spatstat v1.9-6

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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
Kcross.inhom Inhomogeneous Cross K Function
Iest Estimate the I-function
as.matrix.im Convert Pixel Image to Matrix
Kest K-function
gridcentres Rectangular grid of points
corners Corners of a rectangle
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
betacells Beta Ganglion Cells in Cat Retina
as.ppp Convert Data To Class ppp
Pairwise Generic Pairwise Interaction model
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
as.owin Convert Data To Class owin
Gmulti Marked Nearest Neighbour Distance Function
longleaf Longleaf Pines Point Pattern
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
fv.object Data Frames of Function Values
LennardJones The Lennard-Jones Potential
inside.owin Test Whether Points Are Inside A Window
distmap.ppp Distance Map of Point Pattern
nnwhich Nearest neighbour
MultiStrauss The Multitype Strauss Point Process Model
Strauss The Strauss Point Process Model
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
applynbd Apply Function to Every Neighbourhood in a Point Pattern
amacrine Hughes' Amacrine Cell Data
distmap.owin Distance Map of Window
Poisson Poisson Point Process Model
plot.ppm plot a Fitted Point Process Model
rshift.psp Randomly Shift a Line Segment Pattern
plot.splitppp Plot a List of Point Patterns
summary.ppp Summary of a Point Pattern Dataset
is.ppp Test Whether An Object Is A Point Pattern
bramblecanes Hutchings' Bramble Canes data
dilate.owin Dilate a Window
bounding.box Bounding Box of a Window
ants Harkness-Isham ants' nests data
rMatClust Simulate Matern Cluster Process
density.ppp Kernel Smoothed Intensity of Point Pattern
nndist Nearest neighbour distances
intersect.owin Intersection or Union of Two Windows
cells Biological Cells Point Pattern
ppp.object Class of Point Patterns
fitted.ppm Fitted Conditional Intensity for Point Process Model
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
pppdist Optimal Match Between Two Point Patterns
humberside Humberside Data on Childhood Leukaemia and Lymphoma
rNeymanScott Simulate Neyman-Scott Process
reduced.sample Reduced Sample Estimator using Histogram Data
runifpoint Generate N Uniform Random Points
quadscheme Generate a Quadrature Scheme from a Point Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
letterR Window in Shape of Letter R
crossdist.ppp Pairwise distances between two different point patterns
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
distmap Distance Map
rStrauss Perfect Simulation of the Strauss Process
mincontrast Method of Minimum Contrast
rMaternI Simulate Matern Model I
gridweights Compute Quadrature Weights Based on Grid Counts
spatstat-deprecated Deprecated spatstat functions
quad.object Class of Quadrature Schemes
pairdist.ppp Pairwise distances
expand.owin Expand Window By Factor
rpoisline Generate Poisson Random Line Process
simdat Simulated Point Pattern
rmpoint Generate N Random Multitype Points
redwood California Redwoods Point Pattern (Ripley's Subset)
print.ppm Print a Fitted Point Process Model
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
summary.owin Summary of a Spatial Window
selfcrossing.psp Crossing Points in a Line Segment Pattern
eroded.areas Areas of Morphological Erosions
rlabel Random Re-Labelling of Point Pattern
rshift Random Shift
shift.psp Apply Vector Translation To Line Segment Pattern
Jdot Multitype J Function (i-to-any)
plot.quad plot a Spatial Quadrature Scheme
append.psp Combine Two Line Segment Patterns
eval.im Evaluate Expression Involving Pixel Images
hamster Aherne's hamster tumour data
is.owin Test Whether An Object Is A Window
scanpp Read Point Pattern From Data File
complement.owin Take Complement of a Window
subset.fasp Extract Subset of Function Array
pairsat.family Saturated Pairwise Interaction Point Process Family
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
residualspaper Data and Code From JRSS Discussion Paper on Residuals
pcf Pair Correlation Function
split.ppp Divide Point Pattern into Sub-patterns
rmpoispp Generate Multitype Poisson Point Pattern
