spatstat v1.15-3


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


Date 13 May 2009
License GPL (>= 2)
Packaged 2009-05-14 05:28:50 UTC; adrian
Repository CRAN
Date/Publication 2009-05-14 06:57:12

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