spatstat v1.12-4

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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 plotting spatial data, 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
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
Kdot Multitype K Function (i-to-any)
distmap.ppp Distance Map of Point Pattern
Kcross.inhom Inhomogeneous Cross K Function
Kinhom Inhomogeneous K-function
multiplicity.ppp Count Multiplicity of Duplicate Points
ppm Fit Point Process Model to Data
Iest Estimate the I-function
angles.psp Orientation Angles of Line Segments
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
clickppp Interactively Add Points
amacrine Hughes' Amacrine Cell Data
copper Berman-Huntington points and lines data
quantile.im Sample Quantiles of Pixel Image
levelset Level Set of a Pixel Image
crossdist.psp Pairwise distances between two different line segment patterns
as.psp Convert Data To Class psp
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
Jdot Multitype J Function (i-to-any)
Softcore The Soft Core Point Process Model
Kmeasure Reduced Second Moment Measure
im.object Class of Images
plot.splitppp Plot a List of Point Patterns
Fest Estimate the empty space function F
StraussHard The Strauss / Hard Core Point Process Model
allstats Calculate four standard summary functions of a point pattern.
Kest.fft K-function using FFT
rStrauss Perfect Simulation of the Strauss Process
affine.owin Apply Affine Transformation To Window
bei Tropical rain forest trees
LennardJones The Lennard-Jones Potential
ewcdf Weighted Empirical Cumulative Distribution Function
ants Harkness-Isham ants' nests data
anova.ppm ANOVA for Fitted Point Process Models
as.data.frame.ppp Coerce Point Pattern to a Data Frame
affine.ppp Apply Affine Transformation To Point Pattern
bounding.box Bounding Box of a Window or Point Pattern
anemones Beadlet Anemones Data
endpoints.psp Endpoints of Line Segment Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
clickpoly Interactively Define a Polygon
distmap Distance Map
owin.object Class owin
data.ppm Extract Original Data from a Fitted Point Process Model
harmonic Basis for Harmonic Functions
as.rectangle Window Frame
contour.im Contour plot of pixel image
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
nndist Nearest neighbour distances
bdist.pixels Distance to Boundary of Window
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
psp.object Class of Line Segment Patterns
inside.owin Test Whether Points Are Inside A Window
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
centroid.owin Centroid of a window
coef.ppm Coefficients of Fitted Point Process Model
summary.quad Summarizing a Quadrature Scheme
nnwhich Nearest neighbour
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
spatstat The Spatstat Package
persp.im Perspective Plot of Pixel Image
corners Corners of a rectangle
subset.fv Extract Subset of Function Values
fitted.ppm Fitted Conditional Intensity for Point Process Model
bramblecanes Hutchings' Bramble Canes data
pcf.ppp Pair Correlation Function of Point Pattern
is.multitype Test whether Object is Multitype
MultiStrauss The Multitype Strauss Point Process Model
japanesepines Japanese Pines Point Pattern
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
Strauss The Strauss Point Process Model
hist.im Histogram of Pixel Values in an Image
compatible.fv Test Whether Two Function Objects Are Compatible
demopat Artificial Data Point Pattern
clarkevans Clark and Evans Aggregation Index
cut.im Convert Pixel Image from Numeric to Factor
eem Exponential Energy Marks
thomas.estK Fit the Thomas Point Process by Minimum Contrast
localK Neighbourhood density function
ganglia Beta Ganglion Cells in Cat Retina, Old Version
rMaternII Simulate Matern Model II
Gmulti Marked Nearest Neighbour Distance Function
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
matchingdist Distance for a Point Pattern Matching
summary.splitppp Summary of a Split Point Pattern
is.ppm Test Whether An Object Is A Fitted Point Process Model
Jest Estimate the J-function
as.ppp Convert Data To Class ppp
pairdist.default Pairwise distances
nncross Nearest Neighbour in Another Point Pattern
nbfires Point Patterns of New Brunswick Forest Fires
spatstat-deprecated Deprecated spatstat functions
DiggleGratton Diggle-Gratton model
is.marked.ppm Test Whether A Point Process Model is Marked
affine.psp Apply Affine Transformation To Line Segment Pattern
im Create a Pixel Image Object
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
Jmulti Marked J Function
interp.im Interpolate a Pixel Image
bounding.box.xy Convex Hull of Points
as.im Convert to Pixel Image
print.ppm Print a Fitted Point Process Model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
print.psp Print Brief Details of a Line Segment Pattern Dataset
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
print.quad Print a Quadrature Scheme
