spatstat v1.11-8

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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
affine.psp Apply Affine Transformation To Line Segment Pattern
anemones Beadlet Anemones Data
chorley Chorley-Ribble Cancer Data
bramblecanes Hutchings' Bramble Canes data
default.dummy Generate a Default Pattern of Dummy Points
Saturated Saturated Pairwise Interaction model
area.owin Area of a Window
as.mask Pixel Image Approximation of a Window
DiggleGratton Diggle-Gratton model
Kmeasure Reduced Second Moment Measure
bounding.box.xy Convex Hull of Points
affine Apply Affine Transformation
cut.ppp Convert Point Pattern Marks from Numeric to Factor
fv.object Data Frames of Function Values
is.ppm Test Whether An Object Is A Fitted Point Process Model
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
Kmulti Marked K-Function
Softcore The Soft Core Point Process Model
Kest K-function
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
complement.owin Take Complement of a Window
Kest.fft K-function using FFT
im Create a Pixel Image Object
as.owin Convert Data To Class owin
Poisson Poisson Point Process Model
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
StraussHard The Strauss / Hard Core Point Process Model
Kcross Multitype K Function (Cross-type)
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
crossdist.default Pairwise distances between two different sets of points
harmonic Basis for Harmonic Functions
spatstat-internal Internal spatstat functions
bounding.box Bounding Box of a Window or Point Pattern
Kdot Multitype K Function (i-to-any)
data.ppm Extract Original Data from a Fitted Point Process Model
disc Circular Window
finpines Pine saplings in Finland.
Kcross.inhom Inhomogeneous Cross K Function
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
append.psp Combine Two Line Segment Patterns
anova.ppm ANOVA for Fitted Point Process Models
allstats Calculate four standard summary functions of a point pattern.
crossdist Pairwise distances
pcf Pair Correlation Function
is.im Test Whether An Object Is A Pixel Image
angles.psp Orientation Angles of Line Segments
ants Harkness-Isham ants' nests data
pairdist.psp Pairwise distances between line segments
japanesepines Japanese Pines Point Pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
pcf.fv Pair Correlation Function obtained from K Function
plot.listof Plot a List of Things
spatstat-deprecated Deprecated spatstat functions
is.ppp Test Whether An Object Is A Point Pattern
clarkevans Clark and Evans Aggregation Index
logLik.ppm Log Likelihood for Poisson Point Process Model
rlabel Random Re-Labelling of Point Pattern
print.im Print Brief Details of an Image
demopat Artificial Data Point Pattern
distmap.owin Distance Map of Window
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
midpoints.psp Midpoints of Line Segment Pattern
im.object Class of Images
rStrauss Perfect Simulation of the Strauss Process
ewcdf Weighted Empirical Cumulative Distribution Function
fitted.ppm Fitted Conditional Intensity for Point Process Model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
clickpoly Interactively Define a Polygon
compatible.im Test Whether Two Pixel Images Are Compatible
subset.fv Extract Subset of Function Values
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
nztrees New Zealand Trees Point Pattern
Fest Estimate the empty space function F
is.multitype Test whether Object is Multitype
interp.im Interpolate a Pixel Image
rMatClust Simulate Matern Cluster Process
cut.im Convert Pixel Image from Numeric to Factor
plot.quad plot a Spatial Quadrature Scheme
density.ppp Kernel Smoothed Intensity of Point Pattern
nndist Nearest neighbour distances
rmpoint Generate N Random Multitype Points
rSSI Simulate Simple Sequential Inhibition
multiplicity.ppp Count Multiplicity of Duplicate Points
is.multitype.ppm Test Whether A Point Process Model is Multitype
shift Apply Vector Translation
letterR Window in Shape of Letter R
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
levelset Level Set of a Pixel Image
pairwise.family Pairwise Interaction Process Family
ppm.object Class of Fitted Point Process Models
fitin.ppm Extract the Interaction from a Fitted Point Process Model
crossdist.psp Pairwise distances between two different line segment patterns
print.psp Print Brief Details of a Line Segment Pattern Dataset
lansing Lansing Woods Point Pattern
Jdot Multitype J Function (i-to-any)
is.owin Test Whether An Object Is A Window
raster.x Cartesian Coordinates for a Pixel Raster
owin.object Class owin
hist.im Histogram of Pixel Values in an Image
discretise Safely Convert Point Pattern Window to Binary Mask
pairdist.default Pairwise distances
Jest Estimate the J-function
