spatstat v1.14-8

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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
Jdot Multitype J Function (i-to-any)
as.ppp Convert Data To Class ppp
chorley Chorley-Ribble Cancer Data
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
fv.object Data Frames of Function Values
pairdist.default Pairwise distances
print.psp Print Brief Details of a Line Segment Pattern Dataset
summary.quad Summarizing a Quadrature Scheme
Fest Estimate the empty space function F
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
expand.owin Expand Window By Factor
eval.im Evaluate Expression Involving Pixel Images
Pairwise Generic Pairwise Interaction model
Kest.fft K-function using FFT
incircle Find Largest Circle Inside Window
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
OrdThresh Ord's Interaction model
interp.im Interpolate a Pixel Image
mincontrast Method of Minimum Contrast
clickppp Interactively Add Points
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
crossdist Pairwise distances
pcfcross Multitype pair correlation function
dilate.owin Dilate a Window
applynbd Apply Function to Every Neighbourhood in a Point Pattern
Kcross Multitype K Function (Cross-type)
Saturated Saturated Pairwise Interaction model
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
affine.owin Apply Affine Transformation To Window
density.ppp Kernel Smoothed Intensity of Point Pattern
as.mask Pixel Image Approximation of a Window
distmap.ppp Distance Map of Point Pattern
quad.object Class of Quadrature Schemes
bramblecanes Hutchings' Bramble Canes data
complement.owin Take Complement of a Window
eroded.areas Areas of Morphological Erosions
anemones Beadlet Anemones Data
as.tess Convert Data To Tessellation
amacrine Hughes' Amacrine Cell Data
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
compatible.fv Test Whether Two Function Objects Are Compatible
fryplot Fry Plot of Point Pattern
rescue.rectangle Convert Window Back To Rectangle
Jmulti Marked J Function
fasp.object Function Arrays for Spatial Patterns
as.rectangle Window Frame
cut.im Convert Pixel Image from Numeric to Factor
Kdot Multitype K Function (i-to-any)
gridcentres Rectangular grid of points
im.object Class of Images
finpines Pine saplings in Finland.
dirichlet Dirichlet Tessellation of Point Pattern
pcf.fasp Pair Correlation Function obtained from array of K functions
crossdist.default Pairwise distances between two different sets of points
envelope Simulation envelopes of summary function
eval.fv Evaluate Expression Involving Functions
is.multitype.ppp Test Whether A Point Pattern is Multitype
disc Circular Window
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
intersect.tess Intersection of Two Tessellations
crossdist.psp Pairwise distances between two different line segment patterns
spatstat The Spatstat Package
lurking Lurking variable plot
logLik.ppm Log Likelihood for Poisson Point Process Model
cut.ppp Classify Points in a Point Pattern
demopat Artificial Data Point Pattern
coef.ppm Coefficients of Fitted Point Process Model
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
print.ppm Print a Fitted Point Process Model
plot.plotppm Plot a plotppm Object Created by plot.ppm
ewcdf Weighted Empirical Cumulative Distribution Function
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
default.dummy Generate a Default Pattern of Dummy Points
intersect.owin Intersection or Union of Two Windows
matchingdist Distance for a Point Pattern Matching
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
nndist Nearest neighbour distances
murchison Murchison gold deposits
print.owin Print Brief Details of a Spatial Window
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
area.owin Area of a Window
hyperframe Hyper Data Frame
Jest Estimate the J-function
rotate.owin Rotate a Window
as.psp Convert Data To Class psp
kppm Fit cluster point process model
plot.fasp Plot a Function Array
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
pcf.fv Pair Correlation Function obtained from K Function
markcorr Mark Correlation Function
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
nearestsegment Find Line Segment Nearest to Each Point
centroid.owin Centroid of a window
Geyer Geyer's Saturation Point Process Model
DiggleGratton Diggle-Gratton model
pairwise.family Pairwise Interaction Process Family
contour.im Contour plot of pixel image
Gest Nearest Neighbour Distance Function G
fitin.ppm Extract the Interaction from a Fitted Point Process Model
Kmeasure Reduced Second Moment Measure
nearest.raster.point Find Pixel Nearest to a Given Point
plot.tess Plot a tessellation
clickpoly Interactively Define a Polygon
opening.owin Morphological Opening of a Window
fitted.ppm Fitted Conditional Intensity for Point Process Model
diameter Diameter of a Window
inforder.family Infinite Order Interaction Family
