spatstat v1.13-2

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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
Lest L-function
BadGey Hybrid Geyer Point Process Model
LennardJones The Lennard-Jones Potential
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Jdot Multitype J Function (i-to-any)
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
affine.owin Apply Affine Transformation To Window
Fest Estimate the empty space function F
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
anova.ppm ANOVA for Fitted Point Process Models
centroid.owin Centroid of a window
Kcross Multitype K Function (Cross-type)
DiggleGratton Diggle-Gratton model
Kmulti Marked K-Function
affine.psp Apply Affine Transformation To Line Segment Pattern
chorley Chorley-Ribble Cancer Data
Ldot Multitype L-function (i-to-any)
Jest Estimate the J-function
MultiStrauss The Multitype Strauss Point Process Model
spatstat The Spatstat Package
clickpoly Interactively Define a Polygon
as.psp Convert Data To Class psp
cut.ppp Convert Point Pattern Marks from Numeric to Factor
density.psp Kernel Smoothing of Line Segment Pattern
allstats Calculate four standard summary functions of a point pattern.
crossdist.ppp Pairwise distances between two different point patterns
Kest.fft K-function using FFT
Lcross Multitype L-function (cross-type)
ants Harkness-Isham ants' nests data
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
Strauss The Strauss Point Process Model
Saturated Saturated Pairwise Interaction model
distmap Distance Map
affine.ppp Apply Affine Transformation To Point Pattern
Poisson Poisson Point Process Model
Linhom L-function
plot.hyperframe Plot Entries in a Hyperframe
angles.psp Orientation Angles of Line Segments
as.matrix.im Convert Pixel Image to Matrix
convexhull.xy Convex Hull of Points
Kcross.inhom Inhomogeneous Cross K Function
Ord Generic Ord Interaction model
append.psp Combine Two Line Segment Patterns
bounding.box Bounding Box of a Window or Point Pattern
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
distmap.psp Distance Map of Line Segment Pattern
complement.owin Take Complement of a Window
corners Corners of a rectangle
areadiff Difference of Disc Areas
clickppp Interactively Add Points
Kinhom Inhomogeneous K-function
density.ppp Kernel Smoothed Intensity of Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
affine Apply Affine Transformation
as.mask Pixel Image Approximation of a Window
bdist.points Distance to Boundary of Window
betacells Beta Ganglion Cells in Cat Retina
bramblecanes Hutchings' Bramble Canes data
compatible.fasp Test Whether Two Function Arrays Are Compatible
amacrine Hughes' Amacrine Cell Data
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
applynbd Apply Function to Every Neighbourhood in a Point Pattern
Jcross Multitype J Function (i-to-j)
crossdist Pairwise distances
print.ppm Print a Fitted Point Process Model
nbfires Point Patterns of New Brunswick Forest Fires
Kdot Multitype K Function (i-to-any)
Jmulti Marked J Function
crossdist.psp Pairwise distances between two different line segment patterns
cells Biological Cells Point Pattern
distmap.ppp Distance Map of Point Pattern
fasp.object Function Arrays for Spatial Patterns
identify.ppp Identify Points in a Point Pattern
demopat Artificial Data Point Pattern
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
mean.im Mean Pixel Value in an Image
Kmeasure Reduced Second Moment Measure
erode.owin Erode a Window
compatible.fv Test Whether Two Function Objects Are Compatible
coef.ppm Coefficients of Fitted Point Process Model
AreaInter The Area Interaction Point Process Model
lurking Lurking variable plot
harmonic Basis for Harmonic Functions
endpoints.psp Endpoints of Line Segment Pattern
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
bdist.pixels Distance to Boundary of Window
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
dilate.owin Dilate a Window
spatstat-deprecated Deprecated spatstat functions
contour.im Contour plot of pixel image
disc Circular Window
pcf Pair Correlation Function
eval.fasp Evaluate Expression Involving Function Arrays
psp Create a Line Segment Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
fv.object Data Frames of Function Values
reach Interaction Distance of a Point Process
diameter Diameter of a Window
as.rectangle Window Frame
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
eval.fv Evaluate Expression Involving Functions
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
finpines Pine saplings in Finland.
