spatstat v1.12-3

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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
OrdThresh Ord's Interaction model
Pairwise Generic Pairwise Interaction model
is.multitype.ppm Test Whether A Point Process Model is Multitype
is.im Test Whether An Object Is A Pixel Image
im.object Class of Images
Gmulti Marked Nearest Neighbour Distance Function
ord.family Ord Interaction Process Family
affine.ppp Apply Affine Transformation To Point Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
progressreport Print Progress Reports
Kest.fft K-function using FFT
bounding.box Bounding Box of a Window or Point Pattern
Kinhom Inhomogeneous K-function
eval.fv Evaluate Expression Involving Functions
data.ppm Extract Original Data from a Fitted Point Process Model
crossdist Pairwise distances
Saturated Saturated Pairwise Interaction model
distmap.ppp Distance Map of Point Pattern
DiggleGratton Diggle-Gratton model
rotate.ppp Rotate a Point Pattern
rsyst Simulate systematic random point pattern
union.quad Union of Data and Dummy Points
MultiStrauss The Multitype Strauss Point Process Model
as.owin Convert Data To Class owin
ants Harkness-Isham ants' nests data
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Fest Estimate the empty space function F
is.multitype.ppp Test Whether A Point Pattern is Multitype
pairdist Pairwise distances
Jdot Multitype J Function (i-to-any)
kaplan.meier Kaplan-Meier Estimator using Histogram Data
pairdist.psp Pairwise distances between line segments
clickppp Interactively Add Points
gridcentres Rectangular grid of points
plot.splitppp Plot a List of Point Patterns
StraussHard The Strauss / Hard Core Point Process Model
pcf.ppp Pair Correlation Function of Point Pattern
Poisson Poisson Point Process Model
plot.plotppm Plot a plotppm Object Created by plot.ppm
plot.hyperframe Plot Entries in a Hyperframe
print.owin Print Brief Details of a Spatial Window
Gest Nearest Neighbour Distance Function G
as.matrix.im Convert Pixel Image to Matrix
chorley Chorley-Ribble Cancer Data
profilepl Profile Maximum Pseudolikelihood
dilate.owin Dilate a Window
bounding.box.xy Convex Hull of Points
bramblecanes Hutchings' Bramble Canes data
concatxy Concatenate x,y Coordinate Vectors
spatstat The Spatstat Package
envelope Simulation envelopes of summary function
endpoints.psp Endpoints of Line Segment Pattern
distmap.owin Distance Map of Window
distmap.psp Distance Map of Line Segment Pattern
anova.ppm ANOVA for Fitted Point Process Models
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
bdist.points Distance to Boundary of Window
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
Lest L-function
clarkevans Clark and Evans Aggregation Index
allstats Calculate four standard summary functions of a point pattern.
crossdist.psp Pairwise distances between two different line segment patterns
as.mask Pixel Image Approximation of a Window
crossdist.default Pairwise distances between two different sets of points
psp.object Class of Line Segment Patterns
quad.object Class of Quadrature Schemes
as.im Convert to Pixel Image
plot.psp plot a Spatial Line Segment Pattern
rescale Convert dataset to another unit of length
ppm Fit Point Process Model to Data
anemones Beadlet Anemones Data
rThomas Simulate Thomas Process
hyperframe Hyper Data Frame
spatstat-deprecated Deprecated spatstat functions
rlabel Random Re-Labelling of Point Pattern
japanesepines Japanese Pines Point Pattern
rpoispp Generate Poisson Point Pattern
Geyer Geyer's Saturation Point Process Model
applynbd Apply Function to Every Neighbourhood in a Point Pattern
setcov Set Covariance of a Window
ponderosa Ponderosa Pine Tree Point Pattern
Kmulti Marked K-Function
hist.im Histogram of Pixel Values in an Image
Kdot.inhom Inhomogeneous Multitype K Dot Function
Softcore The Soft Core Point Process Model
spokes Spokes pattern of dummy points
psp Create a Line Segment Pattern
raster.x Cartesian Coordinates for a Pixel Raster
inside.owin Test Whether Points Are Inside A Window
coef.ppm Coefficients of Fitted Point Process Model
fitin.ppm Extract the Interaction from a Fitted Point Process Model
markcorr Mark Correlation Function
print.ppm Print a Fitted Point Process Model
identify.ppp Identify Points in a Point Pattern
print.im Print Brief Details of an Image
multiplicity.ppp Count Multiplicity of Duplicate Points
rlinegrid Generate grid of parallel lines with random displacement
rNeymanScott Simulate Neyman-Scott Process
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
residuals.ppm Residuals for Fitted Point Process Model
intersect.owin Intersection or Union of Two Windows
rStrauss Perfect Simulation of the Strauss Process
nearest.raster.point Find Pixel Nearest to a Given Point
simdat Simulated Point Pattern
rescale.psp Convert Line Segment Pattern to Another Unit of Length
