spatstat v1.12-1

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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
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Geyer Geyer's Saturation Point Process Model
Kinhom Inhomogeneous K-function
Pairwise Generic Pairwise Interaction model
Saturated Saturated Pairwise Interaction model
anova.ppm ANOVA for Fitted Point Process Models
angles.psp Orientation Angles of Line Segments
Kmeasure Reduced Second Moment Measure
OrdThresh Ord's Interaction model
copper Berman-Huntington points and lines data
bei Tropical rain forest trees
applynbd Apply Function to Every Neighbourhood in a Point Pattern
Gest Nearest Neighbour Distance Function G
StraussHard The Strauss / Hard Core Point Process Model
contour.im Contour plot of pixel image
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
crossdist.default Pairwise distances between two different sets of points
append.psp Combine Two Line Segment Patterns
corners Corners of a rectangle
inside.owin Test Whether Points Are Inside A Window
Kmulti Marked K-Function
cut.ppp Convert Point Pattern Marks from Numeric to Factor
is.multitype Test whether Object is Multitype
cells Biological Cells Point Pattern
affine.ppp Apply Affine Transformation To Point Pattern
as.im Convert to Pixel Image
default.dummy Generate a Default Pattern of Dummy Points
as.rectangle Window Frame
dilate.owin Dilate a Window
ants Harkness-Isham ants' nests data
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
clarkevans Clark and Evans Aggregation Index
MultiStrauss The Multitype Strauss Point Process Model
envelope Simulation envelopes of summary function
is.owin Test Whether An Object Is A Window
pairdist.ppp Pairwise distances
is.ppp Test Whether An Object Is A Point Pattern
discretise Safely Convert Point Pattern Window to Binary Mask
eval.fv Evaluate Expression Involving Functions
bdist.pixels Distance to Boundary of Window
pppdist Optimal Match Between Two Point Patterns
markcorr Mark Correlation Function
crossdist Pairwise distances
Jdot Multitype J Function (i-to-any)
expand.owin Expand Window By Factor
endpoints.psp Endpoints of Line Segment Pattern
cut.im Convert Pixel Image from Numeric to Factor
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
fitin.ppm Extract the Interaction from a Fitted Point Process Model
data.ppm Extract Original Data from a Fitted Point Process Model
ewcdf Weighted Empirical Cumulative Distribution Function
Poisson Poisson Point Process Model
LennardJones The Lennard-Jones Potential
im Create a Pixel Image Object
DiggleGratton Diggle-Gratton model
midpoints.psp Midpoints of Line Segment Pattern
disc Circular Window
bramblecanes Hutchings' Bramble Canes data
owin.object Class owin
nndist.psp Nearest neighbour distances between line segments
Jest Estimate the J-function
is.marked.ppm Test Whether A Point Process Model is Marked
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
rlabel Random Re-Labelling of Point Pattern
localK Neighbourhood density function
print.ppp Print Brief Details of a Point Pattern Dataset
plot.psp plot a Spatial Line Segment Pattern
plot.hyperframe Plot Entries in a Hyperframe
eval.im Evaluate Expression Involving Pixel Images
rStrauss Perfect Simulation of the Strauss Process
coef.ppm Coefficients of Fitted Point Process Model
vertices Vertices of a Window
humberside Humberside Data on Childhood Leukaemia and Lymphoma
bounding.box.xy Convex Hull of Points
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Strauss The Strauss Point Process Model
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
hist.im Histogram of Pixel Values in an Image
plot.fasp Plot a Function Array
nnwhich Nearest neighbour
distmap.ppp Distance Map of Point Pattern
as.data.frame.ppp Coerce Point Pattern to a Data Frame
distmap Distance Map
bdist.points Distance to Boundary of Window
rMaternII Simulate Matern Model II
rshift Random Shift
print.psp Print Brief Details of a Line Segment Pattern Dataset
lurking Lurking variable plot
erode.owin Erode a Window
pairdist.default Pairwise distances
Jcross Multitype J Function (i-to-j)
Softcore The Soft Core Point Process Model
spatstat-internal Internal spatstat functions
crossing.psp Crossing Points of Two Line Segment Patterns
affine Apply Affine Transformation
print.im Print Brief Details of an Image
Iest Estimate the I-function
print.ppm Print a Fitted Point Process Model
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
nearest.raster.point Find Pixel Nearest to a Given Point
print.owin Print Brief Details of a Spatial Window
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
allstats Calculate four standard summary functions of a point pattern.
