spatstat v1.14-7

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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
unmark Remove Marks
DiggleGratton Diggle-Gratton model
Jmulti Marked J Function
subset.psp Extract Subset of Line Segment Pattern
AreaInter The Area Interaction Point Process Model
MultiStrauss The Multitype Strauss Point Process Model
suffstat Sufficient Statistic of Point Process Model
summary.listof Summary of a List of Things
summary.ppm Summarizing a Fitted Point Process Model
Kest.fft K-function using FFT
as.owin Convert Data To Class owin
summary.ppp Summary of a Point Pattern Dataset
unique.ppp Extract Unique Points from a Spatial Point Pattern
summary.quad Summarizing a Quadrature Scheme
tiles Extract List of Tiles in a Tessellation
diameter Diameter of a Window
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
as.data.frame.ppp Coerce Point Pattern to a Data Frame
with.fv Evaluate an Expression in a Function Table
summary.splitppp Summary of a Split Point Pattern
superimposePSP Superimpose Several Line Segment Patterns
summary.psp Summary of a Line Segment Pattern Dataset
superimpose Superimpose Several Point Patterns
[.tess Extract or Replace Subset of Tessellation
update.kppm Update a Fitted Cluster Point Process Model
trim.rectangle Cut margins from rectangle
inforder.family Infinite Order Interaction Family
tess Create a Tessellation
StraussHard The Strauss / Hard Core Point Process Model
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
markcorr Mark Correlation Function
summary.owin Summary of a Spatial Window
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
union.quad Union of Data and Dummy Points
rstrat Simulate Stratified Random Point Pattern
persp.im Perspective Plot of Pixel Image
summary.im Summarizing a Pixel Image
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
rotate Rotate
update.ppm Update a Fitted Point Process Model
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
urkiola Urkiola Woods Point Pattern
eroded.areas Areas of Morphological Erosions
as.rectangle Window Frame
finpines Pine saplings in Finland.
endpoints.psp Endpoints of Line Segment Pattern
Kdot.inhom Inhomogeneous Multitype K Dot Function
Gmulti Marked Nearest Neighbour Distance Function
Jcross Multitype J Function (i-to-j)
LennardJones The Lennard-Jones Potential
bdist.pixels Distance to Boundary of Window
subsetget.im Reset Values in Subset of Image
disc Circular Window
project2segment Move Point To Nearest Line
spatstat-deprecated Deprecated spatstat functions
quadratcount Quadrat counting for a point pattern
Linhom L-function
Softcore The Soft Core Point Process Model
simulate.kppm Simulate a fitted cluster point process model.
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
Kinhom Inhomogeneous K-function
as.mask Pixel Image Approximation of a Window
bramblecanes Hutchings' Bramble Canes data
mean.im Mean, Median and Range of Pixel Values in an Image
nearest.raster.point Find Pixel Nearest to a Given Point
Jdot Multitype J Function (i-to-any)
fv.object Data Frames of Function Values
hyperframe Hyper Data Frame
eval.im Evaluate Expression Involving Pixel Images
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
BadGey Hybrid Geyer Point Process Model
clickpoly Interactively Define a Polygon
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
nncross Nearest Neighbour in Another Point Pattern
rjitter Random Perturbation of a Point Pattern
Lcross Multitype L-function (cross-type)
rescale.psp Convert Line Segment Pattern to Another Unit of Length
corners Corners of a rectangle
ponderosa Ponderosa Pine Tree Point Pattern
Pairwise Generic Pairwise Interaction model
as.psp Convert Data To Class psp
Iest Estimate the I-function
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
as.im Convert to Pixel Image
compatible.fv Test Whether Two Function Objects Are Compatible
affine.ppp Apply Affine Transformation To Point Pattern
Lest L-function
nearestsegment Find Line Segment Nearest to Each Point
bdist.points Distance to Boundary of Window
Kmulti Marked K-Function
quad.object Class of Quadrature Schemes
applynbd Apply Function to Every Neighbourhood in a Point Pattern
amacrine Hughes' Amacrine Cell Data
Strauss The Strauss Point Process Model
as.tess Convert Data To Tessellation
ants Harkness-Isham ants' nests data
pairdist.ppp Pairwise distances
ord.family Ord Interaction Process Family
quantile.im Sample Quantiles of Pixel Image
distmap.psp Distance Map of Line Segment Pattern
intersect.tess Intersection of Two Tessellations
pppdist Distance Between Two Point Patterns
