spatstat v1.11-6

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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
DiggleGratton Diggle-Gratton model
Kdot Multitype K Function (i-to-any)
as.ppp Convert Data To Class ppp
concatxy Concatenate x,y Coordinate Vectors
crossdist.default Pairwise distances between two different sets of points
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
bdist.points Distance to Boundary of Window
is.im Test Whether An Object Is A Pixel Image
distmap.ppp Distance Map of Point Pattern
intersect.owin Intersection or Union of Two Windows
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
pcf.ppp Pair Correlation Function of Point Pattern
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
plot.fasp Plot a Function Array
plot.splitppp Plot a List of Point Patterns
ppp Create a Point Pattern
Fest Estimate the empty space function F
plot.fv Plot Function Valuesn
Iest Estimate the I-function
append.psp Combine Two Line Segment Patterns
print.quad Print a Quadrature Scheme
print.psp Print Brief Details of a Line Segment Pattern Dataset
data.ppm Extract Original Data from a Fitted Point Process Model
bounding.box.xy Convex Hull of Points
ewcdf Weighted Empirical Cumulative Distribution Function
rStrauss Perfect Simulation of the Strauss Process
rMaternII Simulate Matern Model II
raster.x Cartesian Coordinates for a Pixel Raster
compatible.im Test Whether Two Pixel Images Are Compatible
letterR Window in Shape of Letter R
default.dummy Generate a Default Pattern of Dummy Points
rotate Rotate
setmarks Set or Reset the Marks in a Point Pattern
erode.owin Erode a Window
redwoodfull California Redwoods Point Pattern (Entire Dataset)
unique.ppp Extract Unique Points from a Spatial Point Pattern
residuals.ppm Residuals for Fitted Point Process Model
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
eroded.areas Areas of Morphological Erosions
pairdist.default Pairwise distances
spatstat.options Internal Options in Spatstat Package
plot.psp plot a Spatial Line Segment Pattern
subset.fasp Extract Subset of Function Array
humberside Humberside Data on Childhood Leukaemia and Lymphoma
is.marked Test Whether Marks Are Present
subset.listof Extract or Replace Subset of a List of Things
applynbd Apply Function to Every Neighbourhood in a Point Pattern
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
nncross Nearest Neighbour in Another Point Pattern
density.psp Kernel Smoothing of Line Segment Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
rThomas Simulate Thomas Process
summary.owin Summary of a Spatial Window
distmap.psp Distance Map of Line Segment Pattern
bdist.pixels Distance to Boundary of Window
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
rpoisline Generate Poisson Random Line Process
Kcross.inhom Inhomogeneous Cross K Function
residualspaper Data and Code From JRSS Discussion Paper on Residuals
crossing.psp Crossing Points of Two Line Segment Patterns
plot.owin Plot a Spatial Window
rmh.ppm Simulate from a Fitted Point Process Model
quantile.im Sample Quantiles of Pixel Image
affine.psp Apply Affine Transformation To Line Segment Pattern
rSSI Simulate Simple Sequential Inhibition
density.ppp Kernel Smoothed Intensity of Point Pattern
as.im Convert to Pixel Image
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
rotate.ppp Rotate a Point Pattern
is.ppp Test Whether An Object Is A Point Pattern
subset.ppp Extract or Replace Subset of Point Pattern
owin.object Class owin
crossdist.psp Pairwise distances between two different line segment patterns
Kcross Multitype K Function (Cross-type)
quad.object Class of Quadrature Schemes
copper Berman-Huntington points and lines data
fitin.ppm Extract the Interaction from a Fitted Point Process Model
superimpose Superimpose Several Point Patterns
Saturated Saturated Pairwise Interaction model
angles.psp Orientation Angles of Line Segments
spatstat-internal Internal spatstat functions
is.marked.ppp Test Whether A Point Pattern is Marked
rmpoispp Generate Multitype Poisson Point Pattern
rotate.psp Rotate a Line Segment Pattern
disc Circular Window
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
shift.ppp Apply Vector Translation To Point Pattern
longleaf Longleaf Pines Point Pattern
hamster Aherne's hamster tumour data
mean.im Mean Pixel Value in an Image
gridcentres Rectangular grid of points
hist.im Histogram of Pixel Values in an Image
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
interp.im Interpolate a Pixel Image
spatstat The Spatstat Package
spokes Spokes pattern of dummy points
japanesepines Japanese Pines Point Pattern
Softcore The Soft Core Point Process Model
