spatstat v1.11-5

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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
Jmulti Marked J Function
Kcross Multitype K Function (Cross-type)
as.im Convert to Pixel Image
crossing.psp Crossing Points of Two Line Segment Patterns
OrdThresh Ord's Interaction model
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
Gest Nearest Neighbour Distance Function G
nndist.psp Nearest neighbour distances between line segments
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
cut.im Convert Pixel Image from Numeric to Factor
as.matrix.im Convert Pixel Image to Matrix
Gmulti Marked Nearest Neighbour Distance Function
mincontrast Method of Minimum Contrast
as.psp Convert Data To Class psp
disc Circular Window
density.ppp Kernel Smoothed Intensity of Point Pattern
inside.owin Test Whether Points Are Inside A Window
compatible.fv Test Whether Two Function Objects Are Compatible
intersect.owin Intersection or Union of Two Windows
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
allstats Calculate four standard summary functions of a point pattern.
ripras Estimate window from points alone
Softcore The Soft Core Point Process Model
ppp.object Class of Point Patterns
corners Corners of a rectangle
is.multitype.ppp Test Whether A Point Pattern is Multitype
clickppp Interactively Add Points
centroid.owin Centroid of a window
plot.plotppm Plot a plotppm Object Created by plot.ppm
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
is.subset.owin Determine Whether One Window is Contained In Another
plot.fasp Plot a Function Array
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
distmap.psp Distance Map of Line Segment Pattern
amacrine Hughes' Amacrine Cell Data
reach Interaction Distance of a Point Process
append.psp Combine Two Line Segment Patterns
rpoint Generate N Random Points
area.owin Area of a Window
default.dummy Generate a Default Pattern of Dummy Points
Poisson Poisson Point Process Model
convexhull.xy Convex Hull of Points
print.im Print Brief Details of an Image
compatible.im Test Whether Two Pixel Images Are Compatible
bounding.box.xy Convex Hull of Points
Jest Estimate the J-function
crossdist.ppp Pairwise distances between two different point patterns
distmap.owin Distance Map of Window
subset.fasp Extract Subset of Function Array
fitted.ppm Fitted Conditional Intensity for Point Process Model
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
gridweights Compute Quadrature Weights Based on Grid Counts
expand.owin Expand Window By Factor
demopat Artificial Data Point Pattern
identify.ppp Identify Points in a Point Pattern
eroded.areas Areas of Morphological Erosions
fitin.ppm Extract the Interaction from a Fitted Point Process Model
Kinhom Inhomogeneous K-function
Fest Estimate the empty space function F
Saturated Saturated Pairwise Interaction model
affine Apply Affine Transformation
distmap Distance Map
bramblecanes Hutchings' Bramble Canes data
Kmulti Marked K-Function
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
nearest.raster.point Find Pixel Nearest to a Given Point
Kdot Multitype K Function (i-to-any)
rshift.psp Randomly Shift a Line Segment Pattern
spatstat The Spatstat Package
as.mask Pixel Image Approximation of a Window
crossdist.default Pairwise distances between two different sets of points
ants Harkness-Isham ants' nests data
affine.psp Apply Affine Transformation To Line Segment Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
spatstat-deprecated Deprecated spatstat functions
is.im Test Whether An Object Is A Pixel Image
crossdist.psp Pairwise distances between two different line segment patterns
complement.owin Take Complement of a Window
is.marked Test Whether Marks Are Present
as.ppp Convert Data To Class ppp
longleaf Longleaf Pines Point Pattern
rsyst Simulate systematic random point pattern
DiggleGratton Diggle-Gratton model
is.multitype Test whether Object is Multitype
applynbd Apply Function to Every Neighbourhood in a Point Pattern
is.ppm Test Whether An Object Is A Fitted Point Process Model
ppp Create a Point Pattern
StraussHard The Strauss / Hard Core Point Process Model
LennardJones The Lennard-Jones Potential
print.owin Print Brief Details of a Spatial Window
betacells Beta Ganglion Cells in Cat Retina
