spatstat v1.11-2

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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
suffstat Sufficient Statistic of Point Process Model
rescale.ppp Convert Point Pattern to Another Unit of Length
rcell Simulate Baddeley-Silverman Cell Process
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
MultiStrauss The Multitype Strauss Point Process Model
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
im Create a Pixel Image Object
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
spatstat The Spatstat Package
rNeymanScott Simulate Neyman-Scott Process
multiplicity.ppp Count Multiplicity of Duplicate Points
Jmulti Marked J Function
lengths.psp Lengths of Line Segments
reach Interaction Distance of a Point Process
distmap Distance Map
nncross Nearest Neighbour in Another Point Pattern
japanesepines Japanese Pines Point Pattern
endpoints.psp Endpoints of Line Segment Pattern
is.ppp Test Whether An Object Is A Point Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
gridcentres Rectangular grid of points
diameter Diameter of a Window
ants Harkness-Isham ants' nests data
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
gridweights Compute Quadrature Weights Based on Grid Counts
Pairwise Generic Pairwise Interaction model
im.object Class of Images
eem Exponential Energy Marks
clickppp Interactively Add Points
is.owin Test Whether An Object Is A Window
is.im Test Whether An Object Is A Pixel Image
complement.owin Take Complement of a Window
plot.im Plot a Pixel Image
bounding.box Bounding Box of a Window or Point Pattern
is.subset.owin Determine Whether One Window is Contained In Another
as.mask Pixel Image Approximation of a Window
rescale.owin Convert Window to Another Unit of Length
superimpose Superimpose Several Point Patterns
profilepl Profile Maximum Pseudolikelihood
quadratcount Quadrat counting for a point pattern
ord.family Ord Interaction Process Family
Kmulti Marked K-Function
rshift Random Shift
Jcross Multitype J Function (i-to-j)
levelset Level Set of a Pixel Image
as.psp Convert Data To Class psp
centroid.owin Centroid of a window
copper Berman-Huntington points and lines data
print.psp Print Brief Details of a Line Segment Pattern Dataset
crossdist.default Pairwise distances between two different sets of points
spatstat-internal Internal spatstat functions
Jest Estimate the J-function
split.ppp Divide Point Pattern into Sub-patterns
Saturated Saturated Pairwise Interaction model
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
plot.ppp plot a Spatial Point Pattern
affine Apply Affine Transformation
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
rthin Random Thinning
eroded.areas Areas of Morphological Erosions
shift.im Apply Vector Translation To Pixel Image
crossdist Pairwise distances
print.ppp Print Brief Details of a Point Pattern Dataset
owin.object Class owin
Strauss The Strauss Point Process Model
rmh.ppm Simulate from a Fitted Point Process Model
is.multitype.ppm Test Whether A Point Process Model is Multitype
print.im Print Brief Details of an Image
anova.ppm ANOVA for Fitted Point Process Models
lansing Lansing Woods Point Pattern
subset.psp Extract Subset of Line Segment Pattern
humberside Humberside Data on Childhood Leukaemia and Lymphoma
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
distmap.ppp Distance Map of Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
rotate.psp Rotate a Line Segment Pattern
density.psp Kernel Smoothing of Line Segment Pattern
fv.object Data Frames of Function Values
as.ppp Convert Data To Class ppp
hamster Aherne's hamster tumour data
convexhull.xy Convex Hull of Points
ppp.object Class of Point Patterns
distmap.owin Distance Map of Window
nztrees New Zealand Trees Point Pattern
anemones Beadlet Anemones Data
redwood California Redwoods Point Pattern (Ripley's Subset)
nbfires Point Patterns of New Brunswick Forest Fires
rpoisline Generate Poisson Random Line Process
coef.ppm Coefficients of Fitted Point Process Model
mean.im Mean Pixel Value in an Image
ripras Estimate window from points alone
clickpoly Interactively Define a Polygon
append.psp Combine Two Line Segment Patterns
erode.owin Erode a Window
rotate Rotate
summary.ppp Summary of a Point Pattern Dataset
rshift.psp Randomly Shift a Line Segment Pattern
plot.psp plot a Spatial Line Segment Pattern
longleaf Longleaf Pines Point Pattern
summary.splitppp Summary of a Split Point Pattern
pppdist Optimal Match Between Two Point Patterns
setmarks Set or Reset the Marks in a Point Pattern
simdat Simulated Point Pattern
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
rMaternI Simulate Matern Model I
trim.rectangle Cut margins from rectangle
distmap.psp Distance Map of Line Segment Pattern
midpoints.psp Midpoints of Line Segment Pattern
psp.object Class of Line Segment Patterns
spokes Spokes pattern of dummy points
ppm.object Class of Fitted Point Process Models
