spatstat v1.12-6

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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 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
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
Poisson Poisson Point Process Model
as.im Convert to Pixel Image
Gest Nearest Neighbour Distance Function G
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Jest Estimate the J-function
Kdot Multitype K Function (i-to-any)
coef.ppm Coefficients of Fitted Point Process Model
Linhom L-function
Jcross Multitype J Function (i-to-j)
Softcore The Soft Core Point Process Model
fitted.ppm Fitted Conditional Intensity for Point Process Model
spatstat-deprecated Deprecated spatstat functions
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
bdist.pixels Distance to Boundary of Window
as.psp Convert Data To Class psp
Kmeasure Reduced Second Moment Measure
allstats Calculate four standard summary functions of a point pattern.
as.data.frame.ppp Coerce Point Pattern to a Data Frame
plot.hyperframe Plot Entries in a Hyperframe
affine.owin Apply Affine Transformation To Window
crossdist.psp Pairwise distances between two different line segment patterns
density.ppp Kernel Smoothed Intensity of Point Pattern
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
affine.psp Apply Affine Transformation To Line Segment Pattern
rMaternI Simulate Matern Model I
lansing Lansing Woods Point Pattern
append.psp Combine Two Line Segment Patterns
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
Fest Estimate the empty space function F
plot.ppp plot a Spatial Point Pattern
DiggleGratton Diggle-Gratton model
compatible.fv Test Whether Two Function Objects Are Compatible
affine.ppp Apply Affine Transformation To Point Pattern
AreaInter The Area Interaction Point Process Model
bdist.points Distance to Boundary of Window
default.dummy Generate a Default Pattern of Dummy Points
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
Gmulti Marked Nearest Neighbour Distance Function
gridweights Compute Quadrature Weights Based on Grid Counts
Saturated Saturated Pairwise Interaction model
OrdThresh Ord's Interaction model
as.rectangle Window Frame
LennardJones The Lennard-Jones Potential
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
is.marked.ppm Test Whether A Point Process Model is Marked
midpoints.psp Midpoints of Line Segment Pattern
Pairwise Generic Pairwise Interaction model
spatstat The Spatstat Package
japanesepines Japanese Pines Point Pattern
convexhull.xy Convex Hull of Points
copper Berman-Huntington points and lines data
Lest L-function
density.psp Kernel Smoothing of Line Segment Pattern
nndist.psp Nearest neighbour distances between line segments
Iest Estimate the I-function
applynbd Apply Function to Every Neighbourhood in a Point Pattern
bei Tropical rain forest trees
eval.fv Evaluate Expression Involving Functions
ewcdf Weighted Empirical Cumulative Distribution Function
fitin.ppm Extract the Interaction from a Fitted Point Process Model
ants Harkness-Isham ants' nests data
envelope Simulation envelopes of summary function
contour.im Contour plot of pixel image
crossdist Pairwise distances
anemones Beadlet Anemones Data
clarkevans Clark and Evans Aggregation Index
as.matrix.im Convert Pixel Image to Matrix
superimpose Superimpose Several Point Patterns
betacells Beta Ganglion Cells in Cat Retina
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
identify.ppp Identify Points in a Point Pattern
affine Apply Affine Transformation
expand.owin Expand Window By Factor
MultiStrauss The Multitype Strauss Point Process Model
as.ppp Convert Data To Class ppp
cells Biological Cells Point Pattern
hist.im Histogram of Pixel Values in an Image
anova.ppm ANOVA for Fitted Point Process Models
eval.im Evaluate Expression Involving Pixel Images
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
discretise Safely Convert Point Pattern Window to Binary Mask
quadratcount Quadrat counting for a point pattern
eem Exponential Energy Marks
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
complement.owin Take Complement of a Window
corners Corners of a rectangle
crossing.psp Crossing Points of Two Line Segment Patterns
area.owin Area of a Window
Ord Generic Ord Interaction model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
Jdot Multitype J Function (i-to-any)
concatxy Concatenate x,y Coordinate Vectors
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
areadiff Difference of Disc Areas
is.multitype Test whether Object is Multitype
humberside Humberside Data on Childhood Leukaemia and Lymphoma
inside.owin Test Whether Points Are Inside A Window
im.object Class of Images
Kdot.inhom Inhomogeneous Multitype K Dot Function
Kcross Multitype K Function (Cross-type)
profilepl Profile Maximum Pseudolikelihood
im Create a Pixel Image Object
print.im Print Brief Details of an Image
data.ppm Extract Original Data from a Fitted Point Process Model
angles.psp Orientation Angles of Line Segments