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
affine Apply Affine Transformation
lurking Lurking variable plot
rsyst Simulate systematic random point pattern
amacrine Hughes' Amacrine Cell Data
subset.im Extract Subset of Image
distmap.owin Distance Map of Window
nztrees New Zealand Trees Point Pattern
as.rectangle Window Frame
chorley Chorley-Ribble Cancer Data
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rpoispp Generate Poisson Point Pattern
cells Biological Cells Point Pattern
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
unmark Remove Marks from a Marked Point Pattern
Jmulti Marked J Function
ganglia Beta Ganglion Cells in Cat Retina, Old Version
inside.owin Test Whether Points Are Inside A Window
print.ppm Print a Fitted Point Process Model
summary.quad Summarizing a Quadrature Scheme
pairdist Pairwise distances
Pairwise Generic Pairwise Interaction model
crossdist.ppp Pairwise distances between two different point patterns
pairsat.family Saturated Pairwise Interaction Point Process Family
demopat Artificial Data Point Pattern
profilepl Profile Maximum Pseudolikelihood
envelope Simulation envelopes of summary function
levelset Level Set of a Pixel Image
pcf.fv Pair Correlation Function obtained from K Function
nbfires Point Patterns of New Brunswick Forest Fires
summary.im Summarizing a Pixel Image
subset.psp Extract Subset of Line Segment Pattern
plot.ppp plot a Spatial Point Pattern
pppdist Optimal Match Between Two Point Patterns
ppm Fit Point Process Model to Data
gridweights Compute Quadrature Weights Based on Grid Counts
multiplicity.ppp Count Multiplicity of Duplicate Points
rescale.owin Convert Window to Another Unit of Length
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
quadscheme Generate a Quadrature Scheme from a Point Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
rotate.owin Rotate a Window
plot.listof Plot a List of Things
psp.object Class of Line Segment Patterns
simdat Simulated Point Pattern
bei Tropical rain forest trees
rNeymanScott Simulate Neyman-Scott Process
suffstat Sufficient Statistic of Point Process Model
shift Apply Vector Translation
union.quad Union of Data and Dummy Points
bramblecanes Hutchings' Bramble Canes data
diameter Diameter of a Window
shift.psp Apply Vector Translation To Line Segment Pattern
Kinhom Inhomogeneous K-function
trim.rectangle Cut margins from rectangle
thomas.estK Fit the Thomas Point Process by Minimum Contrast
summary.splitppp Summary of a Split Point Pattern
ants Harkness-Isham ants' nests data
vertices Vertices of a Window
lansing Lansing Woods Point Pattern
owin Create a Window
as.matrix.im Convert Pixel Image to Matrix
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
Geyer Geyer's Saturation Point Process Model
Kdot.inhom Inhomogeneous Multitype K Dot Function
rescue.rectangle Convert Window Back To Rectangle
endpoints.psp Endpoints of Line Segment Pattern
finpines Pine saplings in Finland.
Poisson Poisson Point Process Model
harmonic Basis for Harmonic Functions
area.owin Area of a Window
as.owin Convert Data To Class owin
fv.object Data Frames of Function Values
coef.ppm Coefficients of Fitted Point Process Model
plot.quad plot a Spatial Quadrature Scheme
quadratcount Quadrat counting for a point pattern
runifpoint Generate N Uniform Random Points
dilate.owin Dilate a Window
compatible.fv Test Whether Two Function Objects Are Compatible
fitted.ppm Fitted Conditional Intensity for Point Process Model
swedishpines Swedish Pines Point Pattern
im.object Class of Images
complement.owin Take Complement of a Window
is.owin Test Whether An Object Is A Window
logLik.ppm Log Likelihood for Poisson Point Process Model
nearest.raster.point Find Pixel Nearest to a Given Point
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
mincontrast Method of Minimum Contrast
markcorr Mark Correlation Function
nndist Nearest neighbour distances
pairwise.family Pairwise Interaction Process Family
plot.ppm plot a Fitted Point Process Model
print.im Print Brief Details of an Image
shift.im Apply Vector Translation To Pixel Image
summary.psp Summary of a Line Segment Pattern Dataset
rlabel Random Re-Labelling of Point Pattern
ripras Estimate window from points alone
scanpp Read Point Pattern From Data File
subset.splitppp Extract or Replace Sub-Patterns
shift.owin Apply Vector Translation To Window
Kest K-function
Jcross Multitype J Function (i-to-j)
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
expand.owin Expand Window By Factor
Kest.fft K-function using FFT
betacells Beta Ganglion Cells in Cat Retina
im Create a Pixel Image Object