rmh.ppm Simulate from a Fitted Point Process Model
quadratcount Quadrat counting for a point pattern
Kest K-function
pairsat.family Saturated Pairwise Interaction Point Process Family
affine Apply Affine Transformation
Kmulti Marked K-Function
reach Interaction Distance of a Point Process
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
multiplicity.ppp Count Multiplicity of Duplicate Points
gpc2owin Convert Polygonal Region into Different Format
quadratresample Resample a Point Pattern by Resampling Quadrats
delaunay Delaunay Triangulation of Point Pattern
ants Harkness-Isham ants' nests data
is.ppp Test Whether An Object Is A Point Pattern
pppmatching Create a Point Matching
is.marked.ppp Test Whether A Point Pattern is Marked
summary.im Summarizing a Pixel Image
letterR Window in Shape of Letter R
is.ppm Test Whether An Object Is A Fitted Point Process Model
closing.owin Morphological Closing of a Window
pairdist.psp Pairwise distances between line segments
pppdist Distance Between Two Point Patterns
clarkevans Clark and Evans Aggregation Index
distmap Distance Map
gridweights Compute Quadrature Weights Based on Grid Counts
shift Apply Vector Translation
scanpp Read Point Pattern From Data File
rescale.ppp Convert Point Pattern to Another Unit of Length
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
rMaternI Simulate Matern Model I
plot.splitppp Plot a List of Point Patterns
AreaInter The Area Interaction Point Process Model
mean.im Mean, Median and Range of Pixel Values in an Image
density.psp Kernel Smoothing of Line Segment Pattern
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
rMaternII Simulate Matern Model II
im Create a Pixel Image Object
pixelquad Quadrature Scheme Based on Pixel Grid
japanesepines Japanese Pines Point Pattern
residuals.ppm Residuals for Fitted Point Process Model
psp Create a Line Segment Pattern
hamster Aherne's hamster tumour data
Lest L-function
midpoints.psp Midpoints of Line Segment Pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
nndist.psp Nearest neighbour distances between line segments
model.images Compute Images of Constructed Covariates
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
nnwhich Nearest neighbour
Kdot.inhom Inhomogeneous Multitype K Dot Function
profilepl Profile Maximum Pseudolikelihood
rjitter Random Perturbation of a Point Pattern
rshift.psp Randomly Shift a Line Segment Pattern
levelset Level Set of a Pixel Image
miplot Morishita Index Plot
MultiStrauss The Multitype Strauss Point Process Model
rotate Rotate
as.data.frame.ppp Coerce Point Pattern to a Data Frame
lansing Lansing Woods Point Pattern
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
affine.psp Apply Affine Transformation To Line Segment Pattern
pcf Pair Correlation Function
blur Apply Gaussian Blur to a Pixel Image
plot.quad plot a Spatial Quadrature Scheme
LennardJones The Lennard-Jones Potential
setcov Set Covariance of a Window
convexhull.xy Convex Hull of Points
plot.hyperframe Plot Entries in a Hyperframe
ganglia Beta Ganglion Cells in Cat Retina, Old Version
as.matrix.im Convert Pixel Image to Matrix
Ord Generic Ord Interaction model
affine.ppp Apply Affine Transformation To Point Pattern
rStrauss Perfect Simulation of the Strauss Process
bdist.points Distance to Boundary of Window
psp.object Class of Line Segment Patterns
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
rcell Simulate Baddeley-Silverman Cell Process
rescale Convert dataset to another unit of length
data.ppm Extract Original Data from a Fitted Point Process Model
quadrats Divide Region into Quadrats
discretise Safely Convert Point Pattern Window to Binary Mask
rlinegrid Generate grid of parallel lines with random displacement
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
subsetget.im Reset Values in Subset of Image
endpoints.psp Endpoints of Line Segment Pattern
rmpoispp Generate Multitype Poisson Point Pattern
model.matrix.ppm Extract Design Matrix from Point Process Model
localK Neighbourhood density function
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
Poisson Poisson Point Process Model
owin Create a Window
rstrat Simulate Stratified Random Point Pattern
bei Tropical rain forest trees
bounding.box Bounding Box of a Window or Point Pattern
persp.im Perspective Plot of Pixel Image
ppm.object Class of Fitted Point Process Models
plot.fv Plot Function Valuesn
distmap.owin Distance Map of Window
by.im Apply Function to Image Broken Down by Factor
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
pairdist Pairwise distances
print.im Print Brief Details of an Image
eem Exponential Energy Marks
ord.family Ord Interaction Process Family
Gmulti Marked Nearest Neighbour Distance Function
subset.psp Extract Subset of Line Segment Pattern
allstats Calculate four standard summary functions of a point pattern.