rmh.ppm Simulate from a Fitted Point Process Model
rotate Rotate
pcf.fasp Pair Correlation Function obtained from array of K functions
plot.im Plot a Pixel Image
plot.psp plot a Spatial Line Segment Pattern
print.owin Print Brief Details of a Spatial Window
plot.fv Plot Function Valuesn
print.quad Print a Quadrature Scheme
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
psp.object Class of Line Segment Patterns
psp Create a Line Segment Pattern
ppm.object Class of Fitted Point Process Models
rescue.rectangle Convert Window Back To Rectangle
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
nztrees New Zealand Trees Point Pattern
subset.psp Extract Subset of Line Segment Pattern
rshift.ppp Randomly Shift a Point Pattern
Kest.fft K-function using FFT
rotate.ppp Rotate a Point Pattern
plot.listof Plot a List of Things
raster.x Cartesian Coordinates for a Pixel Raster
residuals.ppm Residuals for Fitted Point Process Model
quadratcount Quadrat counting for a point pattern
setmarks Set or Reset the Marks in a Point Pattern
Jcross Multitype J Function (i-to-j)
Saturated Saturated Pairwise Interaction model
summary.im Summarizing a Pixel Image
affine.ppp Apply Affine Transformation To Point Pattern
hist.im Histogram of Pixel Values in an Image
pcf.ppp Pair Correlation Function of Point Pattern
shift.im Apply Vector Translation To Pixel Image
Ord Generic Ord Interaction model
rpoint Generate N Random Points
pairdist Pairwise distances
angles.psp Orientation Angles of Line Segments
Kmulti Marked K-Function
anova.ppm ANOVA for Fitted Point Process Models
bei Tropical rain forest trees
is.marked.ppp Test Whether A Point Pattern is Marked
shift.ppp Apply Vector Translation To Point Pattern
superimpose Superimpose Several Point Patterns
as.mask Pixel Image Approximation of a Window
area.owin Area of a Window
as.rectangle Window Frame
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
distmap.psp Distance Map of Line Segment Pattern
im Create a Pixel Image Object
ganglia Beta Ganglion Cells in Cat Retina, Old Version
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Gest Nearest Neighbour Distance Function G
crossdist.psp Pairwise distances between two different line segment patterns
erode.owin Erode a Window
affine.owin Apply Affine Transformation To Window
fasp.object Function Arrays for Spatial Patterns
lengths.psp Lengths of Line Segments
lurking Lurking variable plot
eval.fv Evaluate Expression Involving Functions
owin Create a Window
lansing Lansing Woods Point Pattern
square Square Window
ord.family Ord Interaction Process Family
spruces Spruces Point Pattern
pcf.fv Pair Correlation Function obtained from K Function
is.marked Test Whether Marks Are Present
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
plot.ppp plot a Spatial Point Pattern
rotate.psp Rotate a Line Segment Pattern
setcov Set Covariance of a Window
spokes Spokes pattern of dummy points
rsyst Simulate systematic random point pattern
shift.owin Apply Vector Translation To Window
rMaternII Simulate Matern Model II
print.psp Print Brief Details of a Line Segment Pattern Dataset
StraussHard The Strauss / Hard Core Point Process Model
affine Apply Affine Transformation
diameter Diameter of a Window Frame
density.psp Kernel Smoothing of Line Segment Pattern
identify.ppp Identify Points in a Point Pattern
is.subset.owin Determine Whether One Window is Contained In Another
envelope Simulation envelopes of summary function
japanesepines Japanese Pines Point Pattern
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
quantile.im Sample Quantiles of Pixel Image
redwoodfull California Redwoods Point Pattern (Entire Dataset)
spatstat The Spatstat Package
summary.psp Summary of a Line Segment Pattern Dataset
Kdot Multitype K Function (i-to-any)
as.im Convert to Pixel Image
cut.ppp Convert Point Pattern Marks from Numeric to Factor
centroid.owin Centroid of a window
Jest Estimate the J-function
levelset Level Set of a Pixel Image
eem Exponential Energy Marks
pairdist.default Pairwise distances
coef.ppm Coefficients of Fitted Point Process Model
swedishpines Swedish Pines Point Pattern
