spatstat v1.13-4

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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
Softcore The Soft Core Point Process Model
as.matrix.im Convert Pixel Image to Matrix
chorley Chorley-Ribble Cancer Data
Jmulti Marked J Function
Lest L-function
Kcross.inhom Inhomogeneous Cross K Function
Kdot Multitype K Function (i-to-any)
bdist.pixels Distance to Boundary of Window
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
cut.ppp Convert Point Pattern Marks from Numeric to Factor
as.data.frame.ppp Coerce Point Pattern to a Data Frame
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
allstats Calculate four standard summary functions of a point pattern.
humberside Humberside Data on Childhood Leukaemia and Lymphoma
cells Biological Cells Point Pattern
demopat Artificial Data Point Pattern
compatible.fasp Test Whether Two Function Arrays Are Compatible
bramblecanes Hutchings' Bramble Canes data
dilate.owin Dilate a Window
Gest Nearest Neighbour Distance Function G
Kcross Multitype K Function (Cross-type)
Gmulti Marked Nearest Neighbour Distance Function
is.marked Test Whether Marks Are Present
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
append.psp Combine Two Line Segment Patterns
hamster Aherne's hamster tumour data
eem Exponential Energy Marks
eval.im Evaluate Expression Involving Pixel Images
lengths.psp Lengths of Line Segments
Ldot Multitype L-function (i-to-any)
BadGey Hybrid Geyer Point Process Model
StraussHard The Strauss / Hard Core Point Process Model
eval.fv Evaluate Expression Involving Functions
is.marked.ppp Test Whether A Point Pattern is Marked
rotate.psp Rotate a Line Segment Pattern
ord.family Ord Interaction Process Family
rmpoispp Generate Multitype Poisson Point Pattern
Kinhom Inhomogeneous K-function
clarkevans Clark and Evans Aggregation Index
distmap Distance Map
AreaInter The Area Interaction Point Process Model
Strauss The Strauss Point Process Model
Iest Estimate the I-function
pairdist.psp Pairwise distances between line segments
crossdist.default Pairwise distances between two different sets of points
localK Neighbourhood density function
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
scanpp Read Point Pattern From Data File
pcf.fv Pair Correlation Function obtained from K Function
Ord Generic Ord Interaction model
cut.im Convert Pixel Image from Numeric to Factor
distmap.psp Distance Map of Line Segment Pattern
as.mask Pixel Image Approximation of a Window
pcf.fasp Pair Correlation Function obtained from array of K functions
stieltjes Compute Integral of Function Against Cumulative Distribution
distmap.ppp Distance Map of Point Pattern
harmonic Basis for Harmonic Functions
corners Corners of a rectangle
crossdist Pairwise distances
affine.ppp Apply Affine Transformation To Point Pattern
spatstat The Spatstat Package
rotate.ppp Rotate a Point Pattern
areadiff Difference of Disc Areas
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
logLik.ppm Log Likelihood for Poisson Point Process Model
spatstat-deprecated Deprecated spatstat functions
DiggleGratton Diggle-Gratton model
as.ppp Convert Data To Class ppp
as.im Convert to Pixel Image
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
bei Tropical rain forest trees
diameter Diameter of a Window
centroid.owin Centroid of a window
Fest Estimate the empty space function F
print.psp Print Brief Details of a Line Segment Pattern Dataset
pcf Pair Correlation Function
bdist.points Distance to Boundary of Window
ripras Estimate window from points alone
anemones Beadlet Anemones Data
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
rpoisline Generate Poisson Random Line Process
Kest K-function
compatible.im Test Whether Two Pixel Images Are Compatible
data.ppm Extract Original Data from a Fitted Point Process Model
plot.ppm plot a Fitted Point Process Model
plot.fasp Plot a Function Array
Kest.fft K-function using FFT
hyperframe Hyper Data Frame
discretise Safely Convert Point Pattern Window to Binary Mask
Jdot Multitype J Function (i-to-any)
rotate Rotate
convexhull.xy Convex Hull of Points
LennardJones The Lennard-Jones Potential
eroded.areas Areas of Morphological Erosions
rpoispp Generate Poisson Point Pattern
Jest Estimate the J-function
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
bounding.box Bounding Box of a Window or Point Pattern
is.subset.owin Determine Whether One Window is Contained In Another
pairdist.ppp Pairwise distances
density.psp Kernel Smoothing of Line Segment Pattern
OrdThresh Ord's Interaction model
as.rectangle Window Frame
coef.ppm Coefficients of Fitted Point Process Model
as.owin Convert Data To Class owin
ppp Create a Point Pattern
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
im Create a Pixel Image Object
default.dummy Generate a Default Pattern of Dummy Points
im.object Class of Images
levelset Level Set of a Pixel Image
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
quadratcount Quadrat counting for a point pattern
gridweights Compute Quadrature Weights Based on Grid Counts
spokes Spokes pattern of dummy points
plot.splitppp Plot a List of Point Patterns
rescale.psp Convert Line Segment Pattern to Another Unit of Length
rshift.ppp Randomly Shift a Point Pattern
clickpoly Interactively Define a Polygon
fv.object Data Frames of Function Values
Saturated Saturated Pairwise Interaction model
crossdist.ppp Pairwise distances between two different point patterns
distmap.owin Distance Map of Window
gpc2owin Convert Polygonal Region into Different Format
interp.im Interpolate a Pixel Image
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
affine.owin Apply Affine Transformation To Window
is.multitype.ppm Test Whether A Point Process Model is Multitype
is.marked.ppm Test Whether A Point Process Model is Marked
intersect.owin Intersection or Union of Two Windows
identify.ppp Identify Points in a Point Pattern
print.ppm Print a Fitted Point Process Model
Geyer Geyer's Saturation Point Process Model
urkiola Urkiola Woods Point Pattern
is.ppp Test Whether An Object Is A Point Pattern
quad.object Class of Quadrature Schemes
finpines Pine saplings in Finland.
