spatstat v1.10-2

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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
compatible.fv Test Whether Two Function Objects Are Compatible
data.ppm Extract Original Data from a Fitted Point Process Model
density.psp Kernel Smoothing of Line Segment Pattern
chorley Chorley-Ribble Cancer Data
distmap.psp Distance Map of Line Segment Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
lansing Lansing Woods Point Pattern
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
plot.splitppp Plot a List of Point Patterns
quadratcount Quadrat counting for a point pattern
redwood California Redwoods Point Pattern (Ripley's Subset)
rotate Rotate
subset.im Extract Subset of Image
spatstat The Spatstat Package
spokes Spokes pattern of dummy points
unique.ppp Extract Unique Points from a Spatial Point Pattern
MultiStrauss The Multitype Strauss Point Process Model
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
area.owin Area of a Window
crossing.psp Crossing Points of Two Line Segment Patterns
envelope Simulation envelopes of summary function
cut.ppp Convert Point Pattern Marks from Numeric to Factor
is.im Test Whether An Object Is A Pixel Image
pairdist.default Pairwise distances
rMaternII Simulate Matern Model II
plot.owin Plot a Spatial Window
selfcrossing.psp Crossing Points in a Line Segment Pattern
harmonic Basis for Harmonic Functions
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
rcell Simulate Baddeley-Silverman Cell Process
affine.owin Apply Affine Transformation To Window
rpoint Generate N Random Points
summary.ppp Summary of a Point Pattern Dataset
as.im Convert to Pixel Image
quantile.im Sample Quantiles of Pixel Image
pcf.fasp Pair Correlation Function obtained from array of K functions
superimpose Superimpose Several Point Patterns
Kmulti Marked K-Function
StraussHard The Strauss / Hard Core Point Process Model
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
profilepl Profile Maximum Pseudolikelihood
psp.object Class of Line Segment Patterns
quad.object Class of Quadrature Schemes
rshift.splitppp Randomly Shift a List of Point Patterns
runifpoint Generate N Uniform Random Points
pairdist.ppp Pairwise distances
rshift.ppp Randomly Shift a Point Pattern
ppp.object Class of Point Patterns
summary.quad Summarizing a Quadrature Scheme
thomas.estK Fit the Thomas Point Process by Minimum Contrast
as.ppp Convert Data To Class ppp
coef.ppm Coefficients of Fitted Point Process Model
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
distmap.owin Distance Map of Window
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
affine.ppp Apply Affine Transformation To Point Pattern
is.marked Test Whether Marks Are Present
Kest K-function
betacells Beta Ganglion Cells in Cat Retina
complement.owin Take Complement of a Window
nnwhich Nearest neighbour
eem Exponential Energy Marks
spatstat-internal Internal spatstat functions
lengths.psp Lengths of Line Segments
crossdist.psp Pairwise distances between two different line segment patterns
levelset Level Set of a Pixel Image
density.ppp Kernel Smoothed Intensity of Point Pattern
Jdot Multitype J Function (i-to-any)
print.ppp Print Brief Details of a Point Pattern Dataset
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
quadscheme Generate a Quadrature Scheme from a Point Pattern
Kmeasure Reduced Second Moment Measure
residualspaper Data and Code From JRSS Discussion Paper on Residuals
letterR Window in Shape of Letter R
runifdisc Generate N Uniform Random Points in a Disc
crossdist.ppp Pairwise distances between two different point patterns
shift.im Apply Vector Translation To Pixel Image
anova.ppm ANOVA for Fitted Point Process Models
japanesepines Japanese Pines Point Pattern
demopat Artificial Data Point Pattern
lurking Lurking variable plot
subset.fasp Extract Subset of Function Array
pairdist.psp Pairwise distances between line segments
Saturated Saturated Pairwise Interaction model