eval.fasp Evaluate Expression Involving Function Arrays
lengths.psp Lengths of Line Segments
quadscheme Generate a Quadrature Scheme from a Point Pattern
print.quad Print a Quadrature Scheme
hist.im Histogram of Pixel Values in an Image
bdist.pixels Distance to Boundary of Window
angles.psp Orientation Angles of Line Segments
shift.ppp Apply Vector Translation To Point Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rlabel Random Re-Labelling of Point Pattern
progressreport Print Progress Reports
is.owin Test Whether An Object Is A Window
is.multitype Test whether Object is Multitype
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
bounding.box.xy Convex Hull of Points
plot.psp plot a Spatial Line Segment Pattern
ppm Fit Point Process Model to Data
longleaf Longleaf Pines Point Pattern
pcf.ppp Pair Correlation Function of Point Pattern
is.marked Test Whether Marks Are Present
spatstat-deprecated Deprecated spatstat functions
nncross Nearest Neighbour in Another Point Pattern
inside.owin Test Whether Points Are Inside A Window
identify.ppp Identify Points in a Point Pattern
rGaussPoisson Simulate Gauss-Poisson Process
residualspaper Data and Code From JRSS Discussion Paper on Residuals
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
BadGey Hybrid Geyer Point Process Model
rMatClust Simulate Matern Cluster Process
redwoodfull California Redwoods Point Pattern (Entire Dataset)
Strauss The Strauss Point Process Model
Softcore The Soft Core Point Process Model
plot.ppm plot a Fitted Point Process Model
compatible.im Test Whether Two Pixel Images Are Compatible
selfcrossing.psp Crossing Points in a Line Segment Pattern
simulate.kppm Simulate a fitted cluster point process model.
rshift Random Shift
shift.owin Apply Vector Translation To Window
Jcross Multitype J Function (i-to-j)
rSSI Simulate Simple Sequential Inhibition
rThomas Simulate Thomas Process
Kinhom Inhomogeneous K-function
cells Biological Cells Point Pattern
stieltjes Compute Integral of Function Against Cumulative Distribution
rsyst Simulate systematic random point pattern
spruces Spruces Point Pattern
spokes Spokes pattern of dummy points
trim.rectangle Cut margins from rectangle
tiles Extract List of Tiles in a Tessellation
shift.psp Apply Vector Translation To Line Segment Pattern
runifpoint Generate N Uniform Random Points
StraussHard The Strauss / Hard Core Point Process Model
rNeymanScott Simulate Neyman-Scott Process
summary.ppm Summarizing a Fitted Point Process Model
compatible.fasp Test Whether Two Function Arrays Are Compatible
simdat Simulated Point Pattern
square Square Window
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
crossdist.ppp Pairwise distances between two different point patterns
update.ppm Update a Fitted Point Process Model
Ldot Multitype L-function (i-to-any)
summary.psp Summary of a Line Segment Pattern Dataset
spatstat-internal Internal spatstat functions
Linhom L-function
ppp Create a Point Pattern
plot.kppm Plot a fitted cluster point process
ripras Estimate window from points alone
plot.owin Plot a Spatial Window
shift.im Apply Vector Translation To Pixel Image
append.psp Combine Two Line Segment Patterns
plot.im Plot a Pixel Image
thomas.estK Fit the Thomas Point Process by Minimum Contrast
as.owin Convert Data To Class owin
betacells Beta Ganglion Cells in Cat Retina
summary.listof Summary of a List of Things
rmpoint Generate N Random Multitype Points
setmarks Set or Reset the Marks in a Point Pattern
copper Berman-Huntington points and lines data
[.tess Extract or Replace Subset of Tessellation
concatxy Concatenate x,y Coordinate Vectors
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
superimpose Superimpose Several Point Patterns