StraussHard The Strauss / Hard Core Point Process Model
pairdist.default Pairwise distances
is.im Test Whether An Object Is A Pixel Image
matchingdist Distance for a Point Pattern Matching
fasp.object Function Arrays for Spatial Patterns
levelset Level Set of a Pixel Image
plot.splitppp Plot a List of Point Patterns
print.owin Print Brief Details of a Spatial Window
fv.object Data Frames of Function Values
chorley Chorley-Ribble Cancer Data
quantile.im Sample Quantiles of Pixel Image
ord.family Ord Interaction Process Family
runifdisc Generate N Uniform Random Points in a Disc
redwoodfull California Redwoods Point Pattern (Entire Dataset)
diameter Diameter of a Window
crossdist.default Pairwise distances between two different sets of points
nearest.raster.point Find Pixel Nearest to a Given Point
hyperframe Hyper Data Frame
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
print.ppm Print a Fitted Point Process Model
pairdist.psp Pairwise distances between line segments
gridcentres Rectangular grid of points
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
compatible.im Test Whether Two Pixel Images Are Compatible
inforder.family Infinite Order Interaction Family
pcf.fasp Pair Correlation Function obtained from array of K functions
Kinhom Inhomogeneous K-function
dilate.owin Dilate a Window
disc Circular Window
rmpoispp Generate Multitype Poisson Point Pattern
print.quad Print a Quadrature Scheme
interp.im Interpolate a Pixel Image
rshift.splitppp Randomly Shift a List of Point Patterns
distmap.psp Distance Map of Line Segment Pattern
pcf Pair Correlation Function
plot.fv Plot Function Valuesn
rescale.psp Convert Line Segment Pattern to Another Unit of Length
pppmatching Create a Point Matching
plot.ppm plot a Fitted Point Process Model
rescale Convert dataset to another unit of length
setmarks Set or Reset the Marks in a Point Pattern
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
quad.object Class of Quadrature Schemes
pairdist.ppp Pairwise distances
rlinegrid Generate grid of parallel lines with random displacement
eroded.areas Areas of Morphological Erosions
plot.psp plot a Spatial Line Segment Pattern
nztrees New Zealand Trees Point Pattern
ppm.object Class of Fitted Point Process Models
psp Create a Line Segment Pattern
bounding.box Bounding Box of a Window or Point Pattern
rotate.ppp Rotate a Point Pattern
rshift.ppp Randomly Shift a Point Pattern
logLik.ppm Log Likelihood for Poisson Point Process Model
ppp Create a Point Pattern
as.owin Convert Data To Class owin
rpoint Generate N Random Points
lurking Lurking variable plot
finpines Pine saplings in Finland.
nncross Nearest Neighbour in Another Point Pattern
persp.im Perspective Plot of Pixel Image
bounding.box.xy Convex Hull of Points
multiplicity.ppp Count Multiplicity of Duplicate Points
centroid.owin Centroid of a window
suffstat Sufficient Statistic of Point Process Model
summary.quad Summarizing a Quadrature Scheme
reach Interaction Distance of a Point Process
shift.owin Apply Vector Translation To Window
spatstat-internal Internal spatstat functions
trim.rectangle Cut margins from rectangle
pcf.ppp Pair Correlation Function of Point Pattern
plot.plotppm Plot a plotppm Object Created by plot.ppm
localK Neighbourhood density function
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
subsetget.im Reset Values in Subset of Image
pairwise.family Pairwise Interaction Process Family
is.ppp Test Whether An Object Is A Point Pattern
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
owin Create a Window
plot.owin Plot a Spatial Window
kaplan.meier Kaplan-Meier Estimator using Histogram Data
pairsat.family Saturated Pairwise Interaction Point Process Family
plot.im Plot a Pixel Image
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
rotate.psp Rotate a Line Segment Pattern
erode.owin Erode a Window
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
ripras Estimate window from points alone
nnwhich Nearest neighbour
is.subset.owin Determine Whether One Window is Contained In Another
summary.splitppp Summary of a Split Point Pattern
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
update.ppm Update a Fitted Point Process Model
subset.listof Extract or Replace Subset of a List of Things
subset.ppp Extract or Replace Subset of Point Pattern
rcell Simulate Baddeley-Silverman Cell Process
rlabel Random Re-Labelling of Point Pattern
rGaussPoisson Simulate Gauss-Poisson Process
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
rstrat Simulate Stratified Random Point Pattern
summary.im Summarizing a Pixel Image
rsyst Simulate systematic random point pattern
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
subset.psp Extract Subset of Line Segment Pattern
setcov Set Covariance of a Window
scanpp Read Point Pattern From Data File
vertices Vertices of a Window
plot.quad plot a Spatial Quadrature Scheme
rStrauss Perfect Simulation of the Strauss Process
rthin Random Thinning
rNeymanScott Simulate Neyman-Scott Process
