spatstat v1.13-0

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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
Kmeasure Reduced Second Moment Measure
Geyer Geyer's Saturation Point Process Model
BadGey Hybrid Geyer Point Process Model
fv.object Data Frames of Function Values
as.owin Convert Data To Class owin
DiggleGratton Diggle-Gratton model
pairdist.default Pairwise distances
amacrine Hughes' Amacrine Cell Data
Jcross Multitype J Function (i-to-j)
Strauss The Strauss Point Process Model
Jdot Multitype J Function (i-to-any)
inforder.family Infinite Order Interaction Family
distmap.ppp Distance Map of Point Pattern
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
plot.fv Plot Function Valuesn
anemones Beadlet Anemones Data
Gmulti Marked Nearest Neighbour Distance Function
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
eval.im Evaluate Expression Involving Pixel Images
as.matrix.im Convert Pixel Image to Matrix
humberside Humberside Data on Childhood Leukaemia and Lymphoma
bounding.box.xy Convex Hull of Points
Jest Estimate the J-function
allstats Calculate four standard summary functions of a point pattern.
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
spatstat The Spatstat Package
plot.listof Plot a List of Things
print.ppp Print Brief Details of a Point Pattern Dataset
Fest Estimate the empty space function F
kaplan.meier Kaplan-Meier Estimator using Histogram Data
bdist.points Distance to Boundary of Window
Gest Nearest Neighbour Distance Function G
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
nearest.raster.point Find Pixel Nearest to a Given Point
Poisson Poisson Point Process Model
append.psp Combine Two Line Segment Patterns
nbfires Point Patterns of New Brunswick Forest Fires
Kdot.inhom Inhomogeneous Multitype K Dot Function
MultiStrauss The Multitype Strauss Point Process Model
im.object Class of Images
Pairwise Generic Pairwise Interaction model
default.dummy Generate a Default Pattern of Dummy Points
LennardJones The Lennard-Jones Potential
Kcross.inhom Inhomogeneous Cross K Function
nncross Nearest Neighbour in Another Point Pattern
as.data.frame.ppp Coerce Point Pattern to a Data Frame
summary.im Summarizing a Pixel Image
Kinhom Inhomogeneous K-function
rescale.ppp Convert Point Pattern to Another Unit of Length
Kcross Multitype K Function (Cross-type)
expand.owin Expand Window By Factor
multiplicity.ppp Count Multiplicity of Duplicate Points
as.mask Pixel Image Approximation of a Window
as.im Convert to Pixel Image
crossdist Pairwise distances
plot.hyperframe Plot Entries in a Hyperframe
owin.object Class owin
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
Linhom L-function
crossdist.psp Pairwise distances between two different line segment patterns
pairdist.ppp Pairwise distances
anova.ppm ANOVA for Fitted Point Process Models
affine.psp Apply Affine Transformation To Line Segment Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
erode.owin Erode a Window
centroid.owin Centroid of a window
bounding.box Bounding Box of a Window or Point Pattern
is.owin Test Whether An Object Is A Window
complement.owin Take Complement of a Window
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
quadratcount Quadrat counting for a point pattern
rpoispp Generate Poisson Point Pattern
Ord Generic Ord Interaction model
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
pppdist Distance Between Two Point Patterns
runifdisc Generate N Uniform Random Points in a Disc
japanesepines Japanese Pines Point Pattern
smooth.ppp Spatial smoothing of observations at irregular points
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
crossdist.default Pairwise distances between two different sets of points
print.psp Print Brief Details of a Line Segment Pattern Dataset
distmap.owin Distance Map of Window
ants Harkness-Isham ants' nests data
is.subset.owin Determine Whether One Window is Contained In Another
rMaternI Simulate Matern Model I
AreaInter The Area Interaction Point Process Model
eval.fv Evaluate Expression Involving Functions
bdist.pixels Distance to Boundary of Window
Kmulti Marked K-Function
data.ppm Extract Original Data from a Fitted Point Process Model
clickpoly Interactively Define a Polygon
StraussHard The Strauss / Hard Core Point Process Model
gridcentres Rectangular grid of points
betacells Beta Ganglion Cells in Cat Retina
im Create a Pixel Image Object
plot.fasp Plot a Function Array
bramblecanes Hutchings' Bramble Canes data
as.ppp Convert Data To Class ppp
bei Tropical rain forest trees
clarkevans Clark and Evans Aggregation Index
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
endpoints.psp Endpoints of Line Segment Pattern
Jmulti Marked J Function
coef.ppm Coefficients of Fitted Point Process Model
crossing.psp Crossing Points of Two Line Segment Patterns
pppmatching Create a Point Matching
lengths.psp Lengths of Line Segments
discretise Safely Convert Point Pattern Window to Binary Mask
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
quad.object Class of Quadrature Schemes
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
eem Exponential Energy Marks
rmpoint Generate N Random Multitype Points
residuals.ppm Residuals for Fitted Point Process Model
quantile.im Sample Quantiles of Pixel Image
Kdot Multitype K Function (i-to-any)
Lest L-function
finpines Pine saplings in Finland.
