spatstat v1.11-0

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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
Geyer Geyer's Saturation Point Process Model
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Kmulti Marked K-Function
Softcore The Soft Core Point Process Model
default.dummy Generate a Default Pattern of Dummy Points
Kcross Multitype K Function (Cross-type)
Kdot.inhom Inhomogeneous Multitype K Dot Function
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
affine.owin Apply Affine Transformation To Window
append.psp Combine Two Line Segment Patterns
as.im Convert to Pixel Image
as.matrix.im Convert Pixel Image to Matrix
is.marked Test Whether Marks Are Present
distmap.psp Distance Map of Line Segment Pattern
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
clickppp Interactively Add Points
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
compatible.fv Test Whether Two Function Objects Are Compatible
is.marked.ppm Test Whether A Point Process Model is Marked
is.multitype Test whether Object is Multitype
angles.psp Orientation Angles of Line Segments
as.rectangle Window Frame
affine Apply Affine Transformation
owin.object Class owin
plot.ppm plot a Fitted Point Process Model
centroid.owin Centroid of a window
as.owin Convert Data To Class owin
ppp Create a Point Pattern
pppdist Optimal Match Between Two Point Patterns
Kcross.inhom Inhomogeneous Cross K Function
OrdThresh Ord's Interaction model
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
quad.object Class of Quadrature Schemes
plot.splitppp Plot a List of Point Patterns
quadscheme Generate a Quadrature Scheme from a Point Pattern
im.object Class of Images
mean.im Mean Pixel Value in an Image
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
summary.psp Summary of a Line Segment Pattern Dataset
runifdisc Generate N Uniform Random Points in a Disc
spatstat-internal Internal spatstat functions
ants Harkness-Isham ants' nests data
persp.im Perspective Plot of Pixel Image
multiplicity.ppp Count Multiplicity of Duplicate Points
coef.ppm Coefficients of Fitted Point Process Model
rotate.owin Rotate a Window
plot.im Plot a Pixel Image
inside.owin Test Whether Points Are Inside A Window
subset.psp Extract Subset of Line Segment Pattern
dilate.owin Dilate a Window
plot.plotppm Plot a plotppm Object Created by plot.ppm
rotate.psp Rotate a Line Segment Pattern
amacrine Hughes' Amacrine Cell Data
bramblecanes Hutchings' Bramble Canes data
subset.splitppp Extract or Replace Sub-Patterns
eem Exponential Energy Marks
crossdist.ppp Pairwise distances between two different point patterns
kaplan.meier Kaplan-Meier Estimator using Histogram Data
setmarks Set or Reset the Marks in a Point Pattern
im Create a Pixel Image Object
is.owin Test Whether An Object Is A Window
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
lurking Lurking variable plot
profilepl Profile Maximum Pseudolikelihood
DiggleGratton Diggle-Gratton model
pairdist.psp Pairwise distances between line segments
reduced.sample Reduced Sample Estimator using Histogram Data
Kdot Multitype K Function (i-to-any)
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
ppm Fit Point Process Model to Data
gridcentres Rectangular grid of points
rmpoint Generate N Random Multitype Points
humberside Humberside Data on Childhood Leukaemia and Lymphoma
rshift.splitppp Randomly Shift a List of Point Patterns
pcf.fasp Pair Correlation Function obtained from array of K functions
crossdist Pairwise distances
longleaf Longleaf Pines Point Pattern
mincontrast Method of Minimum Contrast
Saturated Saturated Pairwise Interaction model
reach Interaction Distance of a Point Process
plot.owin Plot a Spatial Window
rlabel Random Re-Labelling of Point Pattern
Jcross Multitype J Function (i-to-j)
diameter Diameter of a Window Frame
density.psp Kernel Smoothing of Line Segment Pattern
plot.fv Plot Function Valuesn
rNeymanScott Simulate Neyman-Scott Process
rstrat Simulate Stratified Random Point Pattern
square Square Window
Kest K-function
copper Berman-Huntington points and lines data
crossing.psp Crossing Points of Two Line Segment Patterns
shift.ppp Apply Vector Translation To Point Pattern
pairdist.ppp Pairwise distances
residualspaper Data and Code From JRSS Discussion Paper on Residuals
density.ppp Kernel Smoothed Intensity of Point Pattern
summary.splitppp Summary of a Split Point Pattern
summary.im Summarizing a Pixel Image
