spatstat v1.12-5

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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
Kest K-function
DiggleGratton Diggle-Gratton model
Ord Generic Ord Interaction model
anemones Beadlet Anemones Data
Geyer Geyer's Saturation Point Process Model
Gest Nearest Neighbour Distance Function G
spatstat The Spatstat Package
Jdot Multitype J Function (i-to-any)
MultiStrauss The Multitype Strauss Point Process Model
bei Tropical rain forest trees
Kinhom Inhomogeneous K-function
Softcore The Soft Core Point Process Model
chorley Chorley-Ribble Cancer Data
Jest Estimate the J-function
Strauss The Strauss Point Process Model
bdist.points Distance to Boundary of Window
Saturated Saturated Pairwise Interaction model
applynbd Apply Function to Every Neighbourhood in a Point Pattern
as.matrix.im Convert Pixel Image to Matrix
Kest.fft K-function using FFT
cut.ppp Convert Point Pattern Marks from Numeric to Factor
corners Corners of a rectangle
as.rectangle Window Frame
contour.im Contour plot of pixel image
StraussHard The Strauss / Hard Core Point Process Model
as.owin Convert Data To Class owin
bounding.box.xy Convex Hull of Points
eval.im Evaluate Expression Involving Pixel Images
Kdot Multitype K Function (i-to-any)
area.owin Area of a Window
affine.owin Apply Affine Transformation To Window
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
centroid.owin Centroid of a window
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
Jcross Multitype J Function (i-to-j)
im.object Class of Images
LennardJones The Lennard-Jones Potential
fasp.object Function Arrays for Spatial Patterns
distmap Distance Map
as.ppp Convert Data To Class ppp
as.psp Convert Data To Class psp
compatible.im Test Whether Two Pixel Images Are Compatible
hist.im Histogram of Pixel Values in an Image
convexhull.xy Convex Hull of Points
bounding.box Bounding Box of a Window or Point Pattern
endpoints.psp Endpoints of Line Segment Pattern
Kcross.inhom Inhomogeneous Cross K Function
midpoints.psp Midpoints of Line Segment Pattern
affine.psp Apply Affine Transformation To Line Segment Pattern
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
crossdist.ppp Pairwise distances between two different point patterns
dilate.owin Dilate a Window
Gmulti Marked Nearest Neighbour Distance Function
levelset Level Set of a Pixel Image
ewcdf Weighted Empirical Cumulative Distribution Function
is.marked.ppm Test Whether A Point Process Model is Marked
betacells Beta Ganglion Cells in Cat Retina
ppp.object Class of Point Patterns
eroded.areas Areas of Morphological Erosions
concatxy Concatenate x,y Coordinate Vectors
plot.fv Plot Function Valuesn
OrdThresh Ord's Interaction model
as.im Convert to Pixel Image
cut.im Convert Pixel Image from Numeric to Factor
cells Biological Cells Point Pattern
clickppp Interactively Add Points
ants Harkness-Isham ants' nests data
lansing Lansing Woods Point Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
anova.ppm ANOVA for Fitted Point Process Models
Kdot.inhom Inhomogeneous Multitype K Dot Function
pcf Pair Correlation Function
disc Circular Window
Pairwise Generic Pairwise Interaction model
rescale Convert dataset to another unit of length
distmap.psp Distance Map of Line Segment Pattern
Kmeasure Reduced Second Moment Measure
discretise Safely Convert Point Pattern Window to Binary Mask
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
rsyst Simulate systematic random point pattern
append.psp Combine Two Line Segment Patterns
Jmulti Marked J Function
demopat Artificial Data Point Pattern
bramblecanes Hutchings' Bramble Canes data
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
finpines Pine saplings in Finland.