rescale Convert dataset to another unit of length
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
psp Create a Line Segment Pattern
Kcross Multitype K Function (Cross-type)
Jdot Multitype J Function (i-to-any)
Gest Nearest Neighbour Distance Function G
Kest.fft K-function using FFT
as.owin Convert Data To Class owin
cells Biological Cells Point Pattern
print.quad Print a Quadrature Scheme
shift.owin Apply Vector Translation To Window
subset.fv Extract Subset of Function Values
eval.fv Evaluate Expression Involving Functions
as.im Convert to Pixel Image
rpoint Generate N Random Points
pcf.ppp Pair Correlation Function of Point Pattern
DiggleGratton Diggle-Gratton model
summary.quad Summarizing a Quadrature Scheme
Softcore The Soft Core Point Process Model
area.owin Area of a Window
scanpp Read Point Pattern From Data File
raster.x Cartesian Coordinates for a Pixel Raster
cut.ppp Convert Point Pattern Marks from Numeric to Factor
Kest K-function
concatxy Concatenate x,y Coordinate Vectors
crossdist.psp Pairwise distances between two different line segment patterns
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
letterR Window in Shape of Letter R
as.matrix.im Convert Pixel Image to Matrix
chorley Chorley-Ribble Cancer Data
fasp.object Function Arrays for Spatial Patterns
hist.im Histogram of Pixel Values in an Image
inside.owin Test Whether Points Are Inside A Window
Kmeasure Reduced Second Moment Measure
amacrine Hughes' Amacrine Cell Data
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
compatible.fv Test Whether Two Function Objects Are Compatible
is.multitype Test whether Object is Multitype
is.multitype.ppp Test Whether A Point Pattern is Multitype
plot.splitppp Plot a List of Point Patterns
thomas.estK Fit the Thomas Point Process by Minimum Contrast
shift Apply Vector Translation
is.marked.ppp Test Whether A Point Pattern is Marked
ppm Fit Point Process Model to Data
plot.listof Plot a List of Things
pairdist.default Pairwise distances
nearest.raster.point Find Pixel Nearest to a Given Point
is.ppm Test Whether An Object Is A Fitted Point Process Model
print.ppm Print a Fitted Point Process Model
progressreport Print Progress Reports
contour.im Contour plot of pixel image
affine.ppp Apply Affine Transformation To Point Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
update.ppm Update a Fitted Point Process Model
runifdisc Generate N Uniform Random Points in a Disc
rpoispp Generate Poisson Point Pattern
setcov Set Covariance of a Window
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
pcf.fv Pair Correlation Function obtained from K Function
shift.ppp Apply Vector Translation To Point Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
rotate.owin Rotate a Window
owin Create a Window
rescale.psp Convert Line Segment Pattern to Another Unit of Length
selfcrossing.psp Crossing Points in a Line Segment Pattern
pairdist.psp Pairwise distances between line segments
ewcdf Weighted Empirical Cumulative Distribution Function
plot.plotppm Plot a plotppm Object Created by plot.ppm
summary.im Summarizing a Pixel Image
Fest Estimate the empty space function F
rmpoint Generate N Random Multitype Points
plot.owin Plot a Spatial Window
OrdThresh Ord's Interaction model
default.dummy Generate a Default Pattern of Dummy Points
summary.owin Summary of a Spatial Window
spruces Spruces Point Pattern
residuals.ppm Residuals for Fitted Point Process Model
affine.psp Apply Affine Transformation To Line Segment Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
unique.ppp Extract Unique Points from a Spatial Point Pattern
bei Tropical rain forest trees
shift.psp Apply Vector Translation To Line Segment Pattern
rotate.ppp Rotate a Point Pattern
pairsat.family Saturated Pairwise Interaction Point Process Family
residualspaper Data and Code From JRSS Discussion Paper on Residuals
bramblecanes Hutchings' Bramble Canes data
harmonic Basis for Harmonic Functions
rshift.splitppp Randomly Shift a List of Point Patterns
rSSI Simulate Simple Sequential Inhibition
demopat Artificial Data Point Pattern
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
subset.splitppp Extract or Replace Sub-Patterns
square Square Window
LennardJones The Lennard-Jones Potential
unmark Remove Marks from a Marked Point Pattern
expand.owin Expand Window By Factor
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
persp.im Perspective Plot of Pixel Image
spatstat.options Internal Options in Spatstat Package
crossdist.ppp Pairwise distances between two different point patterns
eval.im Evaluate Expression Involving Pixel Images
lurking Lurking variable plot
mincontrast Method of Minimum Contrast
disc Circular Window
cut.im Convert Pixel Image from Numeric to Factor
plot.quad plot a Spatial Quadrature Scheme
bounding.box.xy Convex Hull of Points
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
bdist.pixels Distance to Boundary of Window
finpines Pine saplings in Finland.