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
subset.listof Extract or Replace Subset of a List of Things
update.ppm Update a Fitted Point Process Model
pairdist Pairwise distances
pairsat.family Saturated Pairwise Interaction Point Process Family
ord.family Ord Interaction Process Family
compatible.im Test Whether Two Pixel Images Are Compatible
subset.fasp Extract Subset of Function Array
psp.object Class of Line Segment Patterns
spatstat-deprecated Deprecated spatstat functions
Fest Estimate the empty space function F
summary.ppp Summary of a Point Pattern Dataset
Strauss The Strauss Point Process Model
Gmulti Marked Nearest Neighbour Distance Function
is.ppm Test Whether An Object Is A Fitted Point Process Model
eval.fv Evaluate Expression Involving Functions
is.multitype.ppp Test Whether A Point Pattern is Multitype
endpoints.psp Endpoints of Line Segment Pattern
Jdot Multitype J Function (i-to-any)
data.ppm Extract Original Data from a Fitted Point Process Model
is.marked.ppp Test Whether A Point Pattern is Marked
is.ppp Test Whether An Object Is A Point Pattern
rcell Simulate Baddeley-Silverman Cell Process
expand.owin Expand Window By Factor
levelset Level Set of a Pixel Image
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
ripras Estimate window from points alone
rshift Random Shift
shift.owin Apply Vector Translation To Window
plot.fasp Plot a Function Array
ganglia Beta Ganglion Cells in Cat Retina, Old Version
Kmeasure Reduced Second Moment Measure
allstats Calculate four standard summary functions of a point pattern.
japanesepines Japanese Pines Point Pattern
pcf.ppp Pair Correlation Function of Point Pattern
cut.ppp Convert Point Pattern Marks from Numeric to Factor
nztrees New Zealand Trees Point Pattern
owin Create a Window
psp Create a Line Segment Pattern
rmh.ppm Simulate from a Fitted Point Process Model
print.ppp Print Brief Details of a Point Pattern Dataset
hist.im Histogram of Pixel Values in an Image
pairwise.family Pairwise Interaction Process Family
print.psp Print Brief Details of a Line Segment Pattern Dataset
eroded.areas Areas of Morphological Erosions
runifpoint Generate N Uniform Random Points
bdist.points Distance to Boundary of Window
subset.im Extract Subset of Image
summary.quad Summarizing a Quadrature Scheme
summary.listof Summary of a List of Things
plot.psp plot a Spatial Line Segment Pattern
finpines Pine saplings in Finland.
ppp.object Class of Point Patterns
harmonic Basis for Harmonic Functions
superimpose Superimpose Several Point Patterns
distmap Distance Map
bei Tropical rain forest trees
bdist.pixels Distance to Boundary of Window
identify.ppp Identify Points in a Point Pattern
rescale Convert dataset to another unit of length
rescale.psp Convert Line Segment Pattern to Another Unit of Length
Gest Nearest Neighbour Distance Function G
letterR Window in Shape of Letter R
eval.im Evaluate Expression Involving Pixel Images
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
erode.owin Erode a Window
shift.im Apply Vector Translation To Pixel Image
Iest Estimate the I-function
Jmulti Marked J Function
print.quad Print a Quadrature Scheme
shift Apply Vector Translation
pcf.fv Pair Correlation Function obtained from K Function
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rMatClust Simulate Matern Cluster Process
print.ppm Print a Fitted Point Process Model
cells Biological Cells Point Pattern
rSSI Simulate Simple Sequential Inhibition
Kinhom Inhomogeneous K-function
raster.x Cartesian Coordinates for a Pixel Raster
LennardJones The Lennard-Jones Potential
MultiStrauss The Multitype Strauss Point Process Model
residuals.ppm Residuals for Fitted Point Process Model
print.owin Print Brief Details of a Spatial Window
affine.psp Apply Affine Transformation To Line Segment Pattern
redwood California Redwoods Point Pattern (Ripley's Subset)
Poisson Poisson Point Process Model
rescue.rectangle Convert Window Back To Rectangle
as.ppp Convert Data To Class ppp
chorley Chorley-Ribble Cancer Data
rsyst Simulate systematic random point pattern
units Name for Unit of Length
spatstat.options Internal Options in Spatstat Package
summary.owin Summary of a Spatial Window
betacells Beta Ganglion Cells in Cat Retina
crossdist.psp Pairwise distances between two different line segment patterns
is.subset.owin Determine Whether One Window is Contained In Another
