spatstat v1.13-3

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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
rSSI Simulate Simple Sequential Inhibition
owin.object Class owin
print.ppm Print a Fitted Point Process Model
pcf Pair Correlation Function
print.im Print Brief Details of an Image
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
rGaussPoisson Simulate Gauss-Poisson Process
rlinegrid Generate grid of parallel lines with random displacement
rescue.rectangle Convert Window Back To Rectangle
rpoisline Generate Poisson Random Line Process
plot.owin Plot a Spatial Window
pairwise.family Pairwise Interaction Process Family
plot.quad plot a Spatial Quadrature Scheme
rStrauss Perfect Simulation of the Strauss Process
plot.fasp Plot a Function Array
rshift.splitppp Randomly Shift a List of Point Patterns
rcell Simulate Baddeley-Silverman Cell Process
plot.hyperframe Plot Entries in a Hyperframe
pcf.fv Pair Correlation Function obtained from K Function
print.psp Print Brief Details of a Line Segment Pattern Dataset
plot.psp plot a Spatial Line Segment Pattern
rMaternII Simulate Matern Model II
owin Create a Window
print.owin Print Brief Details of a Spatial Window
suffstat Sufficient Statistic of Point Process Model
psp.object Class of Line Segment Patterns
ppm Fit Point Process Model to Data
psp Create a Line Segment Pattern
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
ppm.object Class of Fitted Point Process Models
stieltjes Compute Integral of Function Against Cumulative Distribution
pairdist Pairwise distances
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
ponderosa Ponderosa Pine Tree Point Pattern
persp.im Perspective Plot of Pixel Image
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
rshift Random Shift
rpoint Generate N Random Points
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
plot.ppp plot a Spatial Point Pattern
redwood California Redwoods Point Pattern (Ripley's Subset)
pairdist.psp Pairwise distances between line segments
rmpoint Generate N Random Multitype Points
swedishpines Swedish Pines Point Pattern
runifdisc Generate N Uniform Random Points in a Disc
ppp.object Class of Point Patterns
scanpp Read Point Pattern From Data File
quantile.im Sample Quantiles of Pixel Image
quadscheme Generate a Quadrature Scheme from a Point Pattern
ripras Estimate window from points alone
rescale.ppp Convert Point Pattern to Another Unit of Length
pppmatching.object Class of Point Matchings
pppdist Distance Between Two Point Patterns
summary.ppp Summary of a Point Pattern Dataset
rpoispp Generate Poisson Point Pattern
rThomas Simulate Thomas Process
reduced.sample Reduced Sample Estimator using Histogram Data
pppmatching Create a Point Matching
rshift.ppp Randomly Shift a Point Pattern
plot.fv Plot Function Valuesn
shift.ppp Apply Vector Translation To Point Pattern
quad.object Class of Quadrature Schemes
plot.listof Plot a List of Things
rlabel Random Re-Labelling of Point Pattern
subset.ppp Extract or Replace Subset of Point Pattern
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
plot.ppm plot a Fitted Point Process Model
plot.im Plot a Pixel Image
plot.splitppp Plot a List of Point Patterns
rsyst Simulate systematic random point pattern
summary.im Summarizing a Pixel Image
rMatClust Simulate Matern Cluster Process
residuals.ppm Residuals for Fitted Point Process Model
rNeymanScott Simulate Neyman-Scott Process
rescale Convert dataset to another unit of length
progressreport Print Progress Reports
setmarks Set or Reset the Marks in a Point Pattern
profilepl Profile Maximum Pseudolikelihood
rMaternI Simulate Matern Model I
smooth.ppp Spatial smoothing of observations at irregular points
rescale.psp Convert Line Segment Pattern to Another Unit of Length
simdat Simulated Point Pattern
spatstat.options Internal Options in Spatstat Package
summary.ppm Summarizing a Fitted Point Process Model
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
pairdist.default Pairwise distances
print.ppp Print Brief Details of a Point Pattern Dataset
subset.listof Extract or Replace Subset of a List of Things
plot.plotppm Plot a plotppm Object Created by plot.ppm
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rotate Rotate
vertices Vertices of a Window
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
shift Apply Vector Translation
rmh.ppm Simulate from a Fitted Point Process Model
summary.listof Summary of a List of Things
rotate.ppp Rotate a Point Pattern
summary.splitppp Summary of a Split Point Pattern
rstrat Simulate Stratified Random Point Pattern
rotate.owin Rotate a Window
pairsat.family Saturated Pairwise Interaction Point Process Family
quadratcount Quadrat counting for a point pattern
predict.ppm Prediction from a Fitted Point Process Model
superimpose Superimpose Several Point Patterns
spruces Spruces Point Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