convexhull.xy Convex Hull of Points
plot.owin Plot a Spatial Window
envelope Simulation envelopes of summary function
Kcross Multitype K Function (Cross-type)
OrdThresh Ord's Interaction model
plot.listof Plot a List of Things
Kmulti Marked K-Function
rSSI Simulate Simple Sequential Inhibition
Pairwise Generic Pairwise Interaction model
nndist.psp Nearest neighbour distances between line segments
eval.im Evaluate Expression Involving Pixel Images
pppdist Distance Between Two Point Patterns
crossdist Pairwise distances
Poisson Poisson Point Process Model
rotate.ppp Rotate a Point Pattern
lengths.psp Lengths of Line Segments
plot.ppp plot a Spatial Point Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
rcell Simulate Baddeley-Silverman Cell Process
ppm.object Class of Fitted Point Process Models
gridcentres Rectangular grid of points
Kest K-function
density.psp Kernel Smoothing of Line Segment Pattern
Saturated Saturated Pairwise Interaction model
rshift Random Shift
rshift.splitppp Randomly Shift a List of Point Patterns
Jcross Multitype J Function (i-to-j)
humberside Humberside Data on Childhood Leukaemia and Lymphoma
rescue.rectangle Convert Window Back To Rectangle
plot.im Plot a Pixel Image
Kdot.inhom Inhomogeneous Multitype K Dot Function
selfcrossing.psp Crossing Points in a Line Segment Pattern
plot.hyperframe Plot Entries in a Hyperframe
rMaternI Simulate Matern Model I
Lest L-function
psp Create a Line Segment Pattern
residualspaper Data and Code From JRSS Discussion Paper on Residuals
Ord Generic Ord Interaction model
gridweights Compute Quadrature Weights Based on Grid Counts
applynbd Apply Function to Every Neighbourhood in a Point Pattern
rlabel Random Re-Labelling of Point Pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
plot.fv Plot Function Valuesn
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
rescale.owin Convert Window to Another Unit of Length
rThomas Simulate Thomas Process
as.matrix.im Convert Pixel Image to Matrix
longleaf Longleaf Pines Point Pattern
subset.listof Extract or Replace Subset of a List of Things
Gest Nearest Neighbour Distance Function G
spruces Spruces Point Pattern
as.owin Convert Data To Class owin
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
dilate.owin Dilate a Window
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
mincontrast Method of Minimum Contrast
bdist.points Distance to Boundary of Window
suffstat Sufficient Statistic of Point Process Model
append.psp Combine Two Line Segment Patterns
ppp Create a Point Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
quadratcount Quadrat counting for a point pattern
hamster Aherne's hamster tumour data
rotate.psp Rotate a Line Segment Pattern
crossdist.ppp Pairwise distances between two different point patterns
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
subset.splitppp Extract or Replace Sub-Patterns
smooth.ppp Spatial smoothing of observations at irregular points
update.ppm Update a Fitted Point Process Model
reduced.sample Reduced Sample Estimator using Histogram Data
simdat Simulated Point Pattern
discretise Safely Convert Point Pattern Window to Binary Mask
redwood California Redwoods Point Pattern (Ripley's Subset)
spatstat.options Internal Options in Spatstat Package
nztrees New Zealand Trees Point Pattern
concatxy Concatenate x,y Coordinate Vectors
summary.psp Summary of a Line Segment Pattern Dataset
is.marked Test Whether Marks Are Present
fasp.object Function Arrays for Spatial Patterns
summary.ppp Summary of a Point Pattern Dataset
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
rmpoispp Generate Multitype Poisson Point Pattern
subset.ppp Extract or Replace Subset of Point Pattern
pairdist Pairwise distances
subset.psp Extract Subset of Line Segment Pattern
spatstat-internal Internal spatstat functions
summary.ppm Summarizing a Fitted Point Process Model
rotate.owin Rotate a Window
complement.owin Take Complement of a Window
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
as.mask Pixel Image Approximation of a Window
is.multitype.ppp Test Whether A Point Pattern is Multitype
fitin.ppm Extract the Interaction from a Fitted Point Process Model
rstrat Simulate Stratified Random Point Pattern
distmap.psp Distance Map of Line Segment Pattern
area.owin Area of a Window
midpoints.psp Midpoints of Line Segment Pattern
rshift.psp Randomly Shift a Line Segment Pattern
intersect.owin Intersection or Union of Two Windows
ppp.object Class of Point Patterns
chorley Chorley-Ribble Cancer Data
rNeymanScott Simulate Neyman-Scott Process
ripras Estimate window from points alone
shift Apply Vector Translation
fv.object Data Frames of Function Values
lansing Lansing Woods Point Pattern
rMatClust Simulate Matern Cluster Process
rpoisline Generate Poisson Random Line Process
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
default.dummy Generate a Default Pattern of Dummy Points
