subset.fv Extract Subset of Function Values
harmonic Basis for Harmonic Functions
subset.fasp Extract Subset of Function Array
subset.psp Extract Subset of Line Segment Pattern
summary.im Summarizing a Pixel Image
identify.ppp Identify Points in a Point Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
fitted.ppm Fitted Conditional Intensity for Point Process Model
nztrees New Zealand Trees Point Pattern
update.ppm Update a Fitted Point Process Model
rThomas Simulate Thomas Process
rshift.ppp Randomly Shift a Point Pattern
summary.owin Summary of a Spatial Window
summary.ppm Summarizing a Fitted Point Process Model
unique.ppp Extract Unique Points from a Spatial Point Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
affine.owin Apply Affine Transformation To Window
amacrine Hughes' Amacrine Cell Data
demopat Artificial Data Point Pattern
persp.im Perspective Plot of Pixel Image
quad.object Class of Quadrature Schemes
shift Apply Vector Translation
simdat Simulated Point Pattern
Gest Nearest Neighbour Distance Function G
Jdot Multitype J Function (i-to-any)
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
cut.ppp Convert Point Pattern Marks from Numeric to Factor
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
lansing Lansing Woods Point Pattern
reduced.sample Reduced Sample Estimator using Histogram Data
pairwise.family Pairwise Interaction Process Family
rotate Rotate
rpoisline Generate Poisson Random Line Process
rotate.psp Rotate a Line Segment Pattern
summary.quad Summarizing a Quadrature Scheme
units Name for Unit of Length
subset.ppp Extract or Replace Subset of Point Pattern
Kdot Multitype K Function (i-to-any)
as.owin Convert Data To Class owin
envelope Simulation envelopes of summary function
crossing.psp Crossing Points of Two Line Segment Patterns
plot.owin Plot a Spatial Window
print.psp Print Brief Details of a Line Segment Pattern Dataset
rpoispp Generate Poisson Point Pattern
Pairwise Generic Pairwise Interaction model
bdist.pixels Distance to Boundary of Window
clickppp Interactively Add Points
fasp.object Function Arrays for Spatial Patterns
expand.owin Expand Window By Factor
gridweights Compute Quadrature Weights Based on Grid Counts
im Create a Pixel Image Object
plot.ppp plot a Spatial Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
spatstat-internal Internal spatstat functions
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Date 19 October 2006
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Thu Oct 19 18:36:34 2006; adrian

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