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
as.data.frame.ppp Coerce Point Pattern to a Data Frame
amacrine Hughes' Amacrine Cell Data
as.mask Pixel Image Approximation of a Window
compatible.fv Test Whether Two Function Objects Are Compatible
clickpoly Interactively Define a Polygon
Poisson Poisson Point Process Model
intersect.owin Intersection or Union of Two Windows
im Create a Pixel Image Object
complement.owin Take Complement of a Window
clarkevans Clark and Evans Aggregation Index
Kmulti Marked K-Function
Kcross Multitype K Function (Cross-type)
crossdist.default Pairwise distances between two different sets of points
bdist.pixels Distance to Boundary of Window
logLik.ppm Log Likelihood for Poisson Point Process Model
copper Berman-Huntington points and lines data
is.multitype.ppp Test Whether A Point Pattern is Multitype
harmonic Basis for Harmonic Functions
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
distmap.ppp Distance Map of Point Pattern
expand.owin Expand Window By Factor
humberside Humberside Data on Childhood Leukaemia and Lymphoma
fv.object Data Frames of Function Values
ponderosa Ponderosa Pine Tree Point Pattern
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
lengths.psp Lengths of Line Segments
plot.listof Plot a List of Things
pairdist.psp Pairwise distances between line segments
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
gridweights Compute Quadrature Weights Based on Grid Counts
fitted.ppm Fitted Conditional Intensity for Point Process Model
plot.im Plot a Pixel Image
rMaternI Simulate Matern Model I
japanesepines Japanese Pines Point Pattern
pairsat.family Saturated Pairwise Interaction Point Process Family
plot.quad plot a Spatial Quadrature Scheme
is.multitype Test whether Object is Multitype
rescale.psp Convert Line Segment Pattern to Another Unit of Length
plot.ppm plot a Fitted Point Process Model
density.psp Kernel Smoothing of Line Segment Pattern
plot.splitppp Plot a List of Point Patterns
owin Create a Window
summary.listof Summary of a List of Things
shift.psp Apply Vector Translation To Line Segment Pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
nnwhich Nearest neighbour
gridcentres Rectangular grid of points
rThomas Simulate Thomas Process
distmap.owin Distance Map of Window
plot.ppp plot a Spatial Point Pattern
plot.fasp Plot a Function Array
density.ppp Kernel Smoothed Intensity of Point Pattern
letterR Window in Shape of Letter R
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
suffstat Sufficient Statistic of Point Process Model
psp Create a Line Segment Pattern
diameter Diameter of a Window
summary.ppm Summarizing a Fitted Point Process Model
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
setcov Set Covariance of a Window
rshift Random Shift
runifpoint Generate N Uniform Random Points
pcf.fv Pair Correlation Function obtained from K Function
rotate Rotate
lurking Lurking variable plot
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
nndist.psp Nearest neighbour distances between line segments
pcf.fasp Pair Correlation Function obtained from array of K functions
pppdist Distance Between Two Point Patterns
crossing.psp Crossing Points of Two Line Segment Patterns
erode.owin Erode a Window
identify.ppp Identify Points in a Point Pattern
rlinegrid Generate grid of parallel lines with random displacement
ganglia Beta Ganglion Cells in Cat Retina, Old Version
print.ppm Print a Fitted Point Process Model
is.im Test Whether An Object Is A Pixel Image
psp.object Class of Line Segment Patterns
spokes Spokes pattern of dummy points
data.ppm Extract Original Data from a Fitted Point Process Model
default.dummy Generate a Default Pattern of Dummy Points
interp.im Interpolate a Pixel Image
is.marked.ppp Test Whether A Point Pattern is Marked
crossdist Pairwise distances
hamster Aherne's hamster tumour data
spatstat-deprecated Deprecated spatstat functions
redwood California Redwoods Point Pattern (Ripley's Subset)
eval.fv Evaluate Expression Involving Functions
ppm.object Class of Fitted Point Process Models
print.ppp Print Brief Details of a Point Pattern Dataset
predict.ppm Prediction from a Fitted Point Process Model
rmpoispp Generate Multitype Poisson Point Pattern
hyperframe Hyper Data Frame
rshift.ppp Randomly Shift a Point Pattern
is.owin Test Whether An Object Is A Window
is.marked Test Whether Marks Are Present
is.ppp Test Whether An Object Is A Point Pattern
is.subset.owin Determine Whether One Window is Contained In Another
raster.x Cartesian Coordinates for a Pixel Raster
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
owin.object Class owin
mean.im Mean Pixel Value in an Image
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
rthin Random Thinning
ppm Fit Point Process Model to Data
eem Exponential Energy Marks
spruces Spruces Point Pattern
print.im Print Brief Details of an Image
smooth.ppp Spatial smoothing of observations at irregular points
reach Interaction Distance of a Point Process
ord.family Ord Interaction Process Family
setmarks Set or Reset the Marks in a Point Pattern
fitin.ppm Extract the Interaction from a Fitted Point Process Model
rStrauss Perfect Simulation of the Strauss Process
residuals.ppm Residuals for Fitted Point Process Model
pairdist.default Pairwise distances
persp.im Perspective Plot of Pixel Image
rcell Simulate Baddeley-Silverman Cell Process
rmh.ppm Simulate from a Fitted Point Process Model
matchingdist Distance for a Point Pattern Matching
rstrat Simulate Stratified Random Point Pattern
split.ppp Divide Point Pattern into Sub-patterns
markcorr Mark Correlation Function
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
subset.ppp Extract or Replace Subset of Point Pattern
crossdist.psp Pairwise distances between two different line segment patterns
rmpoint Generate N Random Multitype Points
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
plot.owin Plot a Spatial Window
pppmatching Create a Point Matching
Lest L-function
shift.im Apply Vector Translation To Pixel Image
affine Apply Affine Transformation
Fest Estimate the empty space function F
rescue.rectangle Convert Window Back To Rectangle
runifdisc Generate N Uniform Random Points in a Disc
allstats Calculate four standard summary functions of a point pattern.