pcf.fasp Pair Correlation Function obtained from array of K functions
pcf.fv Pair Correlation Function obtained from K Function
interp.im Interpolate a Pixel Image
Jmulti Marked J Function
is.im Test Whether An Object Is A Pixel Image
Kdot.inhom Inhomogeneous Multitype K Dot Function
betacells Beta Ganglion Cells in Cat Retina
rmpoispp Generate Multitype Poisson Point Pattern
rshift.splitppp Randomly Shift a List of Point Patterns
pcf.ppp Pair Correlation Function of Point Pattern
Ord Generic Ord Interaction model
quadscheme Generate a Quadrature Scheme from a Point Pattern
multiplicity.ppp Count Multiplicity of Duplicate Points
psp.object Class of Line Segment Patterns
rotate.psp Rotate a Line Segment Pattern
amacrine Hughes' Amacrine Cell Data
ppp Create a Point Pattern
Fest Estimate the empty space function F
shift.ppp Apply Vector Translation To Point Pattern
rpoint Generate N Random Points
is.multitype.ppm Test Whether A Point Process Model is Multitype
levelset Level Set of a Pixel Image
rshift.ppp Randomly Shift a Point Pattern
affine.owin Apply Affine Transformation To Window
rMaternI Simulate Matern Model I
reduced.sample Reduced Sample Estimator using Histogram Data
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
chorley Chorley-Ribble Cancer Data
psp Create a Line Segment Pattern
setcov Set Covariance of a Window
complement.owin Take Complement of a Window
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
distmap.psp Distance Map of Line Segment Pattern
as.mask Pixel Image Approximation of a Window
scanpp Read Point Pattern From Data File
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
rescale.psp Convert Line Segment Pattern to Another Unit of Length
quantile.im Sample Quantiles of Pixel Image
as.psp Convert Data To Class psp
Kcross.inhom Inhomogeneous Cross K Function
as.ppp Convert Data To Class ppp
square Square Window
affine.psp Apply Affine Transformation To Line Segment Pattern
subset.listof Extract or Replace Subset of a List of Things
eem Exponential Energy Marks
area.owin Area of a Window
as.matrix.im Convert Pixel Image to Matrix
crossdist.psp Pairwise distances between two different line segment patterns
bounding.box Bounding Box of a Window or Point Pattern
anemones Beadlet Anemones Data
rsyst Simulate systematic random point pattern
density.psp Kernel Smoothing of Line Segment Pattern
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
ganglia Beta Ganglion Cells in Cat Retina, Old Version
summary.owin Summary of a Spatial Window
crossdist.ppp Pairwise distances between two different point patterns
finpines Pine saplings in Finland.
simdat Simulated Point Pattern
eroded.areas Areas of Morphological Erosions
subset.splitppp Extract or Replace Sub-Patterns
identify.ppp Identify Points in a Point Pattern
im.object Class of Images
summary.im Summarizing a Pixel Image
subset.im Extract Subset of Image
logLik.ppm Log Likelihood for Poisson Point Process Model
subsetget.im Reset Values in Subset of Image
rescale.owin Convert Window to Another Unit of Length
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
rpoispp Generate Poisson Point Pattern
owin Create a Window
compatible.fv Test Whether Two Function Objects Are Compatible
swedishpines Swedish Pines Point Pattern
is.marked.ppp Test Whether A Point Pattern is Marked
rmpoint Generate N Random Multitype Points
ord.family Ord Interaction Process Family
summary.psp Summary of a Line Segment Pattern Dataset
is.ppm Test Whether An Object Is A Fitted Point Process Model
runifdisc Generate N Uniform Random Points in a Disc
plot.plotppm Plot a plotppm Object Created by plot.ppm
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
lansing Lansing Woods Point Pattern
spatstat-deprecated Deprecated spatstat functions
nncross Nearest Neighbour in Another Point Pattern
rescale Convert dataset to another unit of length
clickppp Interactively Add Points
plot.ppm plot a Fitted Point Process Model
demopat Artificial Data Point Pattern
Kdot Multitype K Function (i-to-any)
compatible.im Test Whether Two Pixel Images Are Compatible
Kcross Multitype K Function (Cross-type)
convexhull.xy Convex Hull of Points
diameter Diameter of a Window
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
selfcrossing.psp Crossing Points in a Line Segment Pattern
split.ppp Divide Point Pattern into Sub-patterns
Kest K-function
hyperframe Hyper Data Frame
pairsat.family Saturated Pairwise Interaction Point Process Family
ppm Fit Point Process Model to Data
Lest L-function
smooth.ppp Spatial smoothing of observations at irregular points
plot.ppp plot a Spatial Point Pattern
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
pairdist Pairwise distances
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
as.owin Convert Data To Class owin
distmap.owin Distance Map of Window
mean.im Mean Pixel Value in an Image
intersect.owin Intersection or Union of Two Windows
hamster Aherne's hamster tumour data
nbfires Point Patterns of New Brunswick Forest Fires