unique.ppp Extract Unique Points from a Spatial Point Pattern
quadratcount Quadrat counting for a point pattern
plot.ppm plot a Fitted Point Process Model
markcorr Mark Correlation Function
pairdist.ppp Pairwise distances
pairdist Pairwise distances
Jcross Multitype J Function (i-to-j)
rpoint Generate N Random Points
eval.fv Evaluate Expression Involving Functions
subset.im Extract Subset of Image
print.ppp Print Brief Details of a Point Pattern Dataset
lengths.psp Lengths of Line Segments
Ord Generic Ord Interaction model
affine.owin Apply Affine Transformation To Window
pairsat.family Saturated Pairwise Interaction Point Process Family
plot.plotppm Plot a plotppm Object Created by plot.ppm
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
print.quad Print a Quadrature Scheme
density.psp Kernel Smoothing of Line Segment Pattern
Iest Estimate the I-function
Geyer Geyer's Saturation Point Process Model
persp.im Perspective Plot of Pixel Image
profilepl Profile Maximum Pseudolikelihood
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
ord.family Ord Interaction Process Family
quad.object Class of Quadrature Schemes
amacrine Hughes' Amacrine Cell Data
rescale Convert dataset to another unit of length
rmh.ppm Simulate from a Fitted Point Process Model
summary.listof Summary of a List of Things
ganglia Beta Ganglion Cells in Cat Retina, Old Version
update.ppm Update a Fitted Point Process Model
erode.owin Erode a Window
psp Create a Line Segment Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
reach Interaction Distance of a Point Process
crossing.psp Crossing Points of Two Line Segment Patterns
simdat Simulated Point Pattern
rThomas Simulate Thomas Process
setmarks Set or Reset the Marks in a Point Pattern
spatstat The Spatstat Package
convexhull.xy Convex Hull of Points
reduced.sample Reduced Sample Estimator using Histogram Data
corners Corners of a rectangle
unmark Remove Marks from a Marked Point Pattern
rshift.ppp Randomly Shift a Point Pattern
Strauss The Strauss Point Process Model
runifpoint Generate N Uniform Random Points
selfcrossing.psp Crossing Points in a Line Segment Pattern
as.matrix.im Convert Pixel Image to Matrix
summary.splitppp Summary of a Split Point Pattern
clickppp Interactively Add Points
predict.ppm Prediction from a Fitted Point Process Model
identify.ppp Identify Points in a Point Pattern
shift.ppp Apply Vector Translation To Point Pattern
envelope Simulation envelopes of summary function
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
eroded.areas Areas of Morphological Erosions
coef.ppm Coefficients of Fitted Point Process Model
residuals.ppm Residuals for Fitted Point Process Model
rcell Simulate Baddeley-Silverman Cell Process
scanpp Read Point Pattern From Data File
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
rpoispp Generate Poisson Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
shift.im Apply Vector Translation To Pixel Image
ppm Fit Point Process Model to Data
distmap.ppp Distance Map of Point Pattern
expand.owin Expand Window By Factor
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
Kinhom Inhomogeneous K-function
longleaf Longleaf Pines Point Pattern
rNeymanScott Simulate Neyman-Scott Process
rescale.owin Convert Window to Another Unit of Length
rshift.psp Randomly Shift a Line Segment Pattern
quantile.im Sample Quantiles of Pixel Image
as.rectangle Window Frame
rthin Random Thinning
is.subset.owin Determine Whether One Window is Contained In Another
rotate.psp Rotate a Line Segment Pattern
OrdThresh Ord's Interaction model
spokes Spokes pattern of dummy points
spruces Spruces Point Pattern
compatible.fv Test Whether Two Function Objects Are Compatible
subset.ppp Extract or Replace Subset of Point Pattern
plot.ppp plot a Spatial Point Pattern
applynbd Apply Function to Every Neighbourhood in a Point Pattern
affine.ppp Apply Affine Transformation To Point Pattern
setcov Set Covariance of a Window
is.marked.ppm Test Whether A Point Process Model is Marked
square Square Window
shift.owin Apply Vector Translation To Window
union.quad Union of Data and Dummy Points
lurking Lurking variable plot
gridweights Compute Quadrature Weights Based on Grid Counts
pppdist Optimal Match Between Two Point Patterns
gridcentres Rectangular grid of points
summary.owin Summary of a Spatial Window
shift.psp Apply Vector Translation To Line Segment Pattern
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
inside.owin Test Whether Points Are Inside A Window
summary.ppm Summarizing a Fitted Point Process Model
as.ppp Convert Data To Class ppp
plot.fasp Plot a Function Array
plot.owin Plot a Spatial Window
betacells Beta Ganglion Cells in Cat Retina
is.marked Test Whether Marks Are Present
ppp Create a Point Pattern
