spatstat v1.12-0

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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
angles.psp Orientation Angles of Line Segments
Kcross.inhom Inhomogeneous Cross K Function
anova.ppm ANOVA for Fitted Point Process Models
Iest Estimate the I-function
DiggleGratton Diggle-Gratton model
affine Apply Affine Transformation
amacrine Hughes' Amacrine Cell Data
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
Geyer Geyer's Saturation Point Process Model
centroid.owin Centroid of a window
Kdot Multitype K Function (i-to-any)
Poisson Poisson Point Process Model
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
Ord Generic Ord Interaction model
applynbd Apply Function to Every Neighbourhood in a Point Pattern
bounding.box Bounding Box of a Window or Point Pattern
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
compatible.im Test Whether Two Pixel Images Are Compatible
spatstat The Spatstat Package
clickppp Interactively Add Points
humberside Humberside Data on Childhood Leukaemia and Lymphoma
ants Harkness-Isham ants' nests data
data.ppm Extract Original Data from a Fitted Point Process Model
area.owin Area of a Window
alltypes Calculate Statistic for All Types in a Multitype Point Pattern
LennardJones The Lennard-Jones Potential
Gest Nearest Neighbour Distance Function G
distmap Distance Map
as.psp Convert Data To Class psp
Fest Estimate the empty space function F
Strauss The Strauss Point Process Model
as.ppp Convert Data To Class ppp
crossdist.default Pairwise distances between two different sets of points
StraussHard The Strauss / Hard Core Point Process Model
append.psp Combine Two Line Segment Patterns
crossing.psp Crossing Points of Two Line Segment Patterns
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
Kmulti Marked K-Function
MultiStrauss The Multitype Strauss Point Process Model
cells Biological Cells Point Pattern
concatxy Concatenate x,y Coordinate Vectors
Jcross Multitype J Function (i-to-j)
affine.psp Apply Affine Transformation To Line Segment Pattern
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
contour.im Contour plot of pixel image
Gmulti Marked Nearest Neighbour Distance Function
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
as.im Convert to Pixel Image
endpoints.psp Endpoints of Line Segment Pattern
affine.ppp Apply Affine Transformation To Point Pattern
Softcore The Soft Core Point Process Model
as.matrix.im Convert Pixel Image to Matrix
demopat Artificial Data Point Pattern
complement.owin Take Complement of a Window
bdist.pixels Distance to Boundary of Window
affine.owin Apply Affine Transformation To Window
erode.owin Erode a Window
hamster Aherne's hamster tumour data
ewcdf Weighted Empirical Cumulative Distribution Function
crossdist.psp Pairwise distances between two different line segment patterns
Kest K-function
eem Exponential Energy Marks
coef.ppm Coefficients of Fitted Point Process Model
gridcentres Rectangular grid of points
corners Corners of a rectangle
ganglia Beta Ganglion Cells in Cat Retina, Old Version
Lest L-function
Kinhom Inhomogeneous K-function
spatstat-deprecated Deprecated spatstat functions
distmap.ppp Distance Map of Point Pattern
betacells Beta Ganglion Cells in Cat Retina
Kdot.inhom Inhomogeneous Multitype K Dot Function
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
fv.object Data Frames of Function Values
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
allstats Calculate four standard summary functions of a point pattern.
pcf.fasp Pair Correlation Function obtained from array of K functions
crossdist.ppp Pairwise distances between two different point patterns
levelset Level Set of a Pixel Image
eval.fv Evaluate Expression Involving Functions
fasp.object Function Arrays for Spatial Patterns
fitted.ppm Fitted Conditional Intensity for Point Process Model
expand.owin Expand Window By Factor
Jmulti Marked J Function
density.ppp Kernel Smoothed Intensity of Point Pattern
bounding.box.xy Convex Hull of Points
cut.im Convert Pixel Image from Numeric to Factor
Jdot Multitype J Function (i-to-any)
is.multitype.ppm Test Whether A Point Process Model is Multitype
as.mask Pixel Image Approximation of a Window
dilate.owin Dilate a Window
envelope Simulation envelopes of summary function
is.owin Test Whether An Object Is A Window
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
Kmeasure Reduced Second Moment Measure
spatstat-internal Internal spatstat functions
print.ppm Print a Fitted Point Process Model
Kcross Multitype K Function (Cross-type)
copper Berman-Huntington points and lines data
Kest.fft K-function using FFT
as.data.frame.ppp Coerce Point Pattern to a Data Frame
