spatstat v1.11-4

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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 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
anova.ppm ANOVA for Fitted Point Process Models
area.owin Area of a Window
Kest.fft K-function using FFT
LennardJones The Lennard-Jones Potential
markcorr Mark Correlation Function
as.owin Convert Data To Class owin
compatible.im Test Whether Two Pixel Images Are Compatible
is.multitype.ppm Test Whether A Point Process Model is Multitype
data.ppm Extract Original Data from a Fitted Point Process Model
angles.psp Orientation Angles of Line Segments
dilate.owin Dilate a Window
copper Berman-Huntington points and lines data
erode.owin Erode a Window
append.psp Combine Two Line Segment Patterns
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
MultiStrauss The Multitype Strauss Point Process Model
Geyer Geyer's Saturation Point Process Model
predict.ppm Prediction from a Fitted Point Process Model
affine Apply Affine Transformation
eval.fv Evaluate Expression Involving Functions
cut.ppp Convert Point Pattern Marks from Numeric to Factor
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
subset.splitppp Extract or Replace Sub-Patterns
nndist Nearest neighbour distances
thomas.estK Fit the Thomas Point Process by Minimum Contrast
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
distmap.ppp Distance Map of Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
hist.im Histogram of Pixel Values in an Image
is.subset.owin Determine Whether One Window is Contained In Another
plot.listof Plot a List of Things
im Create a Pixel Image Object
rstrat Simulate Stratified Random Point Pattern
shift.im Apply Vector Translation To Pixel Image
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
Fest Estimate the empty space function F
density.ppp Kernel Smoothed Intensity of Point Pattern
OrdThresh Ord's Interaction model
plot.fasp Plot a Function Array
plot.owin Plot a Spatial Window
pairdist.ppp Pairwise distances
suffstat Sufficient Statistic of Point Process Model
raster.x Cartesian Coordinates for a Pixel Raster
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
rsyst Simulate systematic random point pattern
eroded.areas Areas of Morphological Erosions
redwood California Redwoods Point Pattern (Ripley's Subset)
is.marked.ppp Test Whether A Point Pattern is Marked
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
mincontrast Method of Minimum Contrast
spatstat-internal Internal spatstat functions
clickpoly Interactively Define a Polygon
Jmulti Marked J Function
plot.plotppm Plot a plotppm Object Created by plot.ppm
betacells Beta Ganglion Cells in Cat Retina
nztrees New Zealand Trees Point Pattern
gridweights Compute Quadrature Weights Based on Grid Counts
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
mean.im Mean Pixel Value in an Image
is.multitype.ppp Test Whether A Point Pattern is Multitype
lansing Lansing Woods Point Pattern
Kmeasure Reduced Second Moment Measure
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
Iest Estimate the I-function
crossdist.default Pairwise distances between two different sets of points
shift.owin Apply Vector Translation To Window
centroid.owin Centroid of a window
clickppp Interactively Add Points
Kmulti Marked K-Function
nncross Nearest Neighbour in Another Point Pattern
bounding.box.xy Convex Hull of Points
intersect.owin Intersection or Union of Two Windows
bramblecanes Hutchings' Bramble Canes data
nnwhich Nearest neighbour
setmarks Set or Reset the Marks in a Point Pattern
reach Interaction Distance of a Point Process
simdat Simulated Point Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
rmpoint Generate N Random Multitype Points
summary.ppp Summary of a Point Pattern Dataset
runifpoint Generate N Uniform Random Points
pairdist Pairwise distances
ants Harkness-Isham ants' nests data
rotate.ppp Rotate a Point Pattern
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
corners Corners of a rectangle
diameter Diameter of a Window
summary.ppm Summarizing a Fitted Point Process Model
summary.listof Summary of a List of Things
rshift Random Shift
persp.im Perspective Plot of Pixel Image
print.ppm Print a Fitted Point Process Model
subsetget.im Reset Values in Subset of Image
rshift.splitppp Randomly Shift a List of Point Patterns
superimpose Superimpose Several Point Patterns
residuals.ppm Residuals for Fitted Point Process Model
selfcrossing.psp Crossing Points in a Line Segment Pattern
rthin Random Thinning
rStrauss Perfect Simulation of the Strauss Process
quadratcount Quadrat counting for a point pattern
plot.im Plot a Pixel Image
rescale.ppp Convert Point Pattern to Another Unit of Length
update.ppm Update a Fitted Point Process Model
summary.quad Summarizing a Quadrature Scheme
rcell Simulate Baddeley-Silverman Cell Process
summary.owin Summary of a Spatial Window
letterR Window in Shape of Letter R
