spatstat v1.14-10

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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
AreaInter The Area Interaction Point Process Model
Geyer Geyer's Saturation Point Process Model
Kest.fft K-function using FFT
by.im Apply Function to Image Broken Down by Factor
Fest Estimate the empty space function F
Kinhom Inhomogeneous K-function
as.im Convert to Pixel Image
as.matrix.im Convert Pixel Image to Matrix
Kcross Multitype K Function (Cross-type)
fv.object Data Frames of Function Values
convexhull.xy Convex Hull of Points
affine Apply Affine Transformation
crossdist.ppp Pairwise distances between two different point patterns
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
LennardJones The Lennard-Jones Potential
harmonic Basis for Harmonic Functions
Pairwise Generic Pairwise Interaction model
DiggleGratton Diggle-Gratton model
Jmulti Marked J Function
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
compatible.fasp Test Whether Two Function Arrays Are Compatible
blur Apply Gaussian Blur to a Pixel Image
pixelquad Quadrature Scheme Based on Pixel Grid
spatstat The Spatstat Package
compatible.im Test Whether Two Pixel Images Are Compatible
StraussHard The Strauss / Hard Core Point Process Model
dirichlet Dirichlet Tessellation of Point Pattern
append.psp Combine Two Line Segment Patterns
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
Gmulti Marked Nearest Neighbour Distance Function
is.im Test Whether An Object Is A Pixel Image
nztrees New Zealand Trees Point Pattern
affine.psp Apply Affine Transformation To Line Segment Pattern
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
pairdist.ppp Pairwise distances
plot.hyperframe Plot Entries in a Hyperframe
clickpoly Interactively Define a Polygon
BadGey Hybrid Geyer Point Process Model
Kest K-function
finpines Pine saplings in Finland.
im Create a Pixel Image Object
kppm Fit cluster point process model
plot.psp plot a Spatial Line Segment Pattern
disc Circular Window
Lest L-function
ewcdf Weighted Empirical Cumulative Distribution Function
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
Jest Estimate the J-function
levelset Level Set of a Pixel Image
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
plot.owin Plot a Spatial Window
Gest Nearest Neighbour Distance Function G
gridweights Compute Quadrature Weights Based on Grid Counts
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
Linhom L-function
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
nearestsegment Find Line Segment Nearest to Each Point
rMaternI Simulate Matern Model I
coef.ppm Coefficients of Fitted Point Process Model
bdist.points Distance to Boundary of Window
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
model.images Compute Images of Constructed Covariates
eval.im Evaluate Expression Involving Pixel Images
Kdot.inhom Inhomogeneous Multitype K Dot Function
cells Biological Cells Point Pattern
bounding.box Bounding Box of a Window or Point Pattern
humberside Humberside Data on Childhood Leukaemia and Lymphoma
distmap.owin Distance Map of Window
Strauss The Strauss Point Process Model
as.tess Convert Data To Tessellation
Kmeasure Reduced Second Moment Measure
print.owin Print Brief Details of a Spatial Window
spatstat-internal Internal spatstat functions
Kdot Multitype K Function (i-to-any)
as.mask Pixel Image Approximation of a Window
quantile.im Sample Quantiles of Pixel Image
affine.ppp Apply Affine Transformation To Point Pattern
anova.ppm ANOVA for Fitted Point Process Models
bramblecanes Hutchings' Bramble Canes data
fitin.ppm Extract the Interaction from a Fitted Point Process Model
rescale Convert dataset to another unit of length
nnwhich Nearest neighbour
density.ppp Kernel Smoothed Intensity of Point Pattern
opening.owin Morphological Opening of a Window
delaunay Delaunay Triangulation of Point Pattern
hamster Aherne's hamster tumour data
pairdist.psp Pairwise distances between line segments
Lcross Multitype L-function (cross-type)
cut.ppp Classify Points in a Point Pattern
Ldot Multitype L-function (i-to-any)
anemones Beadlet Anemones Data
thomas.estK Fit the Thomas Point Process by Minimum Contrast
owin Create a Window
rotate.psp Rotate a Line Segment Pattern
rMatClust Simulate Matern Cluster Process
Ord Generic Ord Interaction model
ants Harkness-Isham ants' nests data
identify.ppp Identify Points in a Point Pattern
