spatstat v1.14-4

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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
as.mask Pixel Image Approximation of a Window
matchingdist Distance for a Point Pattern Matching
chorley Chorley-Ribble Cancer Data
ppp Create a Point Pattern
plot.kppm Plot a fitted cluster point process
OrdThresh Ord's Interaction model
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
murchison Murchison gold deposits
Saturated Saturated Pairwise Interaction model
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
areadiff Difference of Disc Areas
Gest Nearest Neighbour Distance Function G
quantile.im Sample Quantiles of Pixel Image
as.rectangle Window Frame
rMatClust Simulate Matern Cluster Process
Kinhom Inhomogeneous K-function
predict.ppm Prediction from a Fitted Point Process Model
compatible.fv Test Whether Two