shift.psp Apply Vector Translation To Line Segment Pattern
ponderosa Ponderosa Pine Tree Point Pattern
envelope Simulation envelopes of summary function
contour.im Contour plot of pixel image
summary.ppp Summary of a Point Pattern Dataset
as.rectangle Window Frame
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
pcf.fasp Pair Correlation Function obtained from array of K functions
diameter Diameter of a Window
inside.owin Test Whether Points Are Inside A Window
letterR Window in Shape of Letter R
ppm Fit Point Process Model to Data
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
distmap.psp Distance Map of Line Segment Pattern
markcorr Mark Correlation Function
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
pairdist.psp Pairwise distances between line segments
rNeymanScott Simulate Neyman-Scott Process
fasp.object Function Arrays for Spatial Patterns
ewcdf Weighted Empirical Cumulative Distribution Function
Saturated Saturated Pairwise Interaction model
lurking Lurking variable plot
lansing Lansing Woods Point Pattern
rmh.ppm Simulate from a Fitted Point Process Model
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
Softcore The Soft Core Point Process Model
OrdThresh Ord's Interaction model
Iest Estimate the I-function
convexhull.xy Convex Hull of Points
as.psp Convert Data To Class psp
copper Berman-Huntington points and lines data
hist.im Histogram of Pixel Values in an Image
model.matrix.ppm Extract Design Matrix from Point Process Model
rescale.owin Convert Window to Another Unit of Length
vertices Vertices of a Window
setmarks Set or Reset the Marks in a Point Pattern
subset.psp Extract Subset of Line Segment Pattern
cut.im Convert Pixel Image from Numeric to Factor
corners Corners of a rectangle
identify.ppp Identify Points in a Point Pattern
density.psp Kernel Smoothing of Line Segment Pattern
spatstat.options Internal Options in Spatstat Package
plot.quad plot a Spatial Quadrature Scheme
compatible.fv Test Whether Two Function Objects Are Compatible
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
is.multitype.ppp Test Whether A Point Pattern is Multitype
quadscheme Generate a Quadrature Scheme from a Point Pattern
is.marked Test Whether Marks Are Present
spatstat-internal Internal spatstat functions
interp.im Interpolate a Pixel Image
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
nndist Nearest neighbour distances
scanpp Read Point Pattern From Data File
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
fitin.ppm Extract the Interaction from a Fitted Point Process Model
ganglia Beta Ganglion Cells in Cat Retina, Old Version
mincontrast Method of Minimum Contrast
crossdist.ppp Pairwise distances between two different point patterns
gridweights Compute Quadrature Weights Based on Grid Counts
summary.quad Summarizing a Quadrature Scheme
suffstat Sufficient Statistic of Point Process Model
is.ppm Test Whether An Object Is A Fitted Point Process Model
rMatClust Simulate Matern Cluster Process
is.multitype Test whether Object is Multitype
eroded.areas Areas of Morphological Erosions
rcell Simulate Baddeley-Silverman Cell Process
affine.ppp Apply Affine Transformation To Point Pattern
pairwise.family Pairwise Interaction Process Family
pcf.fv Pair Correlation Function obtained from K Function
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
rSSI Simulate Simple Sequential Inhibition
demopat Artificial Data Point Pattern
model.images Compute Images of Constructed Covariates
disc Circular Window
affine.owin Apply Affine Transformation To Window
nnwhich Nearest neighbour
pairdist Pairwise distances
dilate.owin Dilate a Window
clickppp Interactively Add Points
matchingdist Distance for a Point Pattern Matching
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
print.im Print Brief Details of an Image
pairsat.family Saturated Pairwise Interaction Point Process Family
ord.family Ord Interaction Process Family
progressreport Print Progress Reports
thomas.estK Fit the Thomas Point Process by Minimum Contrast
ppm.object Class of Fitted Point Process Models
is.marked.ppp Test Whether A Point Pattern is Marked
intersect.owin Intersection or Union of Two Windows
is.im Test Whether An Object Is A Pixel Image
raster.x Cartesian Coordinates for a Pixel Raster
trim.rectangle Cut margins from rectangle
Kest.fft K-function using FFT
cells Biological Cells Point Pattern
simdat Simulated Point Pattern
plot.im Plot a Pixel Image
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rlabel Random Re-Labelling of Point Pattern
union.quad Union of Data and Dummy Points
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
rlinegrid Generate grid of parallel lines with random displacement
chorley Chorley-Ribble Cancer Data
plot.ppm plot a Fitted Point Process Model
is.multitype.ppm Test Whether A Point Process Model is Multitype
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
