spatstat v1.11-3

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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, 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
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
bounding.box.xy Convex Hull of Points
Gest Nearest Neighbour Distance Function G
OrdThresh Ord's Interaction model
centroid.owin Centroid of a window
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
Jcross Multitype J Function (i-to-j)
crossdist.psp Pairwise distances between two different line segment patterns
copper Berman-Huntington points and lines data
default.dummy Generate a Default Pattern of Dummy Points
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
disc Circular Window
ewcdf Weighted Empirical Cumulative Distribution Function
density.psp Kernel Smoothing of Line Segment Pattern
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
gridcentres Rectangular grid of points
humberside Humberside Data on Childhood Leukaemia and Lymphoma
is.subset.owin Determine Whether One Window is Contained In Another
psp.object Class of Line Segment Patterns
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
pairdist Pairwise distances
progressreport Print Progress Reports
quadratcount Quadrat counting for a point pattern
ppp.object Class of Point Patterns
rescale.owin Convert Window to Another Unit of Length
print.quad Print a Quadrature Scheme
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rescale Convert dataset to another unit of length
subset.fv Extract Subset of Function Values
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
spokes Spokes pattern of dummy points
Pairwise Generic Pairwise Interaction model
rescale.psp Convert Line Segment Pattern to Another Unit of Length
betacells Beta Ganglion Cells in Cat Retina
StraussHard The Strauss / Hard Core Point Process Model
affine.owin Apply Affine Transformation To Window
fasp.object Function Arrays for Spatial Patterns
Kest.fft K-function using FFT
Ord Generic Ord Interaction model
runifpoint Generate N Uniform Random Points
interp.im Interpolate a Pixel Image
MultiStrauss The Multitype Strauss Point Process Model
rlabel Random Re-Labelling of Point Pattern
bei Tropical rain forest trees
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
Poisson Poisson Point Process Model
cut.im Convert Pixel Image from Numeric to Factor
affine.psp Apply Affine Transformation To Line Segment Pattern
update.ppm Update a Fitted Point Process Model
summary.listof Summary of a List of Things
chorley Chorley-Ribble Cancer Data
eval.fv Evaluate Expression Involving Functions
anova.ppm ANOVA for Fitted Point Process Models
letterR Window in Shape of Letter R
is.owin Test Whether An Object Is A Window
rescale.ppp Convert Point Pattern to Another Unit of Length
print.ppm Print a Fitted Point Process Model
is.ppp Test Whether An Object Is A Point Pattern
expand.owin Expand Window By Factor
diameter Diameter of a Window
superimpose Superimpose Several Point Patterns
Iest Estimate the I-function
concatxy Concatenate x,y Coordinate Vectors
plot.psp plot a Spatial Line Segment Pattern
nbfires Point Patterns of New Brunswick Forest Fires
harmonic Basis for Harmonic Functions
lansing Lansing Woods Point Pattern
ganglia Beta Ganglion Cells in Cat Retina, Old Version
plot.quad plot a Spatial Quadrature Scheme
pppdist Optimal Match Between Two Point Patterns
plot.ppm plot a Fitted Point Process Model
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
print.ppp Print Brief Details of a Point Pattern Dataset
plot.ppp plot a Spatial Point Pattern
markcorr Mark Correlation Function
rMaternII Simulate Matern Model II
quantile.im Sample Quantiles of Pixel Image
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
plot.im Plot a Pixel Image
owin.object Class owin
rMatClust Simulate Matern Cluster Process
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
rcell Simulate Baddeley-Silverman Cell Process
print.im Print Brief Details of an Image
ppm.object Class of Fitted Point Process Models
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
nncross Nearest Neighbour in Another Point Pattern
setcov Set Covariance of a Window
psp Create a Line Segment Pattern
print.owin Print Brief Details of a Spatial Window
shift.im Apply Vector Translation To Pixel Image
selfcrossing.psp Crossing Points in a Line Segment Pattern
subset.psp Extract Subset of Line Segment Pattern
as.matrix.im Convert Pixel Image to Matrix
plot.owin Plot a Spatial Window
rpoisline Generate Poisson Random Line Process
summary.quad Summarizing a Quadrature Scheme
rthin Random Thinning
rshift.psp Randomly Shift a Line Segment Pattern
rshift.ppp Randomly Shift a Point Pattern
vertices Vertices of a Window
summary.splitppp Summary of a Split Point Pattern
identify.ppp Identify Points in a Point Pattern
unique.ppp Extract Unique Points from a Spatial Point Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
mean.im Mean Pixel Value in an Image
is.marked.ppp Test Whether A Point Pattern is Marked
shift.ppp Apply Vector Translation To Point Pattern
persp.im Perspective Plot of Pixel Image
corners Corners of a rectangle
crossing.psp Crossing Points of Two Line Segment Patterns
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