density.psp Kernel Smoothing of Line Segment Pattern
is.owin Test Whether An Object Is A Window
bounding.box.xy Convex Hull of Points
complement.owin Take Complement of a Window
mean.im Mean, Median and Range of Pixel Values in an Image
affine.owin Apply Affine Transformation To Window
centroid.owin Centroid of a window
closing.owin Morphological Closing of a Window
rlabel Random Re-Labelling of Point Pattern
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
contour.im Contour plot of pixel image
chorley Chorley-Ribble Cancer Data
letterR Window in Shape of Letter R
ppp.object Class of Point Patterns
nndist.psp Nearest neighbour distances between line segments
pointsOnLines Place Points Evenly Along Specified Lines
Jcross Multitype J Function (i-to-j)
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
Iest Estimate the I-function
hist.im Histogram of Pixel Values in an Image
rthin Random Thinning
Kcross.inhom Inhomogeneous Cross K Function
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
clarkevans Clark and Evans Aggregation Index
runifdisc Generate N Uniform Random Points in a Disc
gpc2owin Convert Polygonal Region into Different Format
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
envelope Simulation envelopes of summary function
areadiff Difference of Disc Areas
pcf.fv Pair Correlation Function obtained from K Function
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
pcf.ppp Pair Correlation Function of Point Pattern
compatible.fv Test Whether Two Function Objects Are Compatible
as.rectangle Window Frame
Softcore The Soft Core Point Process Model
endpoints.psp Endpoints of Line Segment Pattern
ppm.object Class of Fitted Point Process Models
cut.im Convert Pixel Image from Numeric to Factor
clickppp Interactively Add Points
rNeymanScott Simulate Neyman-Scott Process
diameter Diameter of a Window
is.ppp Test Whether An Object Is A Point Pattern
distmap.psp Distance Map of Line Segment Pattern
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
plot.im Plot a Pixel Image
summary.im Summarizing a Pixel Image
rStrauss Perfect Simulation of the Strauss Process
Saturated Saturated Pairwise Interaction model
discretise Safely Convert Point Pattern Window to Binary Mask
concatxy Concatenate x,y Coordinate Vectors
bei Tropical rain forest trees
Kmulti Marked K-Function
corners Corners of a rectangle
expand.owin Expand Window By Factor
plot.splitppp Plot a List of Point Patterns
pppmatching.object Class of Point Matchings
nearest.raster.point Find Pixel Nearest to a Given Point
angles.psp Orientation Angles of Line Segments
copper Berman-Huntington points and lines data
nbfires Point Patterns of New Brunswick Forest Fires
simulate.kppm Simulate a fitted cluster point process model.
quadscheme Generate a Quadrature Scheme from a Point Pattern
default.dummy Generate a Default Pattern of Dummy Points
crossing.psp Crossing Points of Two Line Segment Patterns
square Square Window
quad.object Class of Quadrature Schemes
erode.owin Erode a Window
gridcentres Rectangular grid of points
eroded.areas Areas of Morphological Erosions
Jdot Multitype J Function (i-to-any)
ganglia Beta Ganglion Cells in Cat Retina, Old Version
dilate.owin Dilate a Window
rmpoint Generate N Random Multitype Points
interp.im Interpolate a Pixel Image
ponderosa Ponderosa Pine Tree Point Pattern
fasp.object Function Arrays for Spatial Patterns
is.ppm Test Whether An Object Is A Fitted Point Process Model
MultiStrauss The Multitype Strauss Point Process Model
simdat Simulated Point Pattern
OrdThresh Ord's Interaction model
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
[.quad Subset of Quadrature Scheme
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
applynbd Apply Function to Every Neighbourhood in a Point Pattern
summary.listof Summary of a List of Things
as.owin Convert Data To Class owin
inside.owin Test Whether Points Are Inside A Window
pairdist Pairwise distances
eval.fasp Evaluate Expression Involving Function Arrays
redwoodfull California Redwoods Point Pattern (Entire Dataset)
lengths.psp Lengths of Line Segments
as.psp Convert Data To Class psp
data.ppm Extract Original Data from a Fitted Point Process Model
print.im Print Brief Details of an Image
as.data.frame.ppp Coerce Point Pattern to a Data Frame
crossdist.psp Pairwise distances between two different line segment patterns