is.marked.ppm Test Whether A Point Process Model is Marked
predict.ppm Prediction from a Fitted Point Process Model
bdist.points Distance to Boundary of Window
inside.owin Test Whether Points Are Inside A Window
Pairwise Generic Pairwise Interaction model
kaplan.meier Kaplan-Meier Estimator using Histogram Data
Saturated Saturated Pairwise Interaction model
anemones Beadlet Anemones Data
as.rectangle Window Frame
convexhull.xy Convex Hull of Points
distmap.owin Distance Map of Window
psp Create a Line Segment Pattern
bramblecanes Hutchings' Bramble Canes data
runifpoint Generate N Uniform Random Points
Jest Estimate the J-function
OrdThresh Ord's Interaction model
chorley Chorley-Ribble Cancer Data
bei Tropical rain forest trees
distmap.psp Distance Map of Line Segment Pattern
is.im Test Whether An Object Is A Pixel Image
mean.im Mean Pixel Value in an Image
interp.im Interpolate a Pixel Image
pairwise.family Pairwise Interaction Process Family
plot.fasp Plot a Function Array
clarkevans Clark and Evans Aggregation Index
quadscheme Generate a Quadrature Scheme from a Point Pattern
nearest.raster.point Find Pixel Nearest to a Given Point
fitin.ppm Extract the Interaction from a Fitted Point Process Model
plot.quad plot a Spatial Quadrature Scheme
diameter Diameter of a Window
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
rescale.owin Convert Window to Another Unit of Length
is.multitype Test whether Object is Multitype
im Create a Pixel Image Object
compatible.fv Test Whether Two Function Objects Are Compatible
ppm Fit Point Process Model to Data
persp.im Perspective Plot of Pixel Image
gridweights Compute Quadrature Weights Based on Grid Counts
rshift Random Shift
plot.fv Plot Function Valuesn
pairdist.psp Pairwise distances between line segments
markcorr Mark Correlation Function
rMatClust Simulate Matern Cluster Process
japanesepines Japanese Pines Point Pattern
discretise Safely Convert Point Pattern Window to Binary Mask
pppdist Optimal Match Between Two Point Patterns
plot.owin Plot a Spatial Window
eval.im Evaluate Expression Involving Pixel Images
rescale.ppp Convert Point Pattern to Another Unit of Length
disc Circular Window
plot.plotppm Plot a plotppm Object Created by plot.ppm
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
profilepl Profile Maximum Pseudolikelihood
rStrauss Perfect Simulation of the Strauss Process
hyperframe Hyper Data Frame
quad.object Class of Quadrature Schemes
hist.im Histogram of Pixel Values in an Image
redwood California Redwoods Point Pattern (Ripley's Subset)
lansing Lansing Woods Point Pattern
nndist.psp Nearest neighbour distances between line segments
owin.object Class owin
multiplicity.ppp Count Multiplicity of Duplicate Points
rMaternII Simulate Matern Model II
rmpoint Generate N Random Multitype Points
ponderosa Ponderosa Pine Tree Point Pattern
rSSI Simulate Simple Sequential Inhibition
unmark Remove Marks from a Marked Point Pattern
pairdist.ppp Pairwise distances
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
union.quad Union of Data and Dummy Points
reach Interaction Distance of a Point Process
print.im Print Brief Details of an Image
ks.test.ppm Kolmogorov-Smirnov Test for Point Process Model
shift.ppp Apply Vector Translation To Point Pattern
nncross Nearest Neighbour in Another Point Pattern
rotate.psp Rotate a Line Segment Pattern
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
quadratcount Quadrat counting for a point pattern
pairsat.family Saturated Pairwise Interaction Point Process Family
is.ppm Test Whether An Object Is A Fitted Point Process Model
rstrat Simulate Stratified Random Point Pattern
midpoints.psp Midpoints of Line Segment Pattern
reduced.sample Reduced Sample Estimator using Histogram Data
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
default.dummy Generate a Default Pattern of Dummy Points
vertices Vertices of a Window
shift.im Apply Vector Translation To Pixel Image
cut.ppp Convert Point Pattern Marks from Numeric to Factor
density.psp Kernel Smoothing of Line Segment Pattern
is.marked Test Whether Marks Are Present
nndist Nearest neighbour distances
pairdist Pairwise distances
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
split.ppp Divide Point Pattern into Sub-patterns
update.ppm Update a Fitted Point Process Model
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
is.multitype.ppp Test Whether A Point Pattern is Multitype
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
print.quad Print a Quadrature Scheme
logLik.ppm Log Likelihood for Poisson Point Process Model
lurking Lurking variable plot
nztrees New Zealand Trees Point Pattern
finpines Pine saplings in Finland.
clickpoly Interactively Define a Polygon
is.ppp Test Whether An Object Is A Point Pattern
intersect.owin Intersection or Union of Two Windows
plot.hyperframe Plot Entries in a Hyperframe
subset.im Extract Subset of Image
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
plot.im Plot a Pixel Image
letterR Window in Shape of Letter R
as.owin Convert Data To Class owin
eroded.areas Areas of Morphological Erosions
is.subset.owin Determine Whether One Window is Contained In Another
ord.family Ord Interaction Process Family
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
ppm.object Class of Fitted Point Process Models
rescue.rectangle Convert Window Back To Rectangle
crossdist Pairwise distances
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
shift Apply Vector Translation
im.object Class of Images
plot.listof Plot a List of Things
plot.psp plot a Spatial Line Segment Pattern
localK Neighbourhood density function
harmonic Basis for Harmonic Functions
rotate.owin Rotate a Window
lengths.psp Lengths of Line Segments
shift.owin Apply Vector Translation To Window
subset.ppp Extract or Replace Subset of Point Pattern
rcell Simulate Baddeley-Silverman Cell Process
pcf.fv Pair Correlation Function obtained from K Function
rthin Random Thinning
longleaf Longleaf Pines Point Pattern
nbfires Point Patterns of New Brunswick Forest Fires
swedishpines Swedish Pines Point Pattern
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
subsetget.im Reset Values in Subset of Image
summary.listof Summary of a List of Things
spruces Spruces Point Pattern
print.owin Print Brief Details of a Spatial Window
shift.psp Apply Vector Translation To Line Segment Pattern
rlabel Random Re-Labelling of Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
print.psp Print Brief Details of a Line Segment Pattern Dataset
summary.splitppp Summary of a Split Point Pattern
rlinegrid Generate grid of parallel lines with random displacement
smooth.ppp Spatial smoothing of observations at irregular points
rsyst Simulate systematic random point pattern
pcf Pair Correlation Function
selfcrossing.psp Crossing Points in a Line Segment Pattern
plot.ppm plot a Fitted Point Process Model
plot.ppp plot a Spatial Point Pattern
subset.listof Extract or Replace Subset of a List of Things
summary.ppm Summarizing a Fitted Point Process Model
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
superimpose Superimpose Several Point Patterns
redwoodfull California Redwoods Point Pattern (Entire Dataset)
rotate Rotate
unique.ppp Extract Unique Points from a Spatial Point Pattern
rpoint Generate N Random Points
square Square Window
setcov Set Covariance of a Window
rotate.ppp Rotate a Point Pattern
rshift.splitppp Randomly Shift a List of Point Patterns
thomas.estK Fit the Thomas Point Process by Minimum Contrast
ppp Create a Point Pattern
rNeymanScott Simulate Neyman-Scott Process
trim.rectangle Cut margins from rectangle
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
rescale.psp Convert Line Segment Pattern to Another Unit of Length
identify.ppp Identify Points in a Point Pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
plot.splitppp Plot a List of Point Patterns
owin Create a Window
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
simdat Simulated Point Pattern
is.marked.ppp Test Whether A Point Pattern is Marked
psp.object Class of Line Segment Patterns
progressreport Print Progress Reports
scanpp Read Point Pattern From Data File
rmh.ppm Simulate from a Fitted Point Process Model
raster.x Cartesian Coordinates for a Pixel Raster
rpoispp Generate Poisson Point Pattern
pairdist.default Pairwise distances
mincontrast Method of Minimum Contrast
ppp.object Class of Point Patterns
summary.ppp Summary of a Point Pattern Dataset
spokes Spokes pattern of dummy points
print.ppp Print Brief Details of a Point Pattern Dataset
rescale Convert dataset to another unit of length
quantile.im Sample Quantiles of Pixel Image
runifdisc Generate N Uniform Random Points in a Disc
summary.quad Summarizing a Quadrature Scheme
units Name for Unit of Length
spatstat.options Internal Options in Spatstat Package
rThomas Simulate Thomas Process
rshift.ppp Randomly Shift a Point Pattern
nnwhich Nearest neighbour
pcf.ppp Pair Correlation Function of Point Pattern
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
subset.fv Extract Subset of Function Values
rmpoispp Generate Multitype Poisson Point Pattern
rMaternI Simulate Matern Model I
rpoisline Generate Poisson Random Line Process
rshift.psp Randomly Shift a Line Segment Pattern
setmarks Set or Reset the Marks in a Point Pattern
subset.psp Extract Subset of Line Segment Pattern
subset.splitppp Extract or Replace Sub-Patterns
residualspaper Data and Code From JRSS Discussion Paper on Residuals
ripras Estimate window from points alone
residuals.ppm Residuals for Fitted Point Process Model
suffstat Sufficient Statistic of Point Process Model
subset.fasp Extract Subset of Function Array
summary.owin Summary of a Spatial Window
summary.im Summarizing a Pixel Image
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
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Date 20 August 2007
License GPL version 2 or newer
URL http://www.spatstat.org
Packaged Tue Aug 21 01:58:23 2007; adrian

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