hamster Aherne's hamster tumour data
print.quad Print a Quadrature Scheme
harmonic Basis for Harmonic Functions
rStrauss Perfect Simulation of the Strauss Process
ppp Create a Point Pattern
longleaf Longleaf Pines Point Pattern
psp.object Class of Line Segment Patterns
rescue.rectangle Convert Window Back To Rectangle
rotate Rotate
logLik.ppm Log Likelihood for Poisson Point Process Model
summary.ppm Summarizing a Fitted Point Process Model
reach Interaction Distance of a Point Process
spatstat-deprecated Deprecated spatstat functions
reduced.sample Reduced Sample Estimator using Histogram Data
rsyst Simulate systematic random point pattern
midpoints.psp Midpoints of Line Segment Pattern
distmap Distance Map
rpoint Generate N Random Points
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
rstrat Simulate Stratified Random Point Pattern
ppp.object Class of Point Patterns
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
pppmatching.object Class of Point Matchings
runifpoint Generate N Uniform Random Points
superimpose Superimpose Several Point Patterns
residualspaper Data and Code From JRSS Discussion Paper on Residuals
shift.owin Apply Vector Translation To Window
print.owin Print Brief Details of a Spatial Window
hyperframe Hyper Data Frame
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
subsetget.im Reset Values in Subset of Image
affine Apply Affine Transformation
ripras Estimate window from points alone
localK Neighbourhood density function
rGaussPoisson Simulate Gauss-Poisson Process
summary.listof Summary of a List of Things
area.owin Area of a Window
rescale.psp Convert Line Segment Pattern to Another Unit of Length
rshift.ppp Randomly Shift a Point Pattern
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
areadiff Difference of Disc Areas
fitted.ppm Fitted Conditional Intensity for Point Process Model
setcov Set Covariance of a Window
nztrees New Zealand Trees Point Pattern
summary.owin Summary of a Spatial Window
cut.ppp Convert Point Pattern Marks from Numeric to Factor
predict.ppm Prediction from a Fitted Point Process Model
print.ppm Print a Fitted Point Process Model
levelset Level Set of a Pixel Image
unmark Remove Marks from a Marked Point Pattern
nndist.psp Nearest neighbour distances between line segments
persp.im Perspective Plot of Pixel Image
rpoisline Generate Poisson Random Line Process
shift.ppp Apply Vector Translation To Point Pattern
rmpoispp Generate Multitype Poisson Point Pattern
rshift Random Shift
redwoodfull California Redwoods Point Pattern (Entire Dataset)
Kest K-function
redwood California Redwoods Point Pattern (Ripley's Subset)
angles.psp Orientation Angles of Line Segments
rotate.ppp Rotate a Point Pattern
plot.psp plot a Spatial Line Segment Pattern
rshift.splitppp Randomly Shift a List of Point Patterns
plot.plotppm Plot a plotppm Object Created by plot.ppm
density.ppp Kernel Smoothed Intensity of Point Pattern
subset.fasp Extract Subset of Function Array
psp Create a Line Segment Pattern
subset.fv Extract Subset of Function Values
rotate.psp Rotate a Line Segment Pattern
applynbd Apply Function to Every Neighbourhood in a Point Pattern
subset.im Extract Subset of Image
rshift.psp Randomly Shift a Line Segment Pattern
is.ppp Test Whether An Object Is A Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
plot.splitppp Plot a List of Point Patterns
pcf.ppp Pair Correlation Function of Point Pattern
profilepl Profile Maximum Pseudolikelihood
spruces Spruces Point Pattern
split.ppp Divide Point Pattern into Sub-patterns
rescale Convert dataset to another unit of length
rThomas Simulate Thomas Process
rotate.owin Rotate a Window
shift Apply Vector Translation
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
summary.splitppp Summary of a Split Point Pattern
unique.ppp Extract Unique Points from a Spatial Point Pattern
concatxy Concatenate x,y Coordinate Vectors
is.marked.ppm Test Whether A Point Process Model is Marked
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
shift.im Apply Vector Translation To Pixel Image
mean.im Mean Pixel Value in an Image
square Square Window
spokes Spokes pattern of dummy points
owin Create a Window
subset.listof Extract or Replace Subset of a List of Things
swedishpines Swedish Pines Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
unitname Name for Unit of Length
pcf Pair Correlation Function
plot.owin Plot a Spatial Window
plot.ppp plot a Spatial Point Pattern
rMaternII Simulate Matern Model II
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
rthin Random Thinning
subset.ppp Extract or Replace Subset of Point Pattern
subset.splitppp Extract or Replace Sub-Patterns
update.ppm Update a Fitted Point Process Model
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Date 11 April 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Sat Apr 12 01:09:17 2008; adrian

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