rescale Convert dataset to another unit of length
Kdot.inhom Inhomogeneous Multitype K Dot Function
Strauss The Strauss Point Process Model
StraussHard The Strauss / Hard Core Point Process Model
nbfires Point Patterns of New Brunswick Forest Fires
fitin.ppm Extract the Interaction from a Fitted Point Process Model
is.multitype Test whether Object is Multitype
distmap.owin Distance Map of Window
distmap Distance Map
affine.psp Apply Affine Transformation To Line Segment Pattern
plot.psp plot a Spatial Line Segment Pattern
disc Circular Window
unmark Remove Marks from a Marked Point Pattern
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
psp Create a Line Segment Pattern
bei Tropical rain forest trees
applynbd Apply Function to Every Neighbourhood in a Point Pattern
pairdist.default Pairwise distances
compatible.fv Test Whether Two Function Objects Are Compatible
affine.ppp Apply Affine Transformation To Point Pattern
profilepl Profile Maximum Pseudolikelihood
pairwise.family Pairwise Interaction Process Family
quad.object Class of Quadrature Schemes
ppp.object Class of Point Patterns
spruces Spruces Point Pattern
subset.fasp Extract Subset of Function Array
psp.object Class of Line Segment Patterns
hamster Aherne's hamster tumour data
print.im Print Brief Details of an Image
subset.listof Extract or Replace Subset of a List of Things
midpoints.psp Midpoints of Line Segment Pattern
ppm Fit Point Process Model to Data
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
scanpp Read Point Pattern From Data File
Kest K-function
Jcross Multitype J Function (i-to-j)
rNeymanScott Simulate Neyman-Scott Process
as.im Convert to Pixel Image
eval.im Evaluate Expression Involving Pixel Images
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
bdist.pixels Distance to Boundary of Window
vertices Vertices of a Window
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
rescale.owin Convert Window to Another Unit of Length
subset.psp Extract Subset of Line Segment Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
square Square Window
subset.ppp Extract or Replace Subset of Point Pattern
rpoisline Generate Poisson Random Line Process
expand.owin Expand Window By Factor
summary.psp Summary of a Line Segment Pattern Dataset
redwoodfull California Redwoods Point Pattern (Entire Dataset)
setcov Set Covariance of a Window
DiggleGratton Diggle-Gratton model
as.psp Convert Data To Class psp
cells Biological Cells Point Pattern
envelope Simulation envelopes of summary function
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
shift.psp Apply Vector Translation To Line Segment Pattern
Poisson Poisson Point Process Model
spatstat-deprecated Deprecated spatstat functions
finpines Pine saplings in Finland.
is.marked Test Whether Marks Are Present
rescale.psp Convert Line Segment Pattern to Another Unit of Length
demopat Artificial Data Point Pattern
rMaternII Simulate Matern Model II
gridcentres Rectangular grid of points
is.marked.ppm Test Whether A Point Process Model is Marked
plot.ppp plot a Spatial Point Pattern
reduced.sample Reduced Sample Estimator using Histogram Data
plot.splitppp Plot a List of Point Patterns
japanesepines Japanese Pines Point Pattern
rotate.psp Rotate a Line Segment Pattern
anemones Beadlet Anemones Data
plot.quad plot a Spatial Quadrature Scheme
rSSI Simulate Simple Sequential Inhibition
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
multiplicity.ppp Count Multiplicity of Duplicate Points
amacrine Hughes' Amacrine Cell Data
rotate.owin Rotate a Window
ord.family Ord Interaction Process Family
rpoispp Generate Poisson Point Pattern
summary.splitppp Summary of a Split Point Pattern
affine.owin Apply Affine Transformation To Window
lengths.psp Lengths of Line Segments
harmonic Basis for Harmonic Functions
rshift.ppp Randomly Shift a Point Pattern
Saturated Saturated Pairwise Interaction model
kaplan.meier Kaplan-Meier Estimator using Histogram Data
Ord Generic Ord Interaction model
pcf Pair Correlation Function
print.owin Print Brief Details of a Spatial Window
owin Create a Window
rshift.psp Randomly Shift a Line Segment Pattern
ppm.object Class of Fitted Point Process Models
print.psp Print Brief Details of a Line Segment Pattern Dataset
ripras Estimate window from points alone
rpoint Generate N Random Points
runifdisc Generate N Uniform Random Points in a Disc
subset.im Extract Subset of Image
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
density.psp Kernel Smoothing of Line Segment Pattern
levelset Level Set of a Pixel Image
bounding.box Bounding Box of a Window or Point Pattern
ppp Create a Point Pattern
ganglia Beta Ganglion Cells in Cat Retina, Old Version
units Name for Unit of Length
spokes Spokes pattern of dummy points
crossdist.psp Pairwise distances between two different line segment patterns
interp.im Interpolate a Pixel Image
allstats Calculate four standard summary functions of a point pattern.
