spatstat v1.12-2

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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 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
Geyer Geyer's Saturation Point Process Model
as.ppp Convert Data To Class ppp
cut.ppp Convert Point Pattern Marks from Numeric to Factor
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
midpoints.psp Midpoints of Line Segment Pattern
plot.hyperframe Plot Entries in a Hyperframe
plot.fasp Plot a Function Array
rshift Random Shift
rmpoint Generate N Random Multitype Points
shift.ppp Apply Vector Translation To Point Pattern
affine.ppp Apply Affine Transformation To Point Pattern
corners Corners of a rectangle
clickppp Interactively Add Points
smooth.ppp Spatial smoothing of observations at irregular points
demopat Artificial Data Point Pattern
Fest Estimate the empty space function F
as.data.frame.ppp Coerce Point Pattern to a Data Frame
as.owin Convert Data To Class owin
spruces Spruces Point Pattern
update.ppm Update a Fitted Point Process Model
bounding.box Bounding Box of a Window or Point Pattern
bdist.points Distance to Boundary of Window
Kest K-function
affine.psp Apply Affine Transformation To Line Segment Pattern
clickpoly Interactively Define a Polygon
crossing.psp Crossing Points of Two Line Segment Patterns
im Create a Pixel Image Object
contour.im Contour plot of pixel image
eroded.areas Areas of Morphological Erosions
mean.im Mean Pixel Value in an Image
envelope Simulation envelopes of summary function
pairdist Pairwise distances
hamster Aherne's hamster tumour data
is.multitype.ppp Test Whether A Point Pattern is Multitype
Kdot Multitype K Function (i-to-any)
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
pairdist.psp Pairwise distances between line segments
plot.owin Plot a Spatial Window
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
multiplicity.ppp Count Multiplicity of Duplicate Points
print.im Print Brief Details of an Image
plot.ppp plot a Spatial Point Pattern
density.psp Kernel Smoothing of Line Segment Pattern
spatstat-deprecated Deprecated spatstat functions
Jcross Multitype J Function (i-to-j)
Jdot Multitype J Function (i-to-any)
gridweights Compute Quadrature Weights Based on Grid Counts
plot.plotppm Plot a plotppm Object Created by plot.ppm
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
angles.psp Orientation Angles of Line Segments
as.matrix.im Convert Pixel Image to Matrix
pairsat.family Saturated Pairwise Interaction Point Process Family
fitin.ppm Extract the Interaction from a Fitted Point Process Model
eval.fv Evaluate Expression Involving Functions
diameter Diameter of a Window
discretise Safely Convert Point Pattern Window to Binary Mask
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
plot.splitppp Plot a List of Point Patterns
quad.object Class of Quadrature Schemes
eem Exponential Energy Marks
superimpose Superimpose Several Point Patterns
subset.im Extract Subset of Image
as.psp Convert Data To Class psp
is.marked.ppm Test Whether A Point Process Model is Marked
gridcentres Rectangular grid of points
localK Neighbourhood density function
anemones Beadlet Anemones Data
allstats Calculate four standard summary functions of a point pattern.
ripras Estimate window from points alone
pcf.fasp Pair Correlation Function obtained from array of K functions
print.ppp Print Brief Details of a Point Pattern Dataset
rotate.owin Rotate a Window
fv.object Data Frames of Function Values
rshift.psp Randomly Shift a Line Segment Pattern
rthin Random Thinning
rSSI Simulate Simple Sequential Inhibition
quantile.im Sample Quantiles of Pixel Image
harmonic Basis for Harmonic Functions
Ord Generic Ord Interaction model
redwood California Redwoods Point Pattern (Ripley's Subset)
rescale.ppp Convert Point Pattern to Another Unit of Length
shift.im Apply Vector Translation To Pixel Image
Kmulti Marked K-Function
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Kmeasure Reduced Second Moment Measure
compatible.fv Test Whether Two Function Objects Are Compatible
humberside Humberside Data on Childhood Leukaemia and Lymphoma
as.im Convert to Pixel Image
Kdot.inhom Inhomogeneous Multitype K Dot Function
bramblecanes Hutchings' Bramble Canes data
clarkevans Clark and Evans Aggregation Index
letterR Window in Shape of Letter R
pairwise.family Pairwise Interaction Process Family
im.object Class of Images
as.rectangle Window Frame
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
crossdist Pairwise distances
complement.owin Take Complement of a Window
nbfires Point Patterns of New Brunswick Forest Fires
distmap Distance Map
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
Jest Estimate the J-function
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
bounding.box.xy Convex Hull of Points
owin Create a Window
MultiStrauss The Multitype Strauss Point Process Model