rescue.rectangle Convert Window Back To Rectangle
spatstat-internal Internal spatstat functions
Saturated Saturated Pairwise Interaction model
as.psp Convert Data To Class psp
rstrat Simulate Stratified Random Point Pattern
bounding.box Bounding Box of a Window or Point Pattern
shift.owin Apply Vector Translation To Window
unmark Remove Marks from a Marked Point Pattern
ripras Estimate window from points alone
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
Kest K-function
Fest Estimate the empty space function F
endpoints.psp Endpoints of Line Segment Pattern
demopat Artificial Data Point Pattern
is.im Test Whether An Object Is A Pixel Image
nndist Nearest neighbour distances
pcf.ppp Pair Correlation Function of Point Pattern
plot.plotppm Plot a plotppm Object Created by plot.ppm
ppp Create a Point Pattern
ants Harkness-Isham ants' nests data
as.owin Convert Data To Class owin
rMaternI Simulate Matern Model I
bramblecanes Hutchings' Bramble Canes data
rpoint Generate N Random Points
compatible.im Test Whether Two Pixel Images Are Compatible
rshift Random Shift
Kmeasure Reduced Second Moment Measure
rStrauss Perfect Simulation of the Strauss Process
bdist.pixels Distance to Boundary of Window
rotate.owin Rotate a Window
split.ppp Divide Point Pattern into Sub-patterns
profilepl Profile Maximum Pseudolikelihood
as.im Convert to Pixel Image
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
crossdist Pairwise distances
residuals.ppm Residuals for Fitted Point Process Model
subset.listof Extract or Replace Subset of a List of Things
crossdist.default Pairwise distances between two different sets of points
distmap.ppp Distance Map of Point Pattern
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
envelope Simulation envelopes of summary function
im.object Class of Images
rshift.splitppp Randomly Shift a List of Point Patterns
amacrine Hughes' Amacrine Cell Data
summary.im Summarizing a Pixel Image
union.quad Union of Data and Dummy Points
subset.fasp Extract Subset of Function Array
gridweights Compute Quadrature Weights Based on Grid Counts
append.psp Combine Two Line Segment Patterns
rsyst Simulate systematic random point pattern
trim.rectangle Cut margins from rectangle
as.rectangle Window Frame
suffstat Sufficient Statistic of Point Process Model
compatible.fv Test Whether Two Function Objects Are Compatible
eval.im Evaluate Expression Involving Pixel Images
convexhull.xy Convex Hull of Points
inside.owin Test Whether Points Are Inside A Window
is.marked Test Whether Marks Are Present
pcf.fasp Pair Correlation Function obtained from array of K functions
is.marked.ppm Test Whether A Point Process Model is Marked
pairsat.family Saturated Pairwise Interaction Point Process Family
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
levelset Level Set of a Pixel Image
density.ppp Kernel Smoothed Intensity of Point Pattern
fitted.ppm Fitted Conditional Intensity for Point Process Model
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
pcf.fv Pair Correlation Function obtained from K Function
residualspaper Data and Code From JRSS Discussion Paper on Residuals
reach Interaction Distance of a Point Process
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
summary.ppm Summarizing a Fitted Point Process Model
thomas.estK Fit the Thomas Point Process by Minimum Contrast
redwood California Redwoods Point Pattern (Ripley's Subset)
shift.psp Apply Vector Translation To Line Segment Pattern
square Square Window
subsetget.im Reset Values in Subset of Image
Kdot Multitype K Function (i-to-any)
Geyer Geyer's Saturation Point Process Model
affine.ppp Apply Affine Transformation To Point Pattern
angles.psp Orientation Angles of Line Segments
anemones Beadlet Anemones Data
as.ppp Convert Data To Class ppp
contour.im Contour plot of pixel image
hist.im Histogram of Pixel Values in an Image
erode.owin Erode a Window
im Create a Pixel Image Object
is.multitype Test whether Object is Multitype
japanesepines Japanese Pines Point Pattern
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
plot.fasp Plot a Function Array
ord.family Ord Interaction Process Family
quadscheme Generate a Quadrature Scheme from a Point Pattern
quad.object Class of Quadrature Schemes
rmpoispp Generate Multitype Poisson Point Pattern
rotate Rotate
subset.ppp Extract or Replace Subset of Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
Kdot.inhom Inhomogeneous Multitype K Dot Function
Strauss The Strauss Point Process Model
Softcore The Soft Core Point Process Model
area.owin Area of a Window
DiggleGratton Diggle-Gratton model
complement.owin Take Complement of a Window
eroded.areas Areas of Morphological Erosions
Jmulti Marked J Function
kaplan.meier Kaplan-Meier Estimator using Histogram Data
nnwhich Nearest neighbour
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
pairwise.family Pairwise Interaction Process Family
redwoodfull California Redwoods Point Pattern (Entire Dataset)
reduced.sample Reduced Sample Estimator using Histogram Data
rSSI Simulate Simple Sequential Inhibition
summary.owin Summary of a Spatial Window
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
coef.ppm Coefficients of Fitted Point Process Model
dilate.owin Dilate a Window
finpines Pine saplings in Finland.