summary.owin Summary of a Spatial Window
nbfires Point Patterns of New Brunswick Forest Fires
mincontrast Method of Minimum Contrast
subset.fv Extract Subset of Function Values
square Square Window
swedishpines Swedish Pines Point Pattern
residualspaper Data and Code From JRSS Discussion Paper on Residuals
pairdist Pairwise distances
unmark Remove Marks from a Marked Point Pattern
shift.im Apply Vector Translation To Pixel Image
plot.listof Plot a List of Things
summary.ppm Summarizing a Fitted Point Process Model
nndist Nearest neighbour distances
rpoispp Generate Poisson Point Pattern
rshift.psp Randomly Shift a Line Segment Pattern
pppdist Distance Between Two Point Patterns
mean.im Mean Pixel Value in an Image
markcorr Mark Correlation Function
summary.ppp Summary of a Point Pattern Dataset
spruces Spruces Point Pattern
letterR Window in Shape of Letter R
rMaternII Simulate Matern Model II
psp.object Class of Line Segment Patterns
redwood California Redwoods Point Pattern (Ripley's Subset)
print.ppp Print Brief Details of a Point Pattern Dataset
ponderosa Ponderosa Pine Tree Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
predict.ppm Prediction from a Fitted Point Process Model
rshift Random Shift
is.owin Test Whether An Object Is A Window
progressreport Print Progress Reports
is.multitype.ppm Test Whether A Point Process Model is Multitype
shift.ppp Apply Vector Translation To Point Pattern
subset.splitppp Extract or Replace Sub-Patterns
rescale.owin Convert Window to Another Unit of Length
rMatClust Simulate Matern Cluster Process
spatstat.options Internal Options in Spatstat Package
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rmpoint Generate N Random Multitype Points
spokes Spokes pattern of dummy points
print.psp Print Brief Details of a Line Segment Pattern Dataset
thomas.estK Fit the Thomas Point Process by Minimum Contrast
residuals.ppm Residuals for Fitted Point Process Model
subset.im Extract Subset of Image
raster.x Cartesian Coordinates for a Pixel Raster
ppm Fit Point Process Model to Data
unique.ppp Extract Unique Points from a Spatial Point Pattern
is.marked Test Whether Marks Are Present
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
reduced.sample Reduced Sample Estimator using Histogram Data
hamster Aherne's hamster tumour data
selfcrossing.psp Crossing Points in a Line Segment Pattern
cut.im Convert Pixel Image from Numeric to Factor
simdat Simulated Point Pattern
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
runifpoint Generate N Uniform Random Points
shift Apply Vector Translation
split.ppp Divide Point Pattern into Sub-patterns
rescue.rectangle Convert Window Back To Rectangle
subset.fasp Extract Subset of Function Array
harmonic Basis for Harmonic Functions
rSSI Simulate Simple Sequential Inhibition
distmap.ppp Distance Map of Point Pattern
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
shift.psp Apply Vector Translation To Line Segment Pattern
intersect.owin Intersection or Union of Two Windows
unitname Name for Unit of Length
clickppp Interactively Add Points
Kest K-function
cut.ppp Convert Point Pattern Marks from Numeric to Factor
ganglia Beta Ganglion Cells in Cat Retina, Old Version
distmap.owin Distance Map of Window
ppp.object Class of Point Patterns
lengths.psp Lengths of Line Segments
smooth.ppp Spatial smoothing of observations at irregular points
pppmatching.object Class of Point Matchings
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
rThomas Simulate Thomas Process
union.quad Union of Data and Dummy Points
rmh.ppm Simulate from a Fitted Point Process Model
Kcross.inhom Inhomogeneous Cross K Function
clickpoly Interactively Define a Polygon
amacrine Hughes' Amacrine Cell Data
Kest.fft K-function using FFT
crossdist.ppp Pairwise distances between two different point patterns
demopat Artificial Data Point Pattern
is.multitype.ppp Test Whether A Point Pattern is Multitype
as.mask Pixel Image Approximation of a Window
is.ppm Test Whether An Object Is A Fitted Point Process Model
owin.object Class owin
pcf.fv Pair Correlation Function obtained from K Function
rescale.ppp Convert Point Pattern to Another Unit of Length
Geyer Geyer's Saturation Point Process Model
Kmulti Marked K-Function
distmap Distance Map
endpoints.psp Endpoints of Line Segment Pattern
bramblecanes Hutchings' Bramble Canes data
Jmulti Marked J Function
is.marked.ppp Test Whether A Point Pattern is Marked
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
plot.fasp Plot a Function Array
longleaf Longleaf Pines Point Pattern
rotate.owin Rotate a Window
rpoisline Generate Poisson Random Line Process
rotate Rotate
quadscheme Generate a Quadrature Scheme from a Point Pattern
summary.listof Summary of a List of Things
Strauss The Strauss Point Process Model
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Date 04 February 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Mon Feb 4 23:20:32 2008; adrian

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