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
lengths.psp Lengths of Line Segments
plot.fv Plot Function Valuesn
is.owin Test Whether An Object Is A Window
distmap.owin Distance Map of Window
nndist Nearest neighbour distances
psp.object Class of Line Segment Patterns
rmpoint Generate N Random Multitype Points
hyperframe Hyper Data Frame
pairdist.default Pairwise distances
envelope Simulation envelopes of summary function
im.object Class of Images
is.multitype.ppp Test Whether A Point Pattern is Multitype
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
data.ppm Extract Original Data from a Fitted Point Process Model
levelset Level Set of a Pixel Image
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
crossing.psp Crossing Points of Two Line Segment Patterns
copper Berman-Huntington points and lines data
is.subset.owin Determine Whether One Window is Contained In Another
rpoisline Generate Poisson Random Line Process
longleaf Longleaf Pines Point Pattern
pppmatching Create a Point Matching
nnwhich Nearest neighbour
expand.owin Expand Window By Factor
as.im Convert to Pixel Image
eroded.areas Areas of Morphological Erosions
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
bounding.box.xy Convex Hull of Points
is.multitype Test whether Object is Multitype
humberside Humberside Data on Childhood Leukaemia and Lymphoma
anemones Beadlet Anemones Data
nndist.psp Nearest neighbour distances between line segments
cut.im Convert Pixel Image from Numeric to Factor
ord.family Ord Interaction Process Family
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
markcorr Mark Correlation Function
inside.owin Test Whether Points Are Inside A Window
pairdist Pairwise distances
intersect.owin Intersection or Union of Two Windows
pcf.fasp Pair Correlation Function obtained from array of K functions
trim.rectangle Cut margins from rectangle
rescue.rectangle Convert Window Back To Rectangle
pairwise.family Pairwise Interaction Process Family
matchingdist Distance for a Point Pattern Matching
OrdThresh Ord's Interaction model
spatstat.options Internal Options in Spatstat Package
im Create a Pixel Image Object
logLik.ppm Log Likelihood for Poisson Point Process Model
plot.splitppp Plot a List of Point Patterns
discretise Safely Convert Point Pattern Window to Binary Mask
is.marked Test Whether Marks Are Present
plot.ppp plot a Spatial Point Pattern
default.dummy Generate a Default Pattern of Dummy Points
concatxy Concatenate x,y Coordinate Vectors
eval.im Evaluate Expression Involving Pixel Images
hamster Aherne's hamster tumour data
Gest Nearest Neighbour Distance Function G
as.owin Convert Data To Class owin
residualspaper Data and Code From JRSS Discussion Paper on Residuals
gridcentres Rectangular grid of points
subset.fasp Extract Subset of Function Array
pairdist.psp Pairwise distances between line segments
Pairwise Generic Pairwise Interaction model
quad.object Class of Quadrature Schemes
Iest Estimate the I-function
spatstat-internal Internal spatstat functions
pcf.ppp Pair Correlation Function of Point Pattern
StraussHard The Strauss / Hard Core Point Process Model
plot.plotppm Plot a plotppm Object Created by plot.ppm
ewcdf Weighted Empirical Cumulative Distribution Function
plot.quad plot a Spatial Quadrature Scheme
rGaussPoisson Simulate Gauss-Poisson Process
print.quad Print a Quadrature Scheme
gridweights Compute Quadrature Weights Based on Grid Counts
kaplan.meier Kaplan-Meier Estimator using Histogram Data
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
print.ppp Print Brief Details of a Point Pattern Dataset
subset.im Extract Subset of Image
plot.psp plot a Spatial Line Segment Pattern
rcell Simulate Baddeley-Silverman Cell Process
update.ppm Update a Fitted Point Process Model
is.ppm Test Whether An Object Is A Fitted Point Process Model
ponderosa Ponderosa Pine Tree Point Pattern
rSSI Simulate Simple Sequential Inhibition
rotate.psp Rotate a Line Segment Pattern
pppdist Distance Between Two Point Patterns
Geyer Geyer's Saturation Point Process Model
summary.ppm Summarizing a Fitted Point Process Model
rthin Random Thinning
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
pppmatching.object Class of Point Matchings
rpoint Generate N Random Points
selfcrossing.psp Crossing Points in a Line Segment Pattern
profilepl Profile Maximum Pseudolikelihood
subset.ppp Extract or Replace Subset of Point Pattern
mincontrast Method of Minimum Contrast
is.marked.ppm Test Whether A Point Process Model is Marked
is.im Test Whether An Object Is A Pixel Image
pairdist.ppp Pairwise distances
inforder.family Infinite Order Interaction Family
localK Neighbourhood density function
hist.im Histogram of Pixel Values in an Image
model.images Compute Images of Constructed Covariates
setmarks Set or Reset the Marks in a Point Pattern
superimpose Superimpose Several Point Patterns
quantile.im Sample Quantiles of Pixel Image
plot.im Plot a Pixel Image
rstrat Simulate Stratified Random Point Pattern
summary.splitppp Summary of a Split Point Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
runifpoint Generate N Uniform Random Points
Kdot.inhom Inhomogeneous Multitype K Dot Function
owin.object Class owin
rotate.ppp Rotate a Point Pattern
summary.im Summarizing a Pixel Image
ppp.object Class of Point Patterns
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
Softcore The Soft Core Point Process Model