pairdist.ppp Pairwise distances
setcov Set Covariance of a Window
rshift.psp Randomly Shift a Line Segment Pattern
rescale.owin Convert Window to Another Unit of Length
unique.ppp Extract Unique Points from a Spatial Point Pattern
rotate.psp Rotate a Line Segment Pattern
subset.fasp Extract Subset of Function Array
runifpoint Generate N Uniform Random Points
reach Interaction Distance of a Point Process
shift.im Apply Vector Translation To Pixel Image
pcf.ppp Pair Correlation Function of Point Pattern
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
ppp Create a Point Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
subset.im Extract Subset of Image
redwoodfull California Redwoods Point Pattern (Entire Dataset)
unmark Remove Marks from a Marked Point Pattern
raster.x Cartesian Coordinates for a Pixel Raster
selfcrossing.psp Crossing Points in a Line Segment Pattern
shift.owin Apply Vector Translation To Window
subset.fv Extract Subset of Function Values
shift.psp Apply Vector Translation To Line Segment Pattern
summary.quad Summarizing a Quadrature Scheme
pcf.fasp Pair Correlation Function obtained from array of K functions
residualspaper Data and Code From JRSS Discussion Paper on Residuals
rjitter Random Perturbation of a Point Pattern
rmpoispp Generate Multitype Poisson Point Pattern
split.ppp Divide Point Pattern into Sub-patterns
spatstat The Spatstat Package
Jdot Multitype J Function (i-to-any)
Kmulti Marked K-Function
rthin Random Thinning
with.fv Evaluate an Expression in a Function Table
spokes Spokes pattern of dummy points
summary.psp Summary of a Line Segment Pattern Dataset
trim.rectangle Cut margins from rectangle
update.ppm Update a Fitted Point Process Model
subsetget.im Reset Values in Subset of Image
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
Poisson Poisson Point Process Model
summary.owin Summary of a Spatial Window
as.ppp Convert Data To Class ppp
unitname Name for Unit of Length
union.quad Union of Data and Dummy Points
inforder.family Infinite Order Interaction Family
print.quad Print a Quadrature Scheme
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
Kcross.inhom Inhomogeneous Cross K Function
subset.psp Extract Subset of Line Segment Pattern
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
square Square Window
interp.im Interpolate a Pixel Image
subset.splitppp Extract or Replace Sub-Patterns
Softcore The Soft Core Point Process Model
is.subset.owin Determine Whether One Window is Contained In Another
model.matrix.ppm Extract Design Matrix from Point Process Model
betacells Beta Ganglion Cells in Cat Retina
Kinhom Inhomogeneous K-function
blur Apply Gaussian Blur to a Pixel Image
bounding.box.xy Convex Hull of Points
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
applynbd Apply Function to Every Neighbourhood in a Point Pattern
concatxy Concatenate x,y Coordinate Vectors
Kdot.inhom Inhomogeneous Multitype K Dot Function
Fest Estimate the empty space function F
cut.ppp Convert Point Pattern Marks from Numeric to Factor
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Lcross Multitype L-function (cross-type)
Kest K-function
AreaInter The Area Interaction Point Process Model
DiggleGratton Diggle-Gratton model
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
gridcentres Rectangular grid of points
Gest Nearest Neighbour Distance Function G
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
Ldot Multitype L-function (i-to-any)
affine.psp Apply Affine Transformation To Line Segment Pattern
contour.im Contour plot of pixel image
distmap.owin Distance Map of Window
envelope Simulation envelopes of summary function
clickppp Interactively Add Points
hamster Aherne's hamster tumour data
BadGey Hybrid Geyer Point Process Model
Linhom L-function
Pairwise Generic Pairwise Interaction model
area.owin Area of a Window
japanesepines Japanese Pines Point Pattern
anemones Beadlet Anemones Data
localK Neighbourhood density function
Lest L-function
letterR Window in Shape of Letter R
append.psp Combine Two Line Segment Patterns
Kdot Multitype K Function (i-to-any)
as.psp Convert Data To Class psp
kaplan.meier Kaplan-Meier Estimator using Histogram Data
Strauss The Strauss Point Process Model
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
im.object Class of Images
is.multitype.ppp Test Whether A Point Pattern is Multitype
LennardJones The Lennard-Jones Potential
compatible.fasp Test Whether Two Function Arrays Are Compatible
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
compatible.fv Test Whether Two Function Objects Are Compatible
eroded.areas Areas of Morphological Erosions
ganglia Beta Ganglion Cells in Cat Retina, Old Version
finpines Pine saplings in Finland.
density.psp Kernel Smoothing of Line Segment Pattern
allstats Calculate four standard summary functions of a point pattern.