Iest Estimate the I-function
Kest K-function
owin Create a Window
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
summary.ppp Summary of a Point Pattern Dataset
convexhull.xy Convex Hull of Points
diameter Diameter of a Window
append.psp Combine Two Line Segment Patterns
is.marked Test Whether Marks Are Present
nnwhich Nearest neighbour
Ord Generic Ord Interaction model
betacells Beta Ganglion Cells in Cat Retina
pcf.fv Pair Correlation Function obtained from K Function
crossdist.ppp Pairwise distances between two different point patterns
affine.owin Apply Affine Transformation To Window
pppmatching.object Class of Point Matchings
amacrine Hughes' Amacrine Cell Data
clickpoly Interactively Define a Polygon
shift Apply Vector Translation
lurking Lurking variable plot
selfcrossing.psp Crossing Points in a Line Segment Pattern
density.ppp Kernel Smoothed Intensity of Point Pattern
ppp.object Class of Point Patterns
plot.listof Plot a List of Things
centroid.owin Centroid of a window
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
print.psp Print Brief Details of a Line Segment Pattern Dataset
smooth.ppp Spatial smoothing of observations at irregular points
trim.rectangle Cut margins from rectangle
vertices Vertices of a Window
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
is.ppp Test Whether An Object Is A Point Pattern
rSSI Simulate Simple Sequential Inhibition
rmpoispp Generate Multitype Poisson Point Pattern
default.dummy Generate a Default Pattern of Dummy Points
discretise Safely Convert Point Pattern Window to Binary Mask
rmh.ppm Simulate from a Fitted Point Process Model
square Square Window
subset.ppp Extract or Replace Subset of Point Pattern
ppp Create a Point Pattern
nndist.psp Nearest neighbour distances between line segments
superimpose Superimpose Several Point Patterns
rescue.rectangle Convert Window Back To Rectangle
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
summary.ppm Summarizing a Fitted Point Process Model
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
hamster Aherne's hamster tumour data
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
unmark Remove Marks from a Marked Point Pattern
plot.quad plot a Spatial Quadrature Scheme
humberside Humberside Data on Childhood Leukaemia and Lymphoma
nncross Nearest Neighbour in Another Point Pattern
Strauss The Strauss Point Process Model
pcf.fasp Pair Correlation Function obtained from array of K functions
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
im Create a Pixel Image Object
reduced.sample Reduced Sample Estimator using Histogram Data
Kcross.inhom Inhomogeneous Cross K Function
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
is.subset.owin Determine Whether One Window is Contained In Another
levelset Level Set of a Pixel Image
harmonic Basis for Harmonic Functions
subset.im Extract Subset of Image
runifpoint Generate N Uniform Random Points
rstrat Simulate Stratified Random Point Pattern
subsetget.im Reset Values in Subset of Image
rescale.ppp Convert Point Pattern to Another Unit of Length
residualspaper Data and Code From JRSS Discussion Paper on Residuals
midpoints.psp Midpoints of Line Segment Pattern
shift.owin Apply Vector Translation To Window
compatible.im Test Whether Two Pixel Images Are Compatible
as.psp Convert Data To Class psp
as.ppp Convert Data To Class ppp
nbfires Point Patterns of New Brunswick Forest Fires
mincontrast Method of Minimum Contrast
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
rshift.splitppp Randomly Shift a List of Point Patterns
shift.psp Apply Vector Translation To Line Segment Pattern
disc Circular Window
LennardJones The Lennard-Jones Potential
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
persp.im Perspective Plot of Pixel Image
area.owin Area of a Window
as.data.frame.ppp Coerce Point Pattern to a Data Frame
subset.fv Extract Subset of Function Values
subset.listof Extract or Replace Subset of a List of Things
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
matchingdist Distance for a Point Pattern Matching
contour.im Contour plot of pixel image
affine Apply Affine Transformation
compatible.fv Test Whether Two Function Objects Are Compatible
eval.im Evaluate Expression Involving Pixel Images
summary.im Summarizing a Pixel Image
rshift.ppp Randomly Shift a Point Pattern
cut.ppp Convert Point Pattern Marks from Numeric to Factor
runifdisc Generate N Uniform Random Points in a Disc
logLik.ppm Log Likelihood for Poisson Point Process Model
fitted.ppm Fitted Conditional Intensity for Point Process Model
subset.psp Extract Subset of Line Segment Pattern
summary.quad Summarizing a Quadrature Scheme
eroded.areas Areas of Morphological Erosions
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
pairsat.family Saturated Pairwise Interaction Point Process Family
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