is.marked.ppp Test Whether A Point Pattern is Marked
nbfires Point Patterns of New Brunswick Forest Fires
plot.splitppp Plot a List of Point Patterns
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
pcf.ppp Pair Correlation Function of Point Pattern
summary.im Summarizing a Pixel Image
copper Berman-Huntington points and lines data
hamster Aherne's hamster tumour data
progressreport Print Progress Reports
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
Gest Nearest Neighbour Distance Function G
redwood California Redwoods Point Pattern (Ripley's Subset)
residualspaper Data and Code From JRSS Discussion Paper on Residuals
crossdist.ppp Pairwise distances between two different point patterns
distmap Distance Map
MultiStrauss The Multitype Strauss Point Process Model
rotate Rotate
rshift.splitppp Randomly Shift a List of Point Patterns
Jmulti Marked J Function
distmap.psp Distance Map of Line Segment Pattern
as.psp Convert Data To Class psp
rlinegrid Generate grid of parallel lines with random displacement
plot.psp plot a Spatial Line Segment Pattern
nncross Nearest Neighbour in Another Point Pattern
rescale.psp Convert Line Segment Pattern to Another Unit of Length
plot.fv Plot Function Valuesn
centroid.owin Centroid of a window
rescue.rectangle Convert Window Back To Rectangle
rotate.ppp Rotate a Point Pattern
subset.psp Extract Subset of Line Segment Pattern
eval.im Evaluate Expression Involving Pixel Images
rescale.ppp Convert Point Pattern to Another Unit of Length
mincontrast Method of Minimum Contrast
rstrat Simulate Stratified Random Point Pattern
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
is.multitype.ppp Test Whether A Point Pattern is Multitype
concatxy Concatenate x,y Coordinate Vectors
mean.im Mean Pixel Value in an Image
intersect.owin Intersection or Union of Two Windows
endpoints.psp Endpoints of Line Segment Pattern
plot.im Plot a Pixel Image
nndist.psp Nearest neighbour distances between line segments
subset.splitppp Extract or Replace Sub-Patterns
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
split.ppp Divide Point Pattern into Sub-patterns
nnwhich Nearest neighbour
Pairwise Generic Pairwise Interaction model
summary.ppp Summary of a Point Pattern Dataset
nearest.raster.point Find Pixel Nearest to a Given Point
runifdisc Generate N Uniform Random Points in a Disc
vertices Vertices of a Window
trim.rectangle Cut margins from rectangle
rMaternII Simulate Matern Model II
as.data.frame.ppp Coerce Point Pattern to a Data Frame
ripras Estimate window from points alone
units Name for Unit of Length
rshift Random Shift
as.im Convert to Pixel Image
thomas.estK Fit the Thomas Point Process by Minimum Contrast
superimpose Superimpose Several Point Patterns
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
fasp.object Function Arrays for Spatial Patterns
cells Biological Cells Point Pattern
quadscheme Generate a Quadrature Scheme from a Point Pattern
subset.fasp Extract Subset of Function Array
rotate.owin Rotate a Window
rsyst Simulate systematic random point pattern
summary.quad Summarizing a Quadrature Scheme
spatstat.options Internal Options in Spatstat Package
rmpoispp Generate Multitype Poisson Point Pattern
subset.listof Extract or Replace Subset of a List of Things
swedishpines Swedish Pines Point Pattern
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
summary.psp Summary of a Line Segment Pattern Dataset
kaplan.meier Kaplan-Meier Estimator using Histogram Data
Kdot.inhom Inhomogeneous Multitype K Dot Function
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
subsetget.im Reset Values in Subset of Image
bdist.points Distance to Boundary of Window
LennardJones The Lennard-Jones Potential
bei Tropical rain forest trees
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
print.owin Print Brief Details of a Spatial Window
psp.object Class of Line Segment Patterns
bdist.pixels Distance to Boundary of Window
print.ppm Print a Fitted Point Process Model
contour.im Contour plot of pixel image
diameter Diameter of a Window
dilate.owin Dilate a Window
rMaternI Simulate Matern Model I
eem Exponential Energy Marks
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
owin Create a Window
pcf.fasp Pair Correlation Function obtained from array of K functions
humberside Humberside Data on Childhood Leukaemia and Lymphoma
ppp.object Class of Point Patterns
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
rpoisline Generate Poisson Random Line Process
suffstat Sufficient Statistic of Point Process Model
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Date 26 July 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Fri Jul 27 02:26:55 2007; adrian

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