plot.ppm plot a Fitted Point Process Model
unique.ppp Extract Unique Points from a Spatial Point Pattern
rsyst Simulate systematic random point pattern
is.subset.owin Determine Whether One Window is Contained In Another
profilepl Profile Maximum Pseudolikelihood
setmarks Set or Reset the Marks in a Point Pattern
lurking Lurking variable plot
pairdist.psp Pairwise distances between line segments
scanpp Read Point Pattern From Data File
identify.ppp Identify Points in a Point Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
print.im Print Brief Details of an Image
shift.ppp Apply Vector Translation To Point Pattern
shift.psp Apply Vector Translation To Line Segment Pattern
is.im Test Whether An Object Is A Pixel Image
runifpoint Generate N Uniform Random Points
vertices Vertices of a Window
eroded.areas Areas of Morphological Erosions
swedishpines Swedish Pines Point Pattern
kaplan.meier Kaplan-Meier Estimator using Histogram Data
pcf Pair Correlation Function
letterR Window in Shape of Letter R
affine Apply Affine Transformation
pairsat.family Saturated Pairwise Interaction Point Process Family
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
cells Biological Cells Point Pattern
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
rescale Convert dataset to another unit of length
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
square Square Window
pairdist.ppp Pairwise distances
markcorr Mark Correlation Function
predict.ppm Prediction from a Fitted Point Process Model
plot.psp plot a Spatial Line Segment Pattern
raster.x Cartesian Coordinates for a Pixel Raster
plot.quad plot a Spatial Quadrature Scheme
setcov Set Covariance of a Window
rmpoint Generate N Random Multitype Points
summary.im Summarizing a Pixel Image
rlinegrid Generate grid of parallel lines with random displacement
rotate Rotate
rshift.ppp Randomly Shift a Point Pattern
split.ppp Divide Point Pattern into Sub-patterns
print.owin Print Brief Details of a Spatial Window
ord.family Ord Interaction Process Family
shift.im Apply Vector Translation To Pixel Image
owin Create a Window
pcf.fv Pair Correlation Function obtained from K Function
superimpose Superimpose Several Point Patterns
plot.fasp Plot a Function Array
unmark Remove Marks from a Marked Point Pattern
progressreport Print Progress Reports
rescale.ppp Convert Point Pattern to Another Unit of Length
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
unitname Name for Unit of Length
union.quad Union of Data and Dummy Points
reach Interaction Distance of a Point Process
shift.owin Apply Vector Translation To Window
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
spokes Spokes pattern of dummy points
summary.owin Summary of a Spatial Window
subset.fasp Extract Subset of Function Array
subsetget.im Reset Values in Subset of Image
rmh.ppm Simulate from a Fitted Point Process Model
crossing.psp Crossing Points of Two Line Segment Patterns
density.ppp Kernel Smoothed Intensity of Point Pattern
distmap.owin Distance Map of Window
Geyer Geyer's Saturation Point Process Model
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
erode.owin Erode a Window
expand.owin Expand Window By Factor
eval.fv Evaluate Expression Involving Functions
diameter Diameter of a Window
is.marked.ppp Test Whether A Point Pattern is Marked
is.owin Test Whether An Object Is A Window
logLik.ppm Log Likelihood for Poisson Point Process Model
pcf.fasp Pair Correlation Function obtained from array of K functions
ponderosa Ponderosa Pine Tree Point Pattern
print.ppp Print Brief Details of a Point Pattern Dataset
quadscheme Generate a Quadrature Scheme from a Point Pattern
rpoint Generate N Random Points
rescale.psp Convert Line Segment Pattern to Another Unit of Length
rthin Random Thinning
trim.rectangle Cut margins from rectangle
plot.plotppm Plot a plotppm Object Created by plot.ppm
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
betacells Beta Ganglion Cells in Cat Retina
crossdist.default Pairwise distances between two different sets of points
cut.ppp Convert Point Pattern Marks from Numeric to Factor
disc Circular Window
finpines Pine saplings in Finland.
hyperframe Hyper Data Frame
is.ppp Test Whether An Object Is A Point Pattern
mean.im Mean Pixel Value in an Image
pppmatching.object Class of Point Matchings
quad.object Class of Quadrature Schemes
rpoispp Generate Poisson Point Pattern
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
runifdisc Generate N Uniform Random Points in a Disc
summary.listof Summary of a List of Things
pairwise.family Pairwise Interaction Process Family
pppmatching Create a Point Matching
residuals.ppm Residuals for Fitted Point Process Model
subset.im Extract Subset of Image
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Date 18 December 2007
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Wed Dec 19 01:23:13 2007; adrian

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