Kdot Multitype K Function (i-to-any)
plot.im Plot a Pixel Image
copper Berman-Huntington points and lines data
owin.object Class owin
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
pcf Pair Correlation Function
demopat Artificial Data Point Pattern
plot.ppm plot a Fitted Point Process Model
letterR Window in Shape of Letter R
plot.ppp plot a Spatial Point Pattern
plot.owin Plot a Spatial Window
is.marked.ppp Test Whether A Point Pattern is Marked
interp.im Interpolate a Pixel Image
erode.owin Erode a Window
pppdist Distance Between Two Point Patterns
pairdist.ppp Pairwise distances
ewcdf Weighted Empirical Cumulative Distribution Function
ppm.object Class of Fitted Point Process Models
plot.fv Plot Function Valuesn
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
quadratcount Quadrat counting for a point pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
localK Neighbourhood density function
rotate Rotate
rescale.owin Convert Window to Another Unit of Length
is.owin Test Whether An Object Is A Window
cells Biological Cells Point Pattern
reach Interaction Distance of a Point Process
cut.im Convert Pixel Image from Numeric to Factor
rthin Random Thinning
density.psp Kernel Smoothing of Line Segment Pattern
rpoint Generate N Random Points
shift.im Apply Vector Translation To Pixel Image
rshift.psp Randomly Shift a Line Segment Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
update.ppm Update a Fitted Point Process Model
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
ripras Estimate window from points alone
nndist Nearest neighbour distances
setmarks Set or Reset the Marks in a Point Pattern
scanpp Read Point Pattern From Data File
summary.listof Summary of a List of Things
fasp.object Function Arrays for Spatial Patterns
suffstat Sufficient Statistic of Point Process Model
summary.splitppp Summary of a Split Point Pattern
predict.ppm Prediction from a Fitted Point Process Model
unique.ppp Extract Unique Points from a Spatial Point Pattern
fv.object Data Frames of Function Values
rMaternI Simulate Matern Model I
spruces Spruces Point Pattern
rotate.psp Rotate a Line Segment Pattern
rotate.owin Rotate a Window
complement.owin Take Complement of a Window
corners Corners of a rectangle
plot.fasp Plot a Function Array
pppmatching Create a Point Matching
crossing.psp Crossing Points of Two Line Segment Patterns
is.marked.ppm Test Whether A Point Process Model is Marked
split.ppp Divide Point Pattern into Sub-patterns
longleaf Longleaf Pines Point Pattern
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
rshift Random Shift
rcell Simulate Baddeley-Silverman Cell Process
shift.ppp Apply Vector Translation To Point Pattern
subset.splitppp Extract or Replace Sub-Patterns
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
bdist.pixels Distance to Boundary of Window
Kmeasure Reduced Second Moment Measure
finpines Pine saplings in Finland.
mean.im Mean Pixel Value in an Image
pairwise.family Pairwise Interaction Process Family
print.quad Print a Quadrature Scheme
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
redwood California Redwoods Point Pattern (Ripley's Subset)
quadscheme Generate a Quadrature Scheme from a Point Pattern
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Kcross Multitype K Function (Cross-type)
angles.psp Orientation Angles of Line Segments
ganglia Beta Ganglion Cells in Cat Retina, Old Version
affine.psp Apply Affine Transformation To Line Segment Pattern
gridweights Compute Quadrature Weights Based on Grid Counts
spatstat-internal Internal spatstat functions
eem Exponential Energy Marks
is.multitype Test whether Object is Multitype
expand.owin Expand Window By Factor
is.ppm Test Whether An Object Is A Fitted Point Process Model
lansing Lansing Woods Point Pattern
pairdist.default Pairwise distances
print.ppp Print Brief Details of a Point Pattern Dataset
quantile.im Sample Quantiles of Pixel Image
rmpoint Generate N Random Multitype Points
spatstat.options Internal Options in Spatstat Package
summary.owin Summary of a Spatial Window
unitname Name for Unit of Length
summary.psp Summary of a Line Segment Pattern Dataset
Jest Estimate the J-function
Jmulti Marked J Function
Jcross Multitype J Function (i-to-j)
as.rectangle Window Frame
bei Tropical rain forest trees
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
distmap Distance Map
lengths.psp Lengths of Line Segments
nztrees New Zealand Trees Point Pattern
rMatClust Simulate Matern Cluster Process
rMaternII Simulate Matern Model II
rpoisline Generate Poisson Random Line Process
subset.fasp Extract Subset of Function Array
swedishpines Swedish Pines Point Pattern
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Date 02 November 2007
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Sat Nov 3 06:36:33 2007; adrian

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