erode.owin Erode a Window
plot.listof Plot a List of Things
profilepl Profile Maximum Pseudolikelihood
fasp.object Function Arrays for Spatial Patterns
ants Harkness-Isham ants' nests data
cut.im Convert Pixel Image from Numeric to Factor
inside.owin Test Whether Points Are Inside A Window
setcov Set Covariance of a Window
subset.ppp Extract or Replace Subset of Point Pattern
Kcross.inhom Inhomogeneous Cross K Function
suffstat Sufficient Statistic of Point Process Model
hist.im Histogram of Pixel Values in an Image
subsetget.im Reset Values in Subset of Image
nndist.psp Nearest neighbour distances between line segments
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
unmark Remove Marks from a Marked Point Pattern
owin.object Class owin
Kinhom Inhomogeneous K-function
expand.owin Expand Window By Factor
Strauss The Strauss Point Process Model
subset.splitppp Extract or Replace Sub-Patterns
vertices Vertices of a Window
copper Berman-Huntington points and lines data
Jmulti Marked J Function
identify.ppp Identify Points in a Point Pattern
simdat Simulated Point Pattern
dilate.owin Dilate a Window
endpoints.psp Endpoints of Line Segment Pattern
amacrine Hughes' Amacrine Cell Data
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
ewcdf Weighted Empirical Cumulative Distribution Function
DiggleGratton Diggle-Gratton model
spatstat The Spatstat Package
summary.ppp Summary of a Point Pattern Dataset
japanesepines Japanese Pines Point Pattern
Iest Estimate the I-function
interp.im Interpolate a Pixel Image
ganglia Beta Ganglion Cells in Cat Retina, Old Version
lansing Lansing Woods Point Pattern
OrdThresh Ord's Interaction model
data.ppm Extract Original Data from a Fitted Point Process Model
concatxy Concatenate x,y Coordinate Vectors
nnwhich Nearest neighbour
hyperframe Hyper Data Frame
subset.psp Extract Subset of Line Segment Pattern
ppp Create a Point Pattern
spatstat-internal Internal spatstat functions
summary.listof Summary of a List of Things
ord.family Ord Interaction Process Family
summary.psp Summary of a Line Segment Pattern Dataset
psp Create a Line Segment Pattern
pcf Pair Correlation Function
ppp.object Class of Point Patterns
pcf.fv Pair Correlation Function obtained from K Function
StraussHard The Strauss / Hard Core Point Process Model
pppdist Distance Between Two Point Patterns
rThomas Simulate Thomas Process
append.psp Combine Two Line Segment Patterns
print.quad Print a Quadrature Scheme
crossdist.default Pairwise distances between two different sets of points
redwoodfull California Redwoods Point Pattern (Entire Dataset)
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
is.im Test Whether An Object Is A Pixel Image
fitted.ppm Fitted Conditional Intensity for Point Process Model
is.multitype Test whether Object is Multitype
predict.ppm Prediction from a Fitted Point Process Model
kaplan.meier Kaplan-Meier Estimator using Histogram Data
levelset Level Set of a Pixel Image
is.subset.owin Determine Whether One Window is Contained In Another
swedishpines Swedish Pines Point Pattern
matchingdist Distance for a Point Pattern Matching
mincontrast Method of Minimum Contrast
nndist Nearest neighbour distances
pcf.ppp Pair Correlation Function of Point Pattern
logLik.ppm Log Likelihood for Poisson Point Process Model
rNeymanScott Simulate Neyman-Scott Process
rMaternII Simulate Matern Model II
nztrees New Zealand Trees Point Pattern
plot.quad plot a Spatial Quadrature Scheme
nearest.raster.point Find Pixel Nearest to a Given Point
ponderosa Ponderosa Pine Tree Point Pattern
plot.im Plot a Pixel Image
affine Apply Affine Transformation
residuals.ppm Residuals for Fitted Point Process Model
rstrat Simulate Stratified Random Point Pattern
rStrauss Perfect Simulation of the Strauss Process
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
setmarks Set or Reset the Marks in a Point Pattern
chorley Chorley-Ribble Cancer Data
reduced.sample Reduced Sample Estimator using Histogram Data
convexhull.xy Convex Hull of Points
runifdisc Generate N Uniform Random Points in a Disc
summary.im Summarizing a Pixel Image
subset.fasp Extract Subset of Function Array
is.marked Test Whether Marks Are Present
rescale.owin Convert Window to Another Unit of Length
thomas.estK Fit the Thomas Point Process by Minimum Contrast
reach Interaction Distance of a Point Process
quadratcount Quadrat counting for a point pattern
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
print.owin Print Brief Details of a Spatial Window
print.psp Print Brief Details of a Line Segment Pattern Dataset
Softcore The Soft Core Point Process Model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
print.ppm Print a Fitted Point Process Model
rcell Simulate Baddeley-Silverman Cell Process
quadscheme Generate a Quadrature Scheme from a Point Pattern
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