identify.ppp Identify Points in a Point Pattern
japanesepines Japanese Pines Point Pattern
pairdist.psp Pairwise distances between line segments
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
density.psp Kernel Smoothing of Line Segment Pattern
plot.tess Plot a tessellation
rpoispp Generate Poisson Point Pattern
psp.object Class of Line Segment Patterns
plot.fv Plot Function Valuesn
crossing.psp Crossing Points of Two Line Segment Patterns
pcf.fv Pair Correlation Function obtained from K Function
gpc2owin Convert Polygonal Region into Different Format
convexhull.xy Convex Hull of Points
profilepl Profile Maximum Pseudolikelihood
pcf.ppp Pair Correlation Function of Point Pattern
ppp.object Class of Point Patterns
im.object Class of Images
anova.ppm ANOVA for Fitted Point Process Models
demopat Artificial Data Point Pattern
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
affine.owin Apply Affine Transformation To Window
psp Create a Line Segment Pattern
envelope Simulation envelopes of summary function
erode.owin Erode a Window
centroid.owin Centroid of a window
density.ppp Kernel Smoothed Intensity of Point Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
is.marked.ppp Test Whether A Point Pattern is Marked
OrdThresh Ord's Interaction model
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
crossdist.ppp Pairwise distances between two different point patterns
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
Kmeasure Reduced Second Moment Measure
subset.splitppp Extract or Replace Sub-Patterns
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
as.ppp Convert Data To Class ppp
is.subset.owin Determine Whether One Window is Contained In Another
murchison Murchison gold deposits
rNeymanScott Simulate Neyman-Scott Process
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
print.psp Print Brief Details of a Line Segment Pattern Dataset
shift.im Apply Vector Translation To Pixel Image
runifpoint Generate N Uniform Random Points
eval.fv Evaluate Expression Involving Functions
opening.owin Morphological Opening of a Window
intersect.owin Intersection or Union of Two Windows
shift.owin Apply Vector Translation To Window
crossdist Pairwise distances
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
kppm Fit cluster point process model
cut.ppp Classify Points in a Point Pattern
Ord Generic Ord Interaction model
bei Tropical rain forest trees
bounding.box Bounding Box of a Window or Point Pattern
thomas.estK Fit the Thomas Point Process by Minimum Contrast
is.ppp Test Whether An Object Is A Point Pattern
areadiff Difference of Disc Areas
affine.psp Apply Affine Transformation To Line Segment Pattern
delaunay Delaunay Triangulation of Point Pattern
subset.fv Extract Subset of Function Values
residualspaper Data and Code From JRSS Discussion Paper on Residuals
as.data.frame.psp Coerce Line Segment Pattern to a Data Frame
pcf.fasp Pair Correlation Function obtained from array of K functions
raster.x Cartesian Coordinates for a Pixel Raster
plot.psp plot a Spatial Line Segment Pattern
cut.im Convert Pixel Image from Numeric to Factor
betacells Beta Ganglion Cells in Cat Retina
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
spruces Spruces Point Pattern
lansing Lansing Woods Point Pattern
quadrats Divide Region into Quadrats
interp.im Interpolate a Pixel Image
pcfcross Multitype pair correlation function
chorley Chorley-Ribble Cancer Data
ppm Fit Point Process Model to Data
swedishpines Swedish Pines Point Pattern
selfcrossing.psp Crossing Points in a Line Segment Pattern
matchingdist Distance for a Point Pattern Matching
affine Apply Affine Transformation
bounding.box.xy Convex Hull of Points
rStrauss Perfect Simulation of the Strauss Process
unitname Name for Unit of Length
subset.im Extract Subset of Image
Gest Nearest Neighbour Distance Function G
clickppp Interactively Add Points
pairdist Pairwise distances
rescale Convert dataset to another unit of length
copper Berman-Huntington points and lines data
subset.listof Extract or Replace Subset of a List of Things
discretise Safely Convert Point Pattern Window to Binary Mask
lurking Lurking variable plot
rotate.ppp Rotate a Point Pattern
square Square Window
reduced.sample Reduced Sample Estimator using Histogram Data
shift.psp Apply Vector Translation To Line Segment Pattern
spatstat-internal Internal spatstat functions
nztrees New Zealand Trees Point Pattern
quadratresample Resample a Point Pattern by Resampling Quadrats
ppm.object Class of Fitted Point Process Models
allstats Calculate four standard summary functions of a point pattern.
