spatstat v1.15-1

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

Date 31 March 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Wed Apr 1 16:05:39 2009; adrian
Repository CRAN
Date/Publication 2009-04-01 11:43:18

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