distmap.ppp Distance Map of Point Pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
trim.rectangle Cut margins from rectangle
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rescue.rectangle Convert Window Back To Rectangle
rpoispp Generate Poisson Point Pattern
subset.listof Extract or Replace Subset of a List of Things
pairdist.ppp Pairwise distances
pairdist.default Pairwise distances
rmpoispp Generate Multitype Poisson Point Pattern
rlinegrid Generate grid of parallel lines with random displacement
rsyst Simulate systematic random point pattern
shift.psp Apply Vector Translation To Line Segment Pattern
rpoint Generate N Random Points
rotate.ppp Rotate a Point Pattern
plot.psp plot a Spatial Line Segment Pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
union.quad Union of Data and Dummy Points
rMatClust Simulate Matern Cluster Process
unique.ppp Extract Unique Points from a Spatial Point Pattern
raster.x Cartesian Coordinates for a Pixel Raster
rlabel Random Re-Labelling of Point Pattern
centroid.owin Centroid of a window
bdist.pixels Distance to Boundary of Window
crossdist.psp Pairwise distances between two different line segment patterns
shift Apply Vector Translation
summary.splitppp Summary of a Split Point Pattern
density.ppp Kernel Smoothed Intensity of Point Pattern
eval.im Evaluate Expression Involving Pixel Images
is.ppm Test Whether An Object Is A Fitted Point Process Model
markcorr Mark Correlation Function
ppm Fit Point Process Model to Data
pppmatching.object Class of Point Matchings
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
rpoisline Generate Poisson Random Line Process
split.ppp Divide Point Pattern into Sub-patterns
spatstat.options Internal Options in Spatstat Package
Gest Nearest Neighbour Distance Function G
LennardJones The Lennard-Jones Potential
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
Saturated Saturated Pairwise Interaction model
affine.owin Apply Affine Transformation To Window
crossdist.ppp Pairwise distances between two different point patterns
default.dummy Generate a Default Pattern of Dummy Points
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
distmap.psp Distance Map of Line Segment Pattern
progressreport Print Progress Reports
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
residualspaper Data and Code From JRSS Discussion Paper on Residuals
rmh.ppm Simulate from a Fitted Point Process Model
rshift.splitppp Randomly Shift a List of Point Patterns
runifpoint Generate N Uniform Random Points
subset.fv Extract Subset of Function Values
summary.owin Summary of a Spatial Window
area.owin Area of a Window
bei Tropical rain forest trees
disc Circular Window
is.multitype.ppm Test Whether A Point Process Model is Multitype
is.ppp Test Whether An Object Is A Point Pattern
persp.im Perspective Plot of Pixel Image
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
rescale.psp Convert Line Segment Pattern to Another Unit of Length
rescale Convert dataset to another unit of length
shift.owin Apply Vector Translation To Window
rotate.psp Rotate a Line Segment Pattern
square Square Window
summary.quad Summarizing a Quadrature Scheme
Lest L-function
as.mask Pixel Image Approximation of a Window
Pairwise Generic Pairwise Interaction model
cells Biological Cells Point Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
finpines Pine saplings in Finland.
is.marked.ppp Test Whether A Point Pattern is Marked
lurking Lurking variable plot
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
ppm.object Class of Fitted Point Process Models
rotate Rotate
summary.ppm Summarizing a Fitted Point Process Model
unitname Name for Unit of Length
Gmulti Marked Nearest Neighbour Distance Function
Kest.fft K-function using FFT
betacells Beta Ganglion Cells in Cat Retina
Poisson Poisson Point Process Model
coef.ppm Coefficients of Fitted Point Process Model
distmap.owin Distance Map of Window
nncross Nearest Neighbour in Another Point Pattern
longleaf Longleaf Pines Point Pattern
plot.ppm plot a Fitted Point Process Model
rMaternI Simulate Matern Model I
spokes Spokes pattern of dummy points
Kcross Multitype K Function (Cross-type)
anova.ppm ANOVA for Fitted Point Process Models
applynbd Apply Function to Every Neighbourhood in a Point Pattern
intersect.owin Intersection or Union of Two Windows
is.owin Test Whether An Object Is A Window
pppmatching Create a Point Matching
plot.fv Plot Function Valuesn
lengths.psp Lengths of Line Segments
psp.object Class of Line Segment Patterns
rshift.ppp Randomly Shift a Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
scanpp Read Point Pattern From Data File
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Date 26 October 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Sat Oct 27 01:15:04 2007; adrian

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