MultiStrauss The Multitype Strauss Point Process Model
fasp.object Function Arrays for Spatial Patterns
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
plot.im Plot a Pixel Image
nbfires Point Patterns of New Brunswick Forest Fires
quadscheme Generate a Quadrature Scheme from a Point Pattern
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
Kdot.inhom Inhomogeneous Multitype K Dot Function
erode.owin Erode a Window
raster.x Cartesian Coordinates for a Pixel Raster
Jcross Multitype J Function (i-to-j)
trim.rectangle Cut margins from rectangle
anova.ppm ANOVA for Fitted Point Process Models
nndist.psp Nearest neighbour distances between line segments
mean.im Mean Pixel Value in an Image
expand.owin Expand Window By Factor
is.multitype.ppp Test Whether A Point Pattern is Multitype
spatstat-internal Internal spatstat functions
rMaternI Simulate Matern Model I
model.images Compute Images of Constructed Covariates
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
Poisson Poisson Point Process Model
ants Harkness-Isham ants' nests data
gridcentres Rectangular grid of points
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
affine Apply Affine Transformation
clickppp Interactively Add Points
thomas.estK Fit the Thomas Point Process by Minimum Contrast
plot.psp plot a Spatial Line Segment Pattern
envelope Simulation envelopes of summary function
rsyst Simulate systematic random point pattern
nnwhich Nearest neighbour
contour.im Contour plot of pixel image
ppm.object Class of Fitted Point Process Models
markcorr Mark Correlation Function
plot.ppp plot a Spatial Point Pattern
as.psp Convert Data To Class psp
Kmeasure Reduced Second Moment Measure
kppm Fit cluster point process model
subset.ppp Extract or Replace Subset of Point Pattern
japanesepines Japanese Pines Point Pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
is.im Test Whether An Object Is A Pixel Image
betacells Beta Ganglion Cells in Cat Retina
compatible.fv Test Whether Two Function Objects Are Compatible
area.owin Area of a Window
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rescale Convert dataset to another unit of length
concatxy Concatenate x,y Coordinate Vectors
rescale.owin Convert Window to Another Unit of Length
shift Apply Vector Translation
simulate.kppm Simulate a fitted cluster point process model.
Kmulti Marked K-Function
amacrine Hughes' Amacrine Cell Data
is.owin Test Whether An Object Is A Window
longleaf Longleaf Pines Point Pattern
Linhom L-function
pairwise.family Pairwise Interaction Process Family
crossing.psp Crossing Points of Two Line Segment Patterns
multiplicity.ppp Count Multiplicity of Duplicate Points
nndist Nearest neighbour distances
persp.im Perspective Plot of Pixel Image
mincontrast Method of Minimum Contrast
is.multitype Test whether Object is Multitype
rMatClust Simulate Matern Cluster Process
setcov Set Covariance of a Window
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
blur Apply Gaussian Blur to a Pixel Image
endpoints.psp Endpoints of Line Segment Pattern
Lcross Multitype L-function (cross-type)
complement.owin Take Complement of a Window
vertices Vertices of a Window
rmpoint Generate N Random Multitype Points
rlinegrid Generate grid of parallel lines with random displacement
owin Create a Window
rshift.splitppp Randomly Shift a List of Point Patterns
rGaussPoisson Simulate Gauss-Poisson Process
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
selfcrossing.psp Crossing Points in a Line Segment Pattern
rshift.psp Randomly Shift a Line Segment Pattern
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
summary.listof Summary of a List of Things
Pairwise Generic Pairwise Interaction model
shift.owin Apply Vector Translation To Window
plot.owin Plot a Spatial Window
bounding.box.xy Convex Hull of Points
reduced.sample Reduced Sample Estimator using Histogram Data
update.ppm Update a Fitted Point Process Model
nztrees New Zealand Trees Point Pattern
affine.psp Apply Affine Transformation To Line Segment Pattern
print.quad Print a Quadrature Scheme
rSSI Simulate Simple Sequential Inhibition
rNeymanScott Simulate Neyman-Scott Process
angles.psp Orientation Angles of Line Segments
density.ppp Kernel Smoothed Intensity of Point Pattern
copper Berman-Huntington points and lines data
hist.im Histogram of Pixel Values in an Image
shift.psp Apply Vector Translation To Line Segment Pattern
summary.ppp Summary of a Point Pattern Dataset
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
ppm Fit Point Process Model to Data
shift.ppp Apply Vector Translation To Point Pattern
summary.splitppp Summary of a Split Point Pattern
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
fitted.ppm Fitted Conditional Intensity for Point Process Model
ganglia Beta Ganglion Cells in Cat Retina, Old Version
summary.owin Summary of a Spatial Window
redwoodfull California Redwoods Point Pattern (Entire Dataset)