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
pcf Pair Correlation Function
nndist Nearest neighbour distances
markcorr Mark Correlation Function
predict.ppm Prediction from a Fitted Point Process Model
quantile.im Sample Quantiles of Pixel Image
split.ppp Divide Point Pattern into Sub-patterns
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
simdat Simulated Point Pattern
spruces Spruces Point Pattern
scanpp Read Point Pattern From Data File
rStrauss Perfect Simulation of the Strauss Process
area.owin Area of a Window
suffstat Sufficient Statistic of Point Process Model
rpoisline Generate Poisson Random Line Process
bounding.box Bounding Box of a Window
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
plot.quad plot a Spatial Quadrature Scheme
quadratcount Quadrat counting for a point pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
rmpoispp Generate Multitype Poisson Point Pattern
rpoint Generate N Random Points
rshift.ppp Randomly Shift a Point Pattern
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
cut.im Convert Pixel Image from Numeric to Factor
demopat Artificial Data Point Pattern
distmap.ppp Distance Map of Point Pattern
fasp.object Function Arrays for Spatial Patterns
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
ppm.object Class of Fitted Point Process Models
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rotate.ppp Rotate a Point Pattern
subset.ppp Extract or Replace Subset of Point Pattern
Kest.fft K-function using FFT
affine.ppp Apply Affine Transformation To Point Pattern
crossdist.default Pairwise distances between two different sets of points
spatstat The Spatstat Package
Jest Estimate the J-function
Pairwise Generic Pairwise Interaction model
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
fitted.ppm Fitted Conditional Intensity for Point Process Model
redwoodfull California Redwoods Point Pattern (Entire Dataset)
plot.ppp plot a Spatial Point Pattern
summary.ppm Summarizing a Fitted Point Process Model
rpoispp Generate Poisson Point Pattern
hamster Aherne's hamster tumour data
intersect.owin Intersection or Union of Two Windows
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
union.quad Union of Data and Dummy Points
nncross Nearest Neighbour in Another Point Pattern
plot.listof Plot a List of Things
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
rThomas Simulate Thomas Process
shift.psp Apply Vector Translation To Line Segment Pattern
trim.rectangle Cut margins from rectangle
Ord Generic Ord Interaction model
disc Circular Window
StraussHard The Strauss / Hard Core Point Process Model
rthin Random Thinning
selfcrossing.psp Crossing Points in a Line Segment Pattern
subset.fv Extract Subset of Function Values
spokes Spokes pattern of dummy points
swedishpines Swedish Pines Point Pattern
rMaternII Simulate Matern Model II
as.mask Pixel Image Approximation of a Window
applynbd Apply Function to Every Neighbourhood in a Point Pattern
complement.owin Take Complement of a Window
contour.im Contour plot of pixel image
midpoints.psp Midpoints of Line Segment Pattern
lengths.psp Lengths of Line Segments
rescale.ppp Convert Point Pattern to Another Unit of Length
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
rotate Rotate
unique.ppp Extract Unique Points from a Spatial Point Pattern
unmark Remove Marks from a Marked Point Pattern
anova.ppm ANOVA for Fitted Point Process Models
corners Corners of a rectangle
distmap.owin Distance Map of Window
is.multitype.ppm Test Whether A Point Process Model is Multitype
lansing Lansing Woods Point Pattern
nnwhich Nearest neighbour
nearest.raster.point Find Pixel Nearest to a Given Point
print.im Print Brief Details of an Image
rMaternI Simulate Matern Model I
rescale.owin Convert Window to Another Unit of Length
rshift.psp Randomly Shift a Line Segment Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
as.psp Convert Data To Class psp
concatxy Concatenate x,y Coordinate Vectors
fv.object Data Frames of Function Values
gridweights Compute Quadrature Weights Based on Grid Counts
envelope Simulation envelopes of summary function
pairdist.default Pairwise distances
is.im Test Whether An Object Is A Pixel Image
setcov Set Covariance of a Window
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Date 12 January 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Fri Jan 12 09:40:54 2007; adrian

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