shift.ppp Apply Vector Translation To Point Pattern
subset.splitppp Extract or Replace Sub-Patterns
profilepl Profile Maximum Pseudolikelihood
shift.owin Apply Vector Translation To Window
quadscheme Generate a Quadrature Scheme from a Point Pattern
rescale.owin Convert Window to Another Unit of Length
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
subset.fv Extract Subset of Function Values
quadratcount Quadrat counting for a point pattern
simdat Simulated Point Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
rNeymanScott Simulate Neyman-Scott Process
multiplicity.ppp Count Multiplicity of Duplicate Points
square Square Window
plot.plotppm Plot a plotppm Object Created by plot.ppm
angles.psp Orientation Angles of Line Segments
pcf.ppp Pair Correlation Function of Point Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
nztrees New Zealand Trees Point Pattern
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
ripras Estimate window from points alone
pairwise.family Pairwise Interaction Process Family
rpoint Generate N Random Points
rMaternII Simulate Matern Model II
print.quad Print a Quadrature Scheme
rescale.ppp Convert Point Pattern to Another Unit of Length
plot.psp plot a Spatial Line Segment Pattern
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
residualspaper Data and Code From JRSS Discussion Paper on Residuals
rlabel Random Re-Labelling of Point Pattern
spatstat.options Internal Options in Spatstat Package
progressreport Print Progress Reports
quad.object Class of Quadrature Schemes
pairdist.ppp Pairwise distances
reduced.sample Reduced Sample Estimator using Histogram Data
selfcrossing.psp Crossing Points in a Line Segment Pattern
inside.owin Test Whether Points Are Inside A Window
nncross Nearest Neighbour in Another Point Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
shift Apply Vector Translation
rMatClust Simulate Matern Cluster Process
subset.fasp Extract Subset of Function Array
rotate.psp Rotate a Line Segment Pattern
rpoisline Generate Poisson Random Line Process
nbfires Point Patterns of New Brunswick Forest Fires
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
rSSI Simulate Simple Sequential Inhibition
summary.ppp Summary of a Point Pattern Dataset
summary.psp Summary of a Line Segment Pattern Dataset
subsetget.im Reset Values in Subset of Image
rpoispp Generate Poisson Point Pattern
quantile.im Sample Quantiles of Pixel Image
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
summary.im Summarizing a Pixel Image
summary.owin Summary of a Spatial Window
rshift.psp Randomly Shift a Line Segment Pattern
rotate.owin Rotate a Window
superimpose Superimpose Several Point Patterns
subset.listof Extract or Replace Subset of a List of Things
rotate.ppp Rotate a Point Pattern
subset.im Extract Subset of Image
subset.psp Extract Subset of Line Segment Pattern
swedishpines Swedish Pines Point Pattern
unmark Remove Marks from a Marked Point Pattern
vertices Vertices of a Window
unique.ppp Extract Unique Points from a Spatial Point Pattern
trim.rectangle Cut margins from rectangle
unitname Name for Unit of Length
summary.quad Summarizing a Quadrature Scheme
summary.splitppp Summary of a Split Point Pattern
update.ppm Update a Fitted Point Process Model
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
union.quad Union of Data and Dummy Points
affine.ppp Apply Affine Transformation To Point Pattern
Iest Estimate the I-function
thomas.estK Fit the Thomas Point Process by Minimum Contrast
coef.ppm Coefficients of Fitted Point Process Model
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
envelope Simulation envelopes of summary function
is.ppm Test Whether An Object Is A Fitted Point Process Model
mincontrast Method of Minimum Contrast
pairdist Pairwise distances
plot.hyperframe Plot Entries in a Hyperframe
spatstat-internal Internal spatstat functions
longleaf Longleaf Pines Point Pattern
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
localK Neighbourhood density function
nndist Nearest neighbour distances
print.owin Print Brief Details of a Spatial Window
kaplan.meier Kaplan-Meier Estimator using Histogram Data
rshift.splitppp Randomly Shift a List of Point Patterns
scanpp Read Point Pattern From Data File
ppp Create a Point Pattern
print.psp Print Brief Details of a Line Segment Pattern Dataset
pppmatching.object Class of Point Matchings
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Date 07 January 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Mon Jan 7 18:49:13 2008; adrian

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