bdist.points Distance to Boundary of Window
selfcrossing.psp Crossing Points in a Line Segment Pattern
dilate.owin Dilate a Window
nbfires Point Patterns of New Brunswick Forest Fires
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
owin Create a Window
spatstat-internal Internal spatstat functions
subset.listof Extract or Replace Subset of a List of Things
nnwhich Nearest neighbour
profilepl Profile Maximum Pseudolikelihood
japanesepines Japanese Pines Point Pattern
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
subset.psp Extract Subset of Line Segment Pattern
is.owin Test Whether An Object Is A Window
pcf.fasp Pair Correlation Function obtained from array of K functions
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
pcf.ppp Pair Correlation Function of Point Pattern
Jcross Multitype J Function (i-to-j)
plot.ppm plot a Fitted Point Process Model
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
plot.ppp plot a Spatial Point Pattern
rSSI Simulate Simple Sequential Inhibition
Kest K-function
shift.im Apply Vector Translation To Pixel Image
plot.splitppp Plot a List of Point Patterns
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
bounding.box Bounding Box of a Window or Point Pattern
predict.ppm Prediction from a Fitted Point Process Model
setmarks Set or Reset the Marks in a Point Pattern
plot.fv Plot Function Valuesn
residualspaper Data and Code From JRSS Discussion Paper on Residuals
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
ppm Fit Point Process Model to Data
rescale.psp Convert Line Segment Pattern to Another Unit of Length
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
Kmeasure Reduced Second Moment Measure
data.ppm Extract Original Data from a Fitted Point Process Model
shift Apply Vector Translation
psp Create a Line Segment Pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
Pairwise Generic Pairwise Interaction model
rMaternI Simulate Matern Model I
rMaternII Simulate Matern Model II
plot.psp plot a Spatial Line Segment Pattern
distmap.ppp Distance Map of Point Pattern
pairdist.ppp Pairwise distances
is.marked.ppp Test Whether A Point Pattern is Marked
residuals.ppm Residuals for Fitted Point Process Model
pcf.fv Pair Correlation Function obtained from K Function
rlabel Random Re-Labelling of Point Pattern
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
setcov Set Covariance of a Window
endpoints.psp Endpoints of Line Segment Pattern
envelope Simulation envelopes of summary function
cut.ppp Convert Point Pattern Marks from Numeric to Factor
print.ppp Print Brief Details of a Point Pattern Dataset
summary.quad Summarizing a Quadrature Scheme
rmh.ppm Simulate from a Fitted Point Process Model
psp.object Class of Line Segment Patterns
rotate Rotate
Kdot.inhom Inhomogeneous Multitype K Dot Function
subsetget.im Reset Values in Subset of Image
plot.listof Plot a List of Things
units Name for Unit of Length
ewcdf Weighted Empirical Cumulative Distribution Function
fasp.object Function Arrays for Spatial Patterns
summary.ppm Summarizing a Fitted Point Process Model
Kest.fft K-function using FFT
Kcross.inhom Inhomogeneous Cross K Function
pairdist Pairwise distances
copper Berman-Huntington points and lines data
summary.ppp Summary of a Point Pattern Dataset
progressreport Print Progress Reports
quadscheme Generate a Quadrature Scheme from a Point Pattern
unique.ppp Extract Unique Points from a Spatial Point Pattern
plot.im Plot a Pixel Image
reduced.sample Reduced Sample Estimator using Histogram Data
plot.quad plot a Spatial Quadrature Scheme
chorley Chorley-Ribble Cancer Data
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
Ord Generic Ord Interaction model
diameter Diameter of a Window
rotate.ppp Rotate a Point Pattern
anemones Beadlet Anemones Data
summary.splitppp Summary of a Split Point Pattern
eval.fv Evaluate Expression Involving Functions
Geyer Geyer's Saturation Point Process Model
eem Exponential Energy Marks
angles.psp Orientation Angles of Line Segments
as.owin Convert Data To Class owin
Strauss The Strauss Point Process Model
rmpoispp Generate Multitype Poisson Point Pattern
coef.ppm Coefficients of Fitted Point Process Model
im.object Class of Images
concatxy Concatenate x,y Coordinate Vectors
finpines Pine saplings in Finland.