rMaternI Simulate Matern Model I
rpoispp Generate Poisson Point Pattern
append.psp Combine Two Line Segment Patterns
swedishpines Swedish Pines Point Pattern
as.matrix.im Convert Pixel Image to Matrix
subset.ppp Extract or Replace Subset of Point Pattern
bei Tropical rain forest trees
rThomas Simulate Thomas Process
suffstat Sufficient Statistic of Point Process Model
rstrat Simulate Stratified Random Point Pattern
spatstat-deprecated Deprecated spatstat functions
expand.owin Expand Window By Factor
Iest Estimate the I-function
dilate.owin Dilate a Window
Softcore The Soft Core Point Process Model
Kest.fft K-function using FFT
identify.ppp Identify Points in a Point Pattern
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
midpoints.psp Midpoints of Line Segment Pattern
Strauss The Strauss Point Process Model
summary.psp Summary of a Line Segment Pattern Dataset
Jcross Multitype J Function (i-to-j)
print.ppm Print a Fitted Point Process Model
square Square Window
shift Apply Vector Translation
trim.rectangle Cut margins from rectangle
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
pcf.fv Pair Correlation Function obtained from K Function
crossdist.default Pairwise distances between two different sets of points
fv.object Data Frames of Function Values
unmark Remove Marks from a Marked Point Pattern
plot.fasp Plot a Function Array
ord.family Ord Interaction Process Family
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
print.psp Print Brief Details of a Line Segment Pattern Dataset
raster.x Cartesian Coordinates for a Pixel Raster
shift.psp Apply Vector Translation To Line Segment Pattern
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
applynbd Apply Function to Every Neighbourhood in a Point Pattern
pppdist Optimal Match Between Two Point Patterns
shift.ppp Apply Vector Translation To Point Pattern
rotate.psp Rotate a Line Segment Pattern
clickppp Interactively Add Points
summary.owin Summary of a Spatial Window
summary.ppm Summarizing a Fitted Point Process Model
copper Berman-Huntington points and lines data
subset.fv Extract Subset of Function Values
distmap Distance Map
rNeymanScott Simulate Neyman-Scott Process
diameter Diameter of a Window Frame
eval.fv Evaluate Expression Involving Functions
intersect.owin Intersection or Union of Two Windows
Kdot.inhom Inhomogeneous Multitype K Dot Function
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
plot.ppp plot a Spatial Point Pattern
print.owin Print Brief Details of a Spatial Window
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
Kcross Multitype K Function (Cross-type)
as.mask Pixel Image Approximation of a Window
LennardJones The Lennard-Jones Potential
crossdist Pairwise distances
default.dummy Generate a Default Pattern of Dummy Points
gridcentres Rectangular grid of points
fasp.object Function Arrays for Spatial Patterns
is.ppp Test Whether An Object Is A Point Pattern
Jest Estimate the J-function
Poisson Poisson Point Process Model
nearest.raster.point Find Pixel Nearest to a Given Point
bramblecanes Hutchings' Bramble Canes data
nztrees New Zealand Trees Point Pattern
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
rsyst Simulate systematic random point pattern
is.marked.ppp Test Whether A Point Pattern is Marked
is.ppm Test Whether An Object Is A Fitted Point Process Model
is.multitype.ppp Test Whether A Point Pattern is Multitype
mean.im Mean Pixel Value in an Image
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
ppp Create a Point Pattern
scanpp Read Point Pattern From Data File
ripras Estimate window from points alone
shift.owin Apply Vector Translation To Window
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
summary.im Summarizing a Pixel Image
setcov Set Covariance of a Window
Ord Generic Ord Interaction model
as.psp Convert Data To Class psp
corners Corners of a rectangle
allstats Calculate four standard summary functions of a point pattern.