[.quad Subset of Quadrature Scheme
rmpoint Generate N Random Multitype Points
rshift Random Shift
nbfires Point Patterns of New Brunswick Forest Fires
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
concatxy Concatenate x,y Coordinate Vectors
angles.psp Orientation Angles of Line Segments
rmpoispp Generate Multitype Poisson Point Pattern
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
compatible.fasp Test Whether Two Function Arrays Are Compatible
plot.plotppm Plot a plotppm Object Created by plot.ppm
setcov Set Covariance of a Window
spatstat.options Internal Options in Spatstat Package
mincontrast Method of Minimum Contrast
append.psp Combine Two Line Segment Patterns
pairsat.family Saturated Pairwise Interaction Point Process Family
rpoint Generate N Random Points
spatstat The Spatstat Package
plot.quad plot a Spatial Quadrature Scheme
coef.ppm Coefficients of Fitted Point Process Model
quadscheme Generate a Quadrature Scheme from a Point Pattern
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
Kdot Multitype K Function (i-to-any)
Kest K-function
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rshift.splitppp Randomly Shift a List of Point Patterns
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
rcell Simulate Baddeley-Silverman Cell Process
Jest Estimate the J-function
as.matrix.im Convert Pixel Image to Matrix
Kcross.inhom Inhomogeneous Cross K Function
localK Neighbourhood density function
is.owin Test Whether An Object Is A Window
expand.owin Expand Window By Factor
plot.ppm plot a Fitted Point Process Model
longleaf Longleaf Pines Point Pattern
plot.kppm Plot a fitted cluster point process
split.im Divide Image Into Sub-images
cells Biological Cells Point Pattern
print.im Print Brief Details of an Image
print.ppp Print Brief Details of a Point Pattern Dataset
data.ppm Extract Original Data from a Fitted Point Process Model
closing.owin Morphological Closing of a Window
setmarks Set or Reset the Marks in a Point Pattern
distmap.owin Distance Map of Window
model.images Compute Images of Constructed Covariates
Ldot Multitype L-function (i-to-any)
is.marked Test Whether Marks Are Present
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
redwoodfull California Redwoods Point Pattern (Entire Dataset)
Poisson Poisson Point Process Model
predict.kppm Prediction from a Fitted Cluster Point Process Model
crossdist.default Pairwise distances between two different sets of points
rotate.owin Rotate a Window
eval.fasp Evaluate Expression Involving Function Arrays
crossdist.psp Pairwise distances between two different line segment patterns
by.im Apply Function to Image Broken Down by Factor
plot.im Plot a Pixel Image
contour.im Contour plot of pixel image
blur Apply Gaussian Blur to a Pixel Image
eem Exponential Energy Marks
inside.owin Test Whether Points Are Inside A Window
is.im Test Whether An Object Is A Pixel Image
logLik.ppm Log Likelihood for Poisson Point Process Model
plot.ppp plot a Spatial Point Pattern
rlinegrid Generate grid of parallel lines with random displacement
rMaternII Simulate Matern Model II
rpoisline Generate Poisson Random Line Process
hist.im Histogram of Pixel Values in an Image
predict.ppm Prediction from a Fitted Point Process Model
area.owin Area of a Window
default.dummy Generate a Default Pattern of Dummy Points
is.ppm Test Whether An Object Is A Fitted Point Process Model
pcf Pair Correlation Function
pairwise.family Pairwise Interaction Process Family
humberside Humberside Data on Childhood Leukaemia and Lymphoma
nndist Nearest neighbour distances
Saturated Saturated Pairwise Interaction model
ppp Create a Point Pattern
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
lengths.psp Lengths of Line Segments
kaplan.meier Kaplan-Meier Estimator using Histogram Data
print.ppm Print a Fitted Point Process Model
rMatClust Simulate Matern Cluster Process
is.multitype.ppp Test Whether A Point Pattern is Multitype