nztrees New Zealand Trees Point Pattern
summary.ppp Summary of a Point Pattern Dataset
redwood California Redwoods Point Pattern (Ripley's Subset)
print.psp Print Brief Details of a Line Segment Pattern Dataset
simdat Simulated Point Pattern
model.matrix.ppm Extract Design Matrix from Point Process Model
area.owin Area of a Window
ripras Estimate window from points alone
shift.psp Apply Vector Translation To Line Segment Pattern
print.im Print Brief Details of an Image
fitin.ppm Extract the Interaction from a Fitted Point Process Model
subset.listof Extract or Replace Subset of a List of Things
plot.owin Plot a Spatial Window
as.data.frame.ppp Coerce Point Pattern to a Data Frame
progressreport Print Progress Reports
print.owin Print Brief Details of a Spatial Window
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
rlabel Random Re-Labelling of Point Pattern
pcf.fv Pair Correlation Function obtained from K Function
split.ppp Divide Point Pattern into Sub-patterns
rshift.splitppp Randomly Shift a List of Point Patterns
quadratcount Quadrat counting for a point pattern
nearest.raster.point Find Pixel Nearest to a Given Point
rescale.owin Convert Window to Another Unit of Length
predict.ppm Prediction from a Fitted Point Process Model
nncross Nearest Neighbour in Another Point Pattern
rlinegrid Generate grid of parallel lines with random displacement
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
bei Tropical rain forest trees
rshift Random Shift
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
rMatClust Simulate Matern Cluster Process
reduced.sample Reduced Sample Estimator using Histogram Data
plot.fasp Plot a Function Array
rThomas Simulate Thomas Process
ppm Fit Point Process Model to Data
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
square Square Window
residuals.ppm Residuals for Fitted Point Process Model
rmh.ppm Simulate from a Fitted Point Process Model
rpoispp Generate Poisson Point Pattern
rmpoispp Generate Multitype Poisson Point Pattern
rotate Rotate
clarkevans Clark and Evans Aggregation Index
quadscheme Generate a Quadrature Scheme from a Point Pattern
rshift.psp Randomly Shift a Line Segment Pattern
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
rMaternII Simulate Matern Model II
crossdist.default Pairwise distances between two different sets of points
subset.psp Extract Subset of Line Segment Pattern
rshift.ppp Randomly Shift a Point Pattern
rotate.owin Rotate a Window
interp.im Interpolate a Pixel Image
union.quad Union of Data and Dummy Points
scanpp Read Point Pattern From Data File
rNeymanScott Simulate Neyman-Scott Process
ppp Create a Point Pattern
rStrauss Perfect Simulation of the Strauss Process
summary.quad Summarizing a Quadrature Scheme
spokes Spokes pattern of dummy points
japanesepines Japanese Pines Point Pattern
vertices Vertices of a Window
lansing Lansing Woods Point Pattern
unmark Remove Marks from a Marked Point Pattern
rsyst Simulate systematic random point pattern
raster.x Cartesian Coordinates for a Pixel Raster
rescale Convert dataset to another unit of length
spruces Spruces Point Pattern
shift.owin Apply Vector Translation To Window
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
unique.ppp Extract Unique Points from a Spatial Point Pattern
with.fv Evaluate an Expression in a Function Table
as.ppp Convert Data To Class ppp
fitted.ppm Fitted Conditional Intensity for Point Process Model
smooth.ppp Spatial smoothing of observations at irregular points
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
ganglia Beta Ganglion Cells in Cat Retina, Old Version
is.ppp Test Whether An Object Is A Point Pattern
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
shift.ppp Apply Vector Translation To Point Pattern
is.marked.ppp Test Whether A Point Pattern is Marked
midpoints.psp Midpoints of Line Segment Pattern
subsetget.im Reset Values in Subset of Image
subset.splitppp Extract or Replace Sub-Patterns
plot.listof Plot a List of Things
owin Create a Window
plot.ppm plot a Fitted Point Process Model
shift.im Apply Vector Translation To Pixel Image
swedishpines Swedish Pines Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
unitname Name for Unit of Length
rMaternI Simulate Matern Model I
letterR Window in Shape of Letter R
ppm.object Class of Fitted Point Process Models
persp.im Perspective Plot of Pixel Image
runifdisc Generate N Uniform Random Points in a Disc
multiplicity.ppp Count Multiplicity of Duplicate Points
rescale.psp Convert Line Segment Pattern to Another Unit of Length
setcov Set Covariance of a Window
stieltjes Compute Integral of Function Against Cumulative Distribution
summary.listof Summary of a List of Things
summary.owin Summary of a Spatial Window
suffstat Sufficient Statistic of Point Process Model
eem Exponential Energy Marks
pairsat.family Saturated Pairwise Interaction Point Process Family
rjitter Random Perturbation of a Point Pattern
rescale.ppp Convert Point Pattern to Another Unit of Length
thomas.estK Fit the Thomas Point Process by Minimum Contrast
shift Apply Vector Translation
subset.fv Extract Subset of Function Values
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
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Date 14 May 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Wed May 14 19:29:29 2008; adrian

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