as.owin Convert Data To Class owin
contour.im Contour plot of pixel image
concatxy Concatenate x,y Coordinate Vectors
bdist.points Distance to Boundary of Window
bdist.pixels Distance to Boundary of Window
eroded.areas Areas of Morphological Erosions
ganglia Beta Ganglion Cells in Cat Retina, Old Version
print.im Print Brief Details of an Image
gridweights Compute Quadrature Weights Based on Grid Counts
plot.quad plot a Spatial Quadrature Scheme
pcf Pair Correlation Function
ppm Fit Point Process Model to Data
setmarks Set or Reset the Marks in a Point Pattern
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
reduced.sample Reduced Sample Estimator using Histogram Data
rotate.owin Rotate a Window
Gest Nearest Neighbour Distance Function G
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
ants Harkness-Isham ants' nests data
hamster Aherne's hamster tumour data
plot.im Plot a Pixel Image
plot.listof Plot a List of Things
rlabel Random Re-Labelling of Point Pattern
pairwise.family Pairwise Interaction Process Family
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
rotate.ppp Rotate a Point Pattern
rmpoispp Generate Multitype Poisson Point Pattern
split.ppp Divide Point Pattern into Sub-patterns
update.ppm Update a Fitted Point Process Model
Jmulti Marked J Function
Pairwise Generic Pairwise Interaction model
bounding.box Bounding Box of a Window
cells Biological Cells Point Pattern
is.subset.owin Determine Whether One Window is Contained In Another
as.rectangle Window Frame
owin.object Class owin
predict.ppm Prediction from a Fitted Point Process Model
Fest Estimate the empty space function F
OrdThresh Ord's Interaction model
angles.psp Orientation Angles of Line Segments
cut.im Convert Pixel Image from Numeric to Factor
endpoints.psp Endpoints of Line Segment Pattern
eval.im Evaluate Expression Involving Pixel Images
owin Create a Window
plot.psp plot a Spatial Line Segment Pattern
plot.ppm plot a Fitted Point Process Model
print.quad Print a Quadrature Scheme
spruces Spruces Point Pattern
Gmulti Marked Nearest Neighbour Distance Function
amacrine Hughes' Amacrine Cell Data
disc Circular Window
humberside Humberside Data on Childhood Leukaemia and Lymphoma
inside.owin Test Whether Points Are Inside A Window
is.multitype Test whether Object is Multitype
markcorr Mark Correlation Function
nndist Nearest neighbour distances
mincontrast Method of Minimum Contrast
pairsat.family Saturated Pairwise Interaction Point Process Family
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
ppm.object Class of Fitted Point Process Models
redwoodfull California Redwoods Point Pattern (Entire Dataset)
residuals.ppm Residuals for Fitted Point Process Model
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
DiggleGratton Diggle-Gratton model
affine Apply Affine Transformation
finpines Pine saplings in Finland.
hist.im Histogram of Pixel Values in an Image
is.owin Test Whether An Object Is A Window
rStrauss Perfect Simulation of the Strauss Process
pairdist Pairwise distances
rescue.rectangle Convert Window Back To Rectangle
rshift.psp Randomly Shift a Line Segment Pattern
rshift Random Shift
Kdot Multitype K Function (i-to-any)
distmap.ppp Distance Map of Point Pattern
Kinhom Inhomogeneous K-function
im Create a Pixel Image Object
is.marked.ppm Test Whether A Point Process Model is Marked
rMatClust Simulate Matern Cluster Process
reach Interaction Distance of a Point Process
rmh.ppm Simulate from a Fitted Point Process Model
rmpoint Generate N Random Multitype Points
rthin Random Thinning
units Name for Unit of Length
Geyer Geyer's Saturation Point Process Model
Kcross.inhom Inhomogeneous Cross K Function
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
compatible.im Test Whether Two Pixel Images Are Compatible
erode.owin Erode a Window
fitted.ppm Fitted Conditional Intensity for Point Process Model
multiplicity.ppp Count Multiplicity of Duplicate Points
longleaf Longleaf Pines Point Pattern
plot.fv Plot Function Valuesn
psp Create a Line Segment Pattern
im.object Class of Images
rSSI Simulate Simple Sequential Inhibition
rpoisline Generate Poisson Random Line Process
spatstat.options Internal Options in Spatstat Package
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
union.quad Union of Data and Dummy Points
simdat Simulated Point Pattern
subset.psp Extract Subset of Line Segment Pattern
affine.psp Apply Affine Transformation To Line Segment Pattern
centroid.owin Centroid of a window
kaplan.meier Kaplan-Meier Estimator using Histogram Data
nncross Nearest Neighbour in Another Point Pattern
persp.im Perspective Plot of Pixel Image
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
plot.plotppm Plot a plotppm Object Created by plot.ppm
pcf.ppp Pair Correlation Function of Point Pattern
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Date 06 November 2006
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Mon Nov 6 16:58:39 2006; adrian

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