letterR Window in Shape of Letter R
rescale.owin Convert Window to Another Unit of Length
dirichlet Dirichlet Tessellation of Point Pattern
rlabel Random Re-Labelling of Point Pattern
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
harmonic Basis for Harmonic Functions
fitted.ppm Fitted Conditional Intensity for Point Process Model
rGaussPoisson Simulate Gauss-Poisson Process
midpoints.psp Midpoints of Line Segment Pattern
shift.ppp Apply Vector Translation To Point Pattern
plot.fasp Plot a Function Array
scanpp Read Point Pattern From Data File
shift Apply Vector Translation
subset.ppp Extract or Replace Subset of Point Pattern
rThomas Simulate Thomas Process
distmap Distance Map
ewcdf Weighted Empirical Cumulative Distribution Function
rmh.ppm Simulate from a Fitted Point Process Model
nndist.psp Nearest neighbour distances between line segments
print.quad Print a Quadrature Scheme
pppmatching.object Class of Point Matchings
rescale.ppp Convert Point Pattern to Another Unit of Length
plot.listof Plot a List of Things
rSSI Simulate Simple Sequential Inhibition
rMaternI Simulate Matern Model I
rescale.im Convert Pixel Image to Another Unit of Length
plot.hyperframe Plot Entries in a Hyperframe
pppmatching Create a Point Matching
ganglia Beta Ganglion Cells in Cat Retina, Old Version
print.owin Print Brief Details of a Spatial Window
rsyst Simulate systematic random point pattern
residuals.ppm Residuals for Fitted Point Process Model
split.ppp Divide Point Pattern into Sub-patterns
stieltjes Compute Integral of Function Against Cumulative Distribution
gridcentres Rectangular grid of points
spokes Spokes pattern of dummy points
Fest Estimate the empty space function F
simdat Simulated Point Pattern
rthin Random Thinning
Geyer Geyer's Saturation Point Process Model
rescue.rectangle Convert Window Back To Rectangle
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
anemones Beadlet Anemones Data
levelset Level Set of a Pixel Image
Kcross Multitype K Function (Cross-type)
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
pairdist.default Pairwise distances
subset.fasp Extract Subset of Function Array
incircle Find Largest Circle Inside Window
owin.object Class owin
complement.owin Take Complement of a Window
hamster Aherne's hamster tumour data
nnwhich Nearest neighbour
pixelquad Quadrature Scheme Based on Pixel Grid
clarkevans Clark and Evans Aggregation Index
is.multitype.ppm Test Whether A Point Process Model is Multitype
dilate.owin Dilate a Window
is.multitype Test whether Object is Multitype
distmap.ppp Distance Map of Point Pattern
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
im Create a Pixel Image Object
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
reach Interaction Distance of a Point Process
fasp.object Function Arrays for Spatial Patterns
is.marked.ppm Test Whether A Point Process Model is Marked
plot.splitppp Plot a List of Point Patterns
owin Create a Window
rshift.psp Randomly Shift a Line Segment Pattern
plot.owin Plot a Spatial Window
runifdisc Generate N Uniform Random Points in a Disc
model.matrix.ppm Extract Design Matrix from Point Process Model
multiplicity.ppp Count Multiplicity of Duplicate Points
rshift.ppp Randomly Shift a Point Pattern
rotate.psp Rotate a Line Segment Pattern
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
ripras Estimate window from points alone
progressreport Print Progress Reports
fitin.ppm Extract the Interaction from a Fitted Point Process Model
gridweights Compute Quadrature Weights Based on Grid Counts
redwood California Redwoods Point Pattern (Ripley's Subset)
smooth.ppp Spatial smoothing of observations at irregular points
vertices Vertices of a Window
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Date 17 November 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Tue Nov 18 03:26:00 2008; adrian

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