subset.splitppp Extract or Replace Sub-Patterns
pairdist.ppp Pairwise distances
plot.ppp plot a Spatial Point Pattern
unitname Name for Unit of Length
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
subset.im Extract Subset of Image
split.ppp Divide Point Pattern into Sub-patterns
is.multitype.ppm Test Whether A Point Process Model is Multitype
quantile.im Sample Quantiles of Pixel Image
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
subset.fv Extract Subset of Function Values
humberside Humberside Data on Childhood Leukaemia and Lymphoma
rescale.owin Convert Window to Another Unit of Length
print.ppp Print Brief Details of a Point Pattern Dataset
rpoint Generate N Random Points
raster.x Cartesian Coordinates for a Pixel Raster
is.marked.ppm Test Whether A Point Process Model is Marked
project2segment Move Point To Nearest Line
areadiff Difference of Disc Areas
kaplan.meier Kaplan-Meier Estimator using Histogram Data
rthin Random Thinning
rescale.im Convert Pixel Image to Another Unit of Length
union.quad Union of Data and Dummy Points
crossing.psp Crossing Points of Two Line Segment Patterns
rshift.splitppp Randomly Shift a List of Point Patterns
predict.ppm Prediction from a Fitted Point Process Model
erode.owin Erode a Window
ponderosa Ponderosa Pine Tree Point Pattern
nztrees New Zealand Trees Point Pattern
is.subset.owin Determine Whether One Window is Contained In Another
pppmatching.object Class of Point Matchings
ppp.object Class of Point Patterns
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
urkiola Urkiola Woods Point Pattern
pixellate Convert Point Pattern to Pixel Image
predict.kppm Prediction from a Fitted Cluster Point Process Model
with.fv Evaluate an Expression in a Function Table
rpoispp Generate Poisson Point Pattern
runifdisc Generate N Uniform Random Points in a Disc
Kcross.inhom Inhomogeneous Cross K Function
summary.ppp Summary of a Point Pattern Dataset
distmap.psp Distance Map of Line Segment Pattern
rotate.psp Rotate a Line Segment Pattern
subset.ppp Extract or Replace Subset of Point Pattern
plot.listof Plot a List of Things
summary.owin Summary of a Spatial Window
update.kppm Update a Fitted Cluster Point Process Model
Lcross Multitype L-function (cross-type)
harmonic Basis for Harmonic Functions
[.quad Subset of Quadrature Scheme
nbfires Point Patterns of New Brunswick Forest Fires
split.im Divide Image Into Sub-images
subset.fasp Extract Subset of Function Array
summary.splitppp Summary of a Split Point Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
rescale.psp Convert Line Segment Pattern to Another Unit of Length
Iest Estimate the I-function
subset.listof Extract or Replace Subset of a List of Things
rshift.ppp Randomly Shift a Point Pattern
is.im Test Whether An Object Is A Pixel Image
owin.object Class owin
rotate.ppp Rotate a Point Pattern
suffstat Sufficient Statistic of Point Process Model
rpoisline Generate Poisson Random Line Process
unmark Remove Marks
reduced.sample Reduced Sample Estimator using Histogram Data
smooth.ppp Spatial smoothing of observations at irregular points
tess Create a Tessellation
unique.ppp Extract Unique Points from a Spatial Point Pattern
swedishpines Swedish Pines Point Pattern
anova.ppm ANOVA for Fitted Point Process Models
superimposePSP Superimpose Several Line Segment Patterns
corners Corners of a rectangle
redwood California Redwoods Point Pattern (Ripley's Subset)
as.im Convert to Pixel Image
vertices Vertices of a Window
spatstat.options Internal Options in Spatstat Package
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Date 10 December 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Thu Dec 11 05:09:36 2008; adrian

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