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
pairwise.family Pairwise Interaction Process Family
Kmeasure Reduced Second Moment Measure
subset.fv Extract Subset of Function Values
crossing.psp Crossing Points of Two Line Segment Patterns
print.ppp Print Brief Details of a Point Pattern Dataset
chorley Chorley-Ribble Cancer Data
crossdist Pairwise distances
rshift.splitppp Randomly Shift a List of Point Patterns
subset.ppp Extract or Replace Subset of Point Pattern
nncross Nearest Neighbour in Another Point Pattern
print.im Print Brief Details of an Image
rcell Simulate Baddeley-Silverman Cell Process
Kdot.inhom Inhomogeneous Multitype K Dot Function
Kinhom Inhomogeneous K-function
affine.psp Apply Affine Transformation To Line Segment Pattern
Softcore The Soft Core Point Process Model
concatxy Concatenate x,y Coordinate Vectors
demopat Artificial Data Point Pattern
spatstat-internal Internal spatstat functions
data.ppm Extract Original Data from a Fitted Point Process Model
shift Apply Vector Translation
rstrat Simulate Stratified Random Point Pattern
summary.quad Summarizing a Quadrature Scheme
Geyer Geyer's Saturation Point Process Model
Kcross Multitype K Function (Cross-type)
as.psp Convert Data To Class psp
contour.im Contour plot of pixel image
default.dummy Generate a Default Pattern of Dummy Points
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
is.im Test Whether An Object Is A Pixel Image
multiplicity.ppp Count Multiplicity of Duplicate Points
kaplan.meier Kaplan-Meier Estimator using Histogram Data
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
rThomas Simulate Thomas Process
subset.im Extract Subset of Image
plot.owin Plot a Spatial Window
trim.rectangle Cut margins from rectangle
summary.ppm Summarizing a Fitted Point Process Model
is.marked.ppm Test Whether A Point Process Model is Marked
rthin Random Thinning
compatible.im Test Whether Two Pixel Images Are Compatible
DiggleGratton Diggle-Gratton model
allstats Calculate four standard summary functions of a point pattern.
copper Berman-Huntington points and lines data
ppp Create a Point Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
compatible.fv Test Whether Two Function Objects Are Compatible
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
mean.im Mean Pixel Value in an Image
OrdThresh Ord's Interaction model
Fest Estimate the empty space function F
bdist.points Distance to Boundary of Window
cut.im Convert Pixel Image from Numeric to Factor
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
is.ppm Test Whether An Object Is A Fitted Point Process Model
suffstat Sufficient Statistic of Point Process Model
im.object Class of Images
finpines Pine saplings in Finland.
thomas.estK Fit the Thomas Point Process by Minimum Contrast
rSSI Simulate Simple Sequential Inhibition
Jmulti Marked J Function
clickppp Interactively Add Points
reach Interaction Distance of a Point Process
midpoints.psp Midpoints of Line Segment Pattern
crossdist.default Pairwise distances between two different sets of points
bdist.pixels Distance to Boundary of Window
ppm Fit Point Process Model to Data
ripras Estimate window from points alone
owin.object Class owin
plot.fasp Plot a Function Array
harmonic Basis for Harmonic Functions
endpoints.psp Endpoints of Line Segment Pattern
predict.ppm Prediction from a Fitted Point Process Model
union.quad Union of Data and Dummy Points
update.ppm Update a Fitted Point Process Model
profilepl Profile Maximum Pseudolikelihood
plot.plotppm Plot a plotppm Object Created by plot.ppm
markcorr Mark Correlation Function
rpoispp Generate Poisson Point Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
unique.ppp Extract Unique Points from a Spatial Point Pattern
pairdist.psp Pairwise distances between line segments
persp.im Perspective Plot of Pixel Image
rotate.owin Rotate a Window
unmark Remove Marks from a Marked Point Pattern
spatstat.options Internal Options in Spatstat Package
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Date 27 September 2006
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Wed Sep 27 17:21:44 2006; adrian

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