union.quad Union of Data and Dummy Points
spokes Spokes pattern of dummy points
ord.family Ord Interaction Process Family
rcell Simulate Baddeley-Silverman Cell Process
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
rescale.owin Convert Window to Another Unit of Length
vertices Vertices of a Window
pairdist.psp Pairwise distances between line segments
gridcentres Rectangular grid of points
hist.im Histogram of Pixel Values in an Image
Jdot Multitype J Function (i-to-any)
affine.owin Apply Affine Transformation To Window
rescue.rectangle Convert Window Back To Rectangle
pcf Pair Correlation Function
rmpoint Generate N Random Multitype Points
print.psp Print Brief Details of a Line Segment Pattern Dataset
rThomas Simulate Thomas Process
ganglia Beta Ganglion Cells in Cat Retina, Old Version
eval.im Evaluate Expression Involving Pixel Images
multiplicity.ppp Count Multiplicity of Duplicate Points
levelset Level Set of a Pixel Image
rotate.psp Rotate a Line Segment Pattern
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
nndist Nearest neighbour distances
rotate.owin Rotate a Window
bdist.pixels Distance to Boundary of Window
hamster Aherne's hamster tumour data
im Create a Pixel Image Object
pairsat.family Saturated Pairwise Interaction Point Process Family
crossdist Pairwise distances
fv.object Data Frames of Function Values
markcorr Mark Correlation Function
lurking Lurking variable plot
subset.im Extract Subset of Image
midpoints.psp Midpoints of Line Segment Pattern
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
contour.im Contour plot of pixel image
pairwise.family Pairwise Interaction Process Family
rshift Random Shift
runifdisc Generate N Uniform Random Points in a Disc
bei Tropical rain forest trees
humberside Humberside Data on Childhood Leukaemia and Lymphoma
quantile.im Sample Quantiles of Pixel Image
harmonic Basis for Harmonic Functions
pairdist.default Pairwise distances
rthin Random Thinning
subset.fv Extract Subset of Function Values
owin.object Class owin
summary.psp Summary of a Line Segment Pattern Dataset
letterR Window in Shape of Letter R
nncross Nearest Neighbour in Another Point Pattern
suffstat Sufficient Statistic of Point Process Model
swedishpines Swedish Pines Point Pattern
as.rectangle Window Frame
is.ppp Test Whether An Object Is A Point Pattern
quadratcount Quadrat counting for a point pattern
plot.owin Plot a Spatial Window
redwood California Redwoods Point Pattern (Ripley's Subset)
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
print.ppm Print a Fitted Point Process Model
rpoispp Generate Poisson Point Pattern
shift.psp Apply Vector Translation To Line Segment Pattern
raster.x Cartesian Coordinates for a Pixel Raster
is.marked.ppm Test Whether A Point Process Model is Marked
erode.owin Erode a Window
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
rescale.ppp Convert Point Pattern to Another Unit of Length
summary.im Summarizing a Pixel Image
trim.rectangle Cut margins from rectangle
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
lansing Lansing Woods Point Pattern
rStrauss Perfect Simulation of the Strauss Process
rshift.ppp Randomly Shift a Point Pattern
spruces Spruces Point Pattern
runifpoint Generate N Uniform Random Points
superimpose Superimpose Several Point Patterns
rNeymanScott Simulate Neyman-Scott Process
shift.owin Apply Vector Translation To Window
lengths.psp Lengths of Line Segments
nztrees New Zealand Trees Point Pattern
redwoodfull California Redwoods Point Pattern (Entire Dataset)
Iest Estimate the I-function
affine.ppp Apply Affine Transformation To Point Pattern
rstrat Simulate Stratified Random Point Pattern
MultiStrauss The Multitype Strauss Point Process Model
unmark Remove Marks from a Marked Point Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
shift.ppp Apply Vector Translation To Point Pattern
mean.im Mean Pixel Value in an Image
ppm.object Class of Fitted Point Process Models
persp.im Perspective Plot of Pixel Image
pppdist Optimal Match Between Two Point Patterns
print.quad Print a Quadrature Scheme
rMatClust Simulate Matern Cluster Process
quad.object Class of Quadrature Schemes
scanpp Read Point Pattern From Data File
simdat Simulated Point Pattern
summary.listof Summary of a List of Things
square Square Window
subset.ppp Extract or Replace Subset of Point Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
update.ppm Update a Fitted Point Process Model
anova.ppm ANOVA for Fitted Point Process Models
cells Biological Cells Point Pattern
clickpoly Interactively Define a Polygon
density.psp Kernel Smoothing of Line Segment Pattern
interp.im Interpolate a Pixel Image
kaplan.meier Kaplan-Meier Estimator using Histogram Data
rescale Convert dataset to another unit of length
rshift.splitppp Randomly Shift a List of Point Patterns
rpoisline Generate Poisson Random Line Process
split.ppp Divide Point Pattern into Sub-patterns
subset.splitppp Extract or Replace Sub-Patterns
spatstat.options Internal Options in Spatstat Package
summary.owin Summary of a Spatial Window
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Date 08 May 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Mon May 14 01:36:09 2007; adrian

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