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
eem Exponential Energy Marks
incircle Find Largest Circle Inside Window
fitted.ppm Fitted Conditional Intensity for Point Process Model
betacells Beta Ganglion Cells in Cat Retina
lansing Lansing Woods Point Pattern
is.subset.owin Determine Whether One Window is Contained In Another
rescale.ppp Convert Point Pattern to Another Unit of Length
eval.fv Evaluate Expression Involving Functions
area.owin Area of a Window
setcov Set Covariance of a Window
rshift.psp Randomly Shift a Line Segment Pattern
profilepl Profile Maximum Pseudolikelihood
ripras Estimate window from points alone
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rSSI Simulate Simple Sequential Inhibition
hyperframe Hyper Data Frame
urkiola Urkiola Woods Point Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
spokes Spokes pattern of dummy points
lurking Lurking variable plot
selfcrossing.psp Crossing Points in a Line Segment Pattern
is.marked.ppm Test Whether A Point Process Model is Marked
subset.listof Extract or Replace Subset of a List of Things
subset.im Extract Subset of Image
rstrat Simulate Stratified Random Point Pattern
demopat Artificial Data Point Pattern
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
is.multitype Test whether Object is Multitype
rsyst Simulate systematic random point pattern
bdist.pixels Distance to Boundary of Window
summary.quad Summarizing a Quadrature Scheme
kaplan.meier Kaplan-Meier Estimator using Histogram Data
ppp Create a Point Pattern
union.quad Union of Data and Dummy Points
as.ppp Convert Data To Class ppp
inforder.family Infinite Order Interaction Family
plot.fasp Plot a Function Array
plot.listof Plot a List of Things
amacrine Hughes' Amacrine Cell Data
pppdist Distance Between Two Point Patterns
stieltjes Compute Integral of Function Against Cumulative Distribution
midpoints.psp Midpoints of Line Segment Pattern
pcf.fasp Pair Correlation Function obtained from array of K functions
update.kppm Update a Fitted Cluster Point Process Model
crossdist Pairwise distances
matchingdist Distance for a Point Pattern Matching
plot.ppp plot a Spatial Point Pattern
superimposePSP Superimpose Several Line Segment Patterns
im.object Class of Images
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
quadratcount Quadrat counting for a point pattern
logLik.ppm Log Likelihood for Poisson Point Process Model
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
rjitter Random Perturbation of a Point Pattern
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
predict.kppm Prediction from a Fitted Cluster Point Process Model
intersect.tess Intersection of Two Tessellations
markcorr Mark Correlation Function
distmap Distance Map
pairwise.family Pairwise Interaction Process Family
print.ppm Print a Fitted Point Process Model
rescale.psp Convert Line Segment Pattern to Another Unit of Length
pixellate Convert Point Pattern to Pixel Image
superimpose Superimpose Several Point Patterns
pcfcross Multitype pair correlation function
fryplot Fry Plot of Point Pattern
longleaf Longleaf Pines Point Pattern
localK Neighbourhood density function
unique.ppp Extract Unique Points from a Spatial Point Pattern
miplot Morishita Index Plot
ppm Fit Point Process Model to Data
plot.ppm plot a Fitted Point Process Model
plot.quad plot a Spatial Quadrature Scheme
nncross Nearest Neighbour in Another Point Pattern
plot.tess Plot a tessellation
progressreport Print Progress Reports
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
predict.ppm Prediction from a Fitted Point Process Model
summary.psp Summary of a Line Segment Pattern Dataset
distmap.ppp Distance Map of Point Pattern
psp Create a Line Segment Pattern
ord.family Ord Interaction Process Family
intersect.owin Intersection or Union of Two Windows
residualspaper Data and Code From JRSS Discussion Paper on Residuals
multiplicity.ppp Count Multiplicity of Duplicate Points
plot.kppm Plot a fitted cluster point process
is.marked Test Whether Marks Are Present
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
mincontrast Method of Minimum Contrast
murchison Murchison gold deposits
plot.plotppm Plot a plotppm Object Created by plot.ppm
residuals.ppm Residuals for Fitted Point Process Model
project2segment Move Point To Nearest Line
rotate.owin Rotate a Window
print.psp Print Brief Details of a Line Segment Pattern Dataset