scanpp Read Point Pattern From Data File
intersect.owin Intersection or Union of Two Windows
setmarks Set or Reset the Marks in a Point Pattern
hamster Aherne's hamster tumour data
spruces Spruces Point Pattern
shift Apply Vector Translation
is.ppm Test Whether An Object Is A Fitted Point Process Model
longleaf Longleaf Pines Point Pattern
mincontrast Method of Minimum Contrast
plot.fv Plot Function Valuesn
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
rotate.ppp Rotate a Point Pattern
units Name for Unit of Length
Jdot Multitype J Function (i-to-any)
Kcross.inhom Inhomogeneous Cross K Function
Kmulti Marked K-Function
allstats Calculate four standard summary functions of a point pattern.
bdist.points Distance to Boundary of Window
data.ppm Extract Original Data from a Fitted Point Process Model
distmap Distance Map
midpoints.psp Midpoints of Line Segment Pattern
nztrees New Zealand Trees Point Pattern
pcf Pair Correlation Function
plot.listof Plot a List of Things
predict.ppm Prediction from a Fitted Point Process Model
print.psp Print Brief Details of a Line Segment Pattern Dataset
rNeymanScott Simulate Neyman-Scott Process
rThomas Simulate Thomas Process
runifdisc Generate N Uniform Random Points in a Disc
simdat Simulated Point Pattern
Kinhom Inhomogeneous K-function
Kcross Multitype K Function (Cross-type)
LennardJones The Lennard-Jones Potential
clickpoly Interactively Define a Polygon
eem Exponential Energy Marks
distmap.owin Distance Map of Window
multiplicity.ppp Count Multiplicity of Duplicate Points
rpoispp Generate Poisson Point Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
swedishpines Swedish Pines Point Pattern
Jest Estimate the J-function
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
affine Apply Affine Transformation
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
applynbd Apply Function to Every Neighbourhood in a Point Pattern
crossdist.ppp Pairwise distances between two different point patterns
cells Biological Cells Point Pattern
cut.ppp Convert Point Pattern Marks from Numeric to Factor
clickppp Interactively Add Points
is.multitype.ppp Test Whether A Point Pattern is Multitype
lengths.psp Lengths of Line Segments
lurking Lurking variable plot
plot.splitppp Plot a List of Point Patterns
rmh.ppm Simulate from a Fitted Point Process Model
rmpoint Generate N Random Multitype Points
rotate.psp Rotate a Line Segment Pattern
subset.splitppp Extract or Replace Sub-Patterns
summary.ppp Summary of a Point Pattern Dataset
spatstat The Spatstat Package
as.mask Pixel Image Approximation of a Window
spatstat-deprecated Deprecated spatstat functions
distmap.psp Distance Map of Line Segment Pattern
fv.object Data Frames of Function Values
is.multitype.ppm Test Whether A Point Process Model is Multitype
pairdist.default Pairwise distances
owin Create a Window
pairdist.psp Pairwise distances between line segments
pairdist.ppp Pairwise distances
ppm Fit Point Process Model to Data
nearest.raster.point Find Pixel Nearest to a Given Point
raster.x Cartesian Coordinates for a Pixel Raster
subset.im Extract Subset of Image
spatstat.options Internal Options in Spatstat Package
summary.psp Summary of a Line Segment Pattern Dataset
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Date 19 March 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Mon Mar 19 18:08:23 2007; adrian

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