spatstat v1.15-2

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

Date 14 April 2009
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Fri Apr 17 01:34:44 2009; adrian
Repository CRAN
Date/Publication 2009-04-16 08:22:00

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