bramblecanes Hutchings' Bramble Canes data
corners Corners of a rectangle
bdist.pixels Distance to Boundary of Window
as.matrix.im Convert Pixel Image to Matrix
as.owin Convert Data To Class owin
mean.im Mean Pixel Value in an Image
endpoints.psp Endpoints of Line Segment Pattern
crossdist.psp Pairwise distances between two different line segment patterns
Gmulti Marked Nearest Neighbour Distance Function
is.ppp Test Whether An Object Is A Point Pattern
distmap Distance Map
is.marked.ppp Test Whether A Point Pattern is Marked
affine.owin Apply Affine Transformation To Window
amacrine Hughes' Amacrine Cell Data
centroid.owin Centroid of a window
Geyer Geyer's Saturation Point Process Model
chorley Chorley-Ribble Cancer Data
Jcross Multitype J Function (i-to-j)
dilate.owin Dilate a Window
data.ppm Extract Original Data from a Fitted Point Process Model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
discretise Safely Convert Point Pattern Window to Binary Mask
complement.owin Take Complement of a Window
Iest Estimate the I-function
fv.object Data Frames of Function Values
nztrees New Zealand Trees Point Pattern
ewcdf Weighted Empirical Cumulative Distribution Function
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
is.im Test Whether An Object Is A Pixel Image
bdist.points Distance to Boundary of Window
humberside Humberside Data on Childhood Leukaemia and Lymphoma
harmonic Basis for Harmonic Functions
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
anova.ppm ANOVA for Fitted Point Process Models
is.marked Test Whether Marks Are Present
Kcross Multitype K Function (Cross-type)
crossdist.ppp Pairwise distances between two different point patterns
lengths.psp Lengths of Line Segments
eval.fv Evaluate Expression Involving Functions
is.marked.ppm Test Whether A Point Process Model is Marked
default.dummy Generate a Default Pattern of Dummy Points
levelset Level Set of a Pixel Image
expand.owin Expand Window By Factor
eem Exponential Energy Marks
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
model.images Compute Images of Constructed Covariates
fitted.ppm Fitted Conditional Intensity for Point Process Model
Kest.fft K-function using FFT
crossdist.default Pairwise distances between two different sets of points
im Create a Pixel Image Object
multiplicity.ppp Count Multiplicity of Duplicate Points
nndist.psp Nearest neighbour distances between line segments
ord.family Ord Interaction Process Family
affine.ppp Apply Affine Transformation To Point Pattern
angles.psp Orientation Angles of Line Segments
Jest Estimate the J-function
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
nbfires Point Patterns of New Brunswick Forest Fires
Jmulti Marked J Function
cells Biological Cells Point Pattern
as.rectangle Window Frame
matchingdist Distance for a Point Pattern Matching
Kmeasure Reduced Second Moment Measure
fasp.object Function Arrays for Spatial Patterns
areadiff Difference of Disc Areas
demopat Artificial Data Point Pattern
nnwhich Nearest neighbour
logLik.ppm Log Likelihood for Poisson Point Process Model
hist.im Histogram of Pixel Values in an Image
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
clarkevans Clark and Evans Aggregation Index
compatible.im Test Whether Two Pixel Images Are Compatible
cut.im Convert Pixel Image from Numeric to Factor
gridweights Compute Quadrature Weights Based on Grid Counts
distmap.psp Distance Map of Line Segment Pattern
as.im Convert to Pixel Image
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
Saturated Saturated Pairwise Interaction model
MultiStrauss The Multitype Strauss Point Process Model
crossing.psp Crossing Points of Two Line Segment Patterns
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
as.mask Pixel Image Approximation of a Window
is.multitype.ppm Test Whether A Point Process Model is Multitype
clickpoly Interactively Define a Polygon
StraussHard The Strauss / Hard Core Point Process Model
distmap.ppp Distance Map of Point Pattern
spatstat-deprecated Deprecated spatstat functions
bei Tropical rain forest trees
convexhull.xy Convex Hull of Points
crossdist Pairwise distances
mincontrast Method of Minimum Contrast
Ord Generic Ord Interaction model
nncross Nearest Neighbour in Another Point Pattern
OrdThresh Ord's Interaction model
is.multitype Test whether Object is Multitype
lurking Lurking variable plot
ants Harkness-Isham ants' nests data
affine Apply Affine Transformation
eval.fasp Evaluate Expression Involving Function Arrays
eval.im Evaluate Expression Involving Pixel Images
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
diameter Diameter of a Window
longleaf Longleaf Pines Point Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
hyperframe Hyper Data Frame
erode.owin Erode a Window
coef.ppm Coefficients of Fitted Point Process Model
intersect.owin Intersection or Union of Two Windows
copper Berman-Huntington points and lines data
as.data.frame.ppp Coerce Point Pattern to a Data Frame
density.ppp Kernel Smoothed Intensity of Point Pattern
bounding.box Bounding Box of a Window or Point Pattern
fitin.ppm Extract the Interaction from a Fitted Point Process Model
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
identify.ppp Identify Points in a Point Pattern
is.ppm Test Whether An Object Is A Fitted Point Process Model
disc Circular Window
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
lansing Lansing Woods Point Pattern
is.owin Test Whether An Object Is A Window
spatstat-internal Internal spatstat functions
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
nndist Nearest neighbour distances
inside.owin Test Whether Points Are Inside A Window
midpoints.psp Midpoints of Line Segment Pattern
markcorr Mark Correlation Function
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Date 24 June 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Mon Jun 23 10:12:23 2008; adrian

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