plot.im Plot a Pixel Image
ppp.object Class of Point Patterns
is.multitype.ppp Test Whether A Point Pattern is Multitype
rotate.ppp Rotate a Point Pattern
fv.object Data Frames of Function Values
gridcentres Rectangular grid of points
plot.splitppp Plot a List of Point Patterns
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
harmonic Basis for Harmonic Functions
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
progressreport Print Progress Reports
pcf Pair Correlation Function
fasp.object Function Arrays for Spatial Patterns
redwood California Redwoods Point Pattern (Ripley's Subset)
spruces Spruces Point Pattern
is.marked Test Whether Marks Are Present
is.subset.owin Determine Whether One Window is Contained In Another
persp.im Perspective Plot of Pixel Image
profilepl Profile Maximum Pseudolikelihood
plot.fv Plot Function Valuesn
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
nztrees New Zealand Trees Point Pattern
unmark Remove Marks from a Marked Point Pattern
rThomas Simulate Thomas Process
ripras Estimate window from points alone
rcell Simulate Baddeley-Silverman Cell Process
ppm.object Class of Fitted Point Process Models
mincontrast Method of Minimum Contrast
quadratcount Quadrat counting for a point pattern
pairdist.psp Pairwise distances between line segments
density.ppp Kernel Smoothed Intensity of Point Pattern
pairwise.family Pairwise Interaction Process Family
update.ppm Update a Fitted Point Process Model
reach Interaction Distance of a Point Process
lengths.psp Lengths of Line Segments
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
rNeymanScott Simulate Neyman-Scott Process
plot.listof Plot a List of Things
rshift.psp Randomly Shift a Line Segment Pattern
summary.ppp Summary of a Point Pattern Dataset
setmarks Set or Reset the Marks in a Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
kaplan.meier Kaplan-Meier Estimator using Histogram Data
summary.listof Summary of a List of Things
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
summary.ppm Summarizing a Fitted Point Process Model
thomas.estK Fit the Thomas Point Process by Minimum Contrast
unique.ppp Extract Unique Points from a Spatial Point Pattern
shift.owin Apply Vector Translation To Window
clickpoly Interactively Define a Polygon
predict.ppm Prediction from a Fitted Point Process Model
summary.splitppp Summary of a Split Point Pattern
letterR Window in Shape of Letter R
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
rMatClust Simulate Matern Cluster Process
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
raster.x Cartesian Coordinates for a Pixel Raster
nndist Nearest neighbour distances
centroid.owin Centroid of a window
rmh.ppm Simulate from a Fitted Point Process Model
gridweights Compute Quadrature Weights Based on Grid Counts
plot.quad plot a Spatial Quadrature Scheme
spatstat The Spatstat Package
residuals.ppm Residuals for Fitted Point Process Model
Kest.fft K-function using FFT
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
shift.im Apply Vector Translation To Pixel Image
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
rotate Rotate
concatxy Concatenate x,y Coordinate Vectors
rotate.owin Rotate a Window
units Name for Unit of Length
longleaf Longleaf Pines Point Pattern
rstrat Simulate Stratified Random Point Pattern
fitted.ppm Fitted Conditional Intensity for Point Process Model
plot.owin Plot a Spatial Window
redwoodfull California Redwoods Point Pattern (Entire Dataset)
rescue.rectangle Convert Window Back To Rectangle
spokes Spokes pattern of dummy points
ponderosa Ponderosa Pine Tree Point Pattern
print.quad Print a Quadrature Scheme
rescale.ppp Convert Point Pattern to Another Unit of Length
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
japanesepines Japanese Pines Point Pattern
quad.object Class of Quadrature Schemes
subset.ppp Extract or Replace Subset of Point Pattern
residualspaper Data and Code From JRSS Discussion Paper on Residuals
rlinegrid Generate grid of parallel lines with random displacement
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
rpoisline Generate Poisson Random Line Process
summary.quad Summarizing a Quadrature Scheme
runifpoint Generate N Uniform Random Points
superimpose Superimpose Several Point Patterns
shift.psp Apply Vector Translation To Line Segment Pattern
rthin Random Thinning
subset.psp Extract Subset of Line Segment Pattern
rSSI Simulate Simple Sequential Inhibition
suffstat Sufficient Statistic of Point Process Model
union.quad Union of Data and Dummy Points
shift Apply Vector Translation
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
subset.fasp Extract Subset of Function Array
spatstat.options Internal Options in Spatstat Package
subset.fv Extract Subset of Function Values
trim.rectangle Cut margins from rectangle
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Date 22 September 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Fri Sep 28 23:26:30 2007; adrian

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