intersect.owin Intersection or Union of Two Windows
print.owin Print Brief Details of a Spatial Window
rlabel Random Re-Labelling of Point Pattern
swedishpines Swedish Pines Point Pattern
rescue.rectangle Convert Window Back To Rectangle
quad.object Class of Quadrature Schemes
subsetget.im Reset Values in Subset of Image
data.ppm Extract Original Data from a Fitted Point Process Model
allstats Calculate four standard summary functions of a point pattern.
Gmulti Marked Nearest Neighbour Distance Function
Iest Estimate the I-function
bdist.points Distance to Boundary of Window
fitted.ppm Fitted Conditional Intensity for Point Process Model
ganglia Beta Ganglion Cells in Cat Retina, Old Version
is.marked Test Whether Marks Are Present
envelope Simulation envelopes of summary function
identify.ppp Identify Points in a Point Pattern
quantile.im Sample Quantiles of Pixel Image
spatstat-deprecated Deprecated spatstat functions
Kdot Multitype K Function (i-to-any)
markcorr Mark Correlation Function
ppp Create a Point Pattern
pairwise.family Pairwise Interaction Process Family
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
quadscheme Generate a Quadrature Scheme from a Point Pattern
is.marked.ppm Test Whether A Point Process Model is Marked
rshift.ppp Randomly Shift a Point Pattern
summary.ppm Summarizing a Fitted Point Process Model
affine.owin Apply Affine Transformation To Window
corners Corners of a rectangle
kaplan.meier Kaplan-Meier Estimator using Histogram Data
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
nndist Nearest neighbour distances
Geyer Geyer's Saturation Point Process Model
nnwhich Nearest neighbour
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
pcf.fasp Pair Correlation Function obtained from array of K functions
subset.fasp Extract Subset of Function Array
summary.listof Summary of a List of Things
Kcross.inhom Inhomogeneous Cross K Function
StraussHard The Strauss / Hard Core Point Process Model
Kinhom Inhomogeneous K-function
crossing.psp Crossing Points of Two Line Segment Patterns
applynbd Apply Function to Every Neighbourhood in a Point Pattern
plot.fv Plot Function Valuesn
rStrauss Perfect Simulation of the Strauss Process
runifpoint Generate N Uniform Random Points
rmpoispp Generate Multitype Poisson Point Pattern
reduced.sample Reduced Sample Estimator using Histogram Data
plot.ppm plot a Fitted Point Process Model
rMatClust Simulate Matern Cluster Process
Kdot.inhom Inhomogeneous Multitype K Dot Function
as.rectangle Window Frame
rThomas Simulate Thomas Process
betacells Beta Ganglion Cells in Cat Retina
Poisson Poisson Point Process Model
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
predict.ppm Prediction from a Fitted Point Process Model
pairdist Pairwise distances
pcf Pair Correlation Function
rsyst Simulate systematic random point pattern
plot.fasp Plot a Function Array
subset.im Extract Subset of Image
rstrat Simulate Stratified Random Point Pattern
vertices Vertices of a Window
rMaternII Simulate Matern Model II
dilate.owin Dilate a Window
subset.ppp Extract or Replace Subset of Point Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
angles.psp Orientation Angles of Line Segments
density.ppp Kernel Smoothed Intensity of Point Pattern
pairdist.ppp Pairwise distances
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
Ord Generic Ord Interaction model
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
union.quad Union of Data and Dummy Points
units Name for Unit of Length
subset.listof Extract or Replace Subset of a List of Things
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Date 10 March 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Mon Mar 12 09:35:27 2007; adrian

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