kaplan.meier Kaplan-Meier Estimator using Histogram Data
plot.im Plot a Pixel Image
rescale Convert dataset to another unit of length
anova.ppm ANOVA for Fitted Point Process Models
MultiStrauss The Multitype Strauss Point Process Model
clickpoly Interactively Define a Polygon
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
rstrat Simulate Stratified Random Point Pattern
summary.ppp Summary of a Point Pattern Dataset
ord.family Ord Interaction Process Family
summary.ppm Summarizing a Fitted Point Process Model
is.marked.ppm Test Whether A Point Process Model is Marked
psp Create a Line Segment Pattern
rMatClust Simulate Matern Cluster Process
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rthin Random Thinning
rshift.splitppp Randomly Shift a List of Point Patterns
split.ppp Divide Point Pattern into Sub-patterns
square Square Window
units Name for Unit of Length
fasp.object Function Arrays for Spatial Patterns
eval.fv Evaluate Expression Involving Functions
is.multitype Test whether Object is Multitype
is.subset.owin Determine Whether One Window is Contained In Another
pcf Pair Correlation Function
Ord Generic Ord Interaction model
contour.im Contour plot of pixel image
ppm.object Class of Fitted Point Process Models
corners Corners of a rectangle
cut.im Convert Pixel Image from Numeric to Factor
print.owin Print Brief Details of a Spatial Window
rescale.psp Convert Line Segment Pattern to Another Unit of Length
rescale.ppp Convert Point Pattern to Another Unit of Length
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
spatstat-deprecated Deprecated spatstat functions
eval.im Evaluate Expression Involving Pixel Images
lengths.psp Lengths of Line Segments
rshift.ppp Randomly Shift a Point Pattern
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
setcov Set Covariance of a Window
nnwhich Nearest neighbour
plot.plotppm Plot a plotppm Object Created by plot.ppm
predict.ppm Prediction from a Fitted Point Process Model
rMaternI Simulate Matern Model I
rcell Simulate Baddeley-Silverman Cell Process
reach Interaction Distance of a Point Process
redwood California Redwoods Point Pattern (Ripley's Subset)
runifdisc Generate N Uniform Random Points in a Disc
rmpoint Generate N Random Multitype Points
spruces Spruces Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
Gest Nearest Neighbour Distance Function G
Jest Estimate the J-function
Gmulti Marked Nearest Neighbour Distance Function
Strauss The Strauss Point Process Model
affine.owin Apply Affine Transformation To Window
allstats Calculate four standard summary functions of a point pattern.
bounding.box Bounding Box of a Window or Point Pattern
convexhull.xy Convex Hull of Points
centroid.owin Centroid of a window
cut.ppp Convert Point Pattern Marks from Numeric to Factor
as.mask Pixel Image Approximation of a Window
is.multitype.ppm Test Whether A Point Process Model is Multitype
nndist.psp Nearest neighbour distances between line segments
is.multitype.ppp Test Whether A Point Pattern is Multitype
pairdist.ppp Pairwise distances
pairdist.psp Pairwise distances between line segments
pcf.fasp Pair Correlation Function obtained from array of K functions
persp.im Perspective Plot of Pixel Image
print.ppp Print Brief Details of a Point Pattern Dataset
update.ppm Update a Fitted Point Process Model
Jdot Multitype J Function (i-to-any)
anemones Beadlet Anemones Data
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
distmap Distance Map
eem Exponential Energy Marks
is.ppm Test Whether An Object Is A Fitted Point Process Model
midpoints.psp Midpoints of Line Segment Pattern
ppp.object Class of Point Patterns
rpoint Generate N Random Points
subset.fv Extract Subset of Function Values
LennardJones The Lennard-Jones Potential
Kmulti Marked K-Function
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
rshift Random Shift
rshift.psp Randomly Shift a Line Segment Pattern
subsetget.im Reset Values in Subset of Image
OrdThresh Ord's Interaction model
affine.ppp Apply Affine Transformation To Point Pattern
Kmeasure Reduced Second Moment Measure
StraussHard The Strauss / Hard Core Point Process Model
as.psp Convert Data To Class psp
clickppp Interactively Add Points
crossdist Pairwise distances
identify.ppp Identify Points in a Point Pattern
progressreport Print Progress Reports
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
reduced.sample Reduced Sample Estimator using Histogram Data
summary.listof Summary of a List of Things
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Date 18 May 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Fri May 18 20:13:37 2007; adrian

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