pcf.fasp Pair Correlation Function obtained from array of K functions
Jest Estimate the J-function
crossing.psp Crossing Points of Two Line Segment Patterns
coef.ppm Coefficients of Fitted Point Process Model
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
plot.fv Plot Function Valuesn
Pairwise Generic Pairwise Interaction model
lurking Lurking variable plot
pairdist.psp Pairwise distances between line segments
im.object Class of Images
chorley Chorley-Ribble Cancer Data
unique.ppp Extract Unique Points from a Spatial Point Pattern
Kcross Multitype K Function (Cross-type)
is.ppm Test Whether An Object Is A Fitted Point Process Model
rmpoispp Generate Multitype Poisson Point Pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
spatstat.options Internal Options in Spatstat Package
swedishpines Swedish Pines Point Pattern
union.quad Union of Data and Dummy Points
longleaf Longleaf Pines Point Pattern
summary.im Summarizing a Pixel Image
rMaternI Simulate Matern Model I
shift.ppp Apply Vector Translation To Point Pattern
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
bdist.points Distance to Boundary of Window
is.im Test Whether An Object Is A Pixel Image
inside.owin Test Whether Points Are Inside A Window
is.ppp Test Whether An Object Is A Point Pattern
distmap.psp Distance Map of Line Segment Pattern
complement.owin Take Complement of a Window
endpoints.psp Endpoints of Line Segment Pattern
crossdist.ppp Pairwise distances between two different point patterns
humberside Humberside Data on Childhood Leukaemia and Lymphoma
as.mask Pixel Image Approximation of a Window
residualspaper Data and Code From JRSS Discussion Paper on Residuals
pppdist Optimal Match Between Two Point Patterns
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
rThomas Simulate Thomas Process
Softcore The Soft Core Point Process Model
spatstat The Spatstat Package
Kinhom Inhomogeneous K-function
Kcross.inhom Inhomogeneous Cross K Function
ewcdf Weighted Empirical Cumulative Distribution Function
as.ppp Convert Data To Class ppp
fv.object Data Frames of Function Values
eem Exponential Energy Marks
Gest Nearest Neighbour Distance Function G
crossdist Pairwise distances
owin.object Class owin
quantile.im Sample Quantiles of Pixel Image
nndist.psp Nearest neighbour distances between line segments
rmh.ppm Simulate from a Fitted Point Process Model
rMatClust Simulate Matern Cluster Process
convexhull.xy Convex Hull of Points
pairsat.family Saturated Pairwise Interaction Point Process Family
Jdot Multitype J Function (i-to-any)
default.dummy Generate a Default Pattern of Dummy Points
as.rectangle Window Frame
contour.im Contour plot of pixel image
fasp.object Function Arrays for Spatial Patterns
Kdot Multitype K Function (i-to-any)
is.owin Test Whether An Object Is A Window
pcf.fv Pair Correlation Function obtained from K Function
cut.im Convert Pixel Image from Numeric to Factor
quadscheme Generate a Quadrature Scheme from a Point Pattern
progressreport Print Progress Reports
rescue.rectangle Convert Window Back To Rectangle
rlabel Random Re-Labelling of Point Pattern
subset.fv Extract Subset of Function Values
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
trim.rectangle Cut margins from rectangle
shift Apply Vector Translation
pcf.ppp Pair Correlation Function of Point Pattern
concatxy Concatenate x,y Coordinate Vectors
as.matrix.im Convert Pixel Image to Matrix
identify.ppp Identify Points in a Point Pattern
print.quad Print a Quadrature Scheme
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
plot.ppm plot a Fitted Point Process Model
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
rotate Rotate
fitted.ppm Fitted Conditional Intensity for Point Process Model
split.ppp Divide Point Pattern into Sub-patterns
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
print.ppp Print Brief Details of a Point Pattern Dataset
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
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Date 16 March 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Mon Apr 16 17:13:00 2007; adrian

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