print.owin Print Brief Details of a Spatial Window
rshift Random Shift
applynbd Apply Function to Every Neighbourhood in a Point Pattern
owin.object Class owin
crossdist.psp Pairwise distances between two different line segment patterns
square Square Window
ewcdf Weighted Empirical Cumulative Distribution Function
plot.quad plot a Spatial Quadrature Scheme
inside.owin Test Whether Points Are Inside A Window
plot.kppm Plot a fitted cluster point process
plot.listof Plot a List of Things
rMaternII Simulate Matern Model II
letterR Window in Shape of Letter R
rjitter Random Perturbation of a Point Pattern
psp Create a Line Segment Pattern
spatstat.options Internal Options in Spatstat Package
rStrauss Perfect Simulation of the Strauss Process
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
rstrat Simulate Stratified Random Point Pattern
profilepl Profile Maximum Pseudolikelihood
rescale.ppp Convert Point Pattern to Another Unit of Length
rmh.ppm Simulate from a Fitted Point Process Model
rcell Simulate Baddeley-Silverman Cell Process
eval.fasp Evaluate Expression Involving Function Arrays
midpoints.psp Midpoints of Line Segment Pattern
redwood California Redwoods Point Pattern (Ripley's Subset)
fitin.ppm Extract the Interaction from a Fitted Point Process Model
is.ppm Test Whether An Object Is A Fitted Point Process Model
matchingdist Distance for a Point Pattern Matching
kaplan.meier Kaplan-Meier Estimator using Histogram Data
lurking Lurking variable plot
plot.fv Plot Function Valuesn
subset.fasp Extract Subset of Function Array
pppdist Distance Between Two Point Patterns
residualspaper Data and Code From JRSS Discussion Paper on Residuals
ppp.object Class of Point Patterns
model.matrix.ppm Extract Design Matrix from Point Process Model
print.im Print Brief Details of an Image
rpoint Generate N Random Points
disc Circular Window
rthin Random Thinning
union.quad Union of Data and Dummy Points
pppmatching.object Class of Point Matchings
predict.kppm Prediction from a Fitted Cluster Point Process Model
nncross Nearest Neighbour in Another Point Pattern
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
unmark Remove Marks from a Marked Point Pattern
update.kppm Update a Fitted Cluster Point Process Model
subset.psp Extract Subset of Line Segment Pattern
setmarks Set or Reset the Marks in a Point Pattern
superimpose Superimpose Several Point Patterns
subsetget.im Reset Values in Subset of Image
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
lansing Lansing Woods Point Pattern
runifdisc Generate N Uniform Random Points in a Disc
inforder.family Infinite Order Interaction Family
predict.ppm Prediction from a Fitted Point Process Model
plot.plotppm Plot a plotppm Object Created by plot.ppm
rotate.owin Rotate a Window
pairdist Pairwise distances
suffstat Sufficient Statistic of Point Process Model
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
rThomas Simulate Thomas Process
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
quantile.im Sample Quantiles of Pixel Image
plot.hyperframe Plot Entries in a Hyperframe
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
rlabel Random Re-Labelling of Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
print.ppp Print Brief Details of a Point Pattern Dataset
pcf.ppp Pair Correlation Function of Point Pattern
shift.im Apply Vector Translation To Pixel Image
rescue.rectangle Convert Window Back To Rectangle
with.fv Evaluate an Expression in a Function Table
progressreport Print Progress Reports
summary.im Summarizing a Pixel Image
pairdist.default Pairwise distances
subset.fv Extract Subset of Function Values
pairsat.family Saturated Pairwise Interaction Point Process Family
residuals.ppm Residuals for Fitted Point Process Model
reach Interaction Distance of a Point Process
runifpoint Generate N Uniform Random Points
subset.listof Extract or Replace Subset of a List of Things
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
spruces Spruces Point Pattern
unitname Name for Unit of Length
subset.splitppp Extract or Replace Sub-Patterns
simdat Simulated Point Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
smooth.ppp Spatial smoothing of observations at irregular points
ponderosa Ponderosa Pine Tree Point Pattern
pppmatching Create a Point Matching
psp.object Class of Line Segment Patterns
swedishpines Swedish Pines Point Pattern
split.ppp Divide Point Pattern into Sub-patterns
subset.im Extract Subset of Image
unique.ppp Extract Unique Points from a Spatial Point Pattern
summary.quad Summarizing a Quadrature Scheme
summary.ppm Summarizing a Fitted Point Process Model
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
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Date 18 July 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Fri Jul 18 12:29:36 2008; adrian

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