print.ppp Print Brief Details of a Point Pattern Dataset
rThomas Simulate Thomas Process
runifpointOnLines Generate N Uniform Random Points On Line Segments
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
model.matrix.ppm Extract Design Matrix from Point Process Model
pppmatching Create a Point Matching
psp.object Class of Line Segment Patterns
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rmh.ppm Simulate from a Fitted Point Process Model
is.marked.ppp Test Whether A Point Pattern is Marked
quadrats Divide Region into Quadrats
is.multitype.ppp Test Whether A Point Pattern is Multitype
rpoisline Generate Poisson Random Line Process
subsetget.im Reset Values in Subset of Image
rcell Simulate Baddeley-Silverman Cell Process
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
reduced.sample Reduced Sample Estimator using Histogram Data
quadrat.test.splitppp Chi-Squared Test of CSR for Split Point Pattern
rescale.owin Convert Window to Another Unit of Length
rlinegrid Generate grid of parallel lines with random displacement
update.ppm Update a Fitted Point Process Model
summary.splitppp Summary of a Split Point Pattern
quadratresample Resample a Point Pattern by Resampling Quadrats
redwood California Redwoods Point Pattern (Ripley's Subset)
rGaussPoisson Simulate Gauss-Poisson Process
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
rescale.im Convert Pixel Image to Another Unit of Length
runifpoint Generate N Uniform Random Points
rshift.splitppp Randomly Shift a List of Point Patterns
owin.object Class owin
nndist Nearest neighbour distances
shift.owin Apply Vector Translation To Window
japanesepines Japanese Pines Point Pattern
rmpoispp Generate Multitype Poisson Point Pattern
rpoispp Generate Poisson Point Pattern
shift.im Apply Vector Translation To Pixel Image
shift.psp Apply Vector Translation To Line Segment Pattern
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
rpoisppOnLines Generate Poisson Point Pattern on Line Segments
persp.im Perspective Plot of Pixel Image
rshift.ppp Randomly Shift a Point Pattern
pairsat.family Saturated Pairwise Interaction Point Process Family
pairdist.default Pairwise distances
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
swedishpines Swedish Pines Point Pattern
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
split.ppp Divide Point Pattern into Sub-patterns
smooth.ppp Spatial smoothing of observations at irregular points
split.im Divide Image Into Sub-images
spatstat.options Internal Options in Spatstat Package
subset.fasp Extract Subset of Function Array
rescue.rectangle Convert Window Back To Rectangle
[.tess Extract or Replace Subset of Tessellation
subset.psp Extract Subset of Line Segment Pattern
summary.owin Summary of a Spatial Window
suffstat Sufficient Statistic of Point Process Model
spruces Spruces Point Pattern
unmark Remove Marks
tess Create a Tessellation
print.quad Print a Quadrature Scheme
trim.rectangle Cut margins from rectangle
raster.x Cartesian Coordinates for a Pixel Raster
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
unitname Name for Unit of Length
Poisson Poisson Point Process Model
allstats Calculate four standard summary functions of a point pattern.
vertices Vertices of a Window
subset.fv Extract Subset of Function Values
reach Interaction Distance of a Point Process
rotate Rotate
spatstat-deprecated Deprecated spatstat functions
crossdist.default Pairwise distances between two different sets of points
rshift Random Shift
scanpp Read Point Pattern From Data File
plot.fv Plot Function Valuesn
summary.ppm Summarizing a Fitted Point Process Model
summary.ppp Summary of a Point Pattern Dataset
rpoint Generate N Random Points
subset.ppp Extract or Replace Subset of Point Pattern
with.fv Evaluate an Expression in a Function Table
tiles Extract List of Tiles in a Tessellation
shift Apply Vector Translation
shift.ppp Apply Vector Translation To Point Pattern
rMaternII Simulate Matern Model II
rotate.ppp Rotate a Point Pattern
setmarks Set or Reset the Marks in a Point Pattern
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
subset.splitppp Extract or Replace Sub-Patterns
pcf Pair Correlation Function
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Date 30 January 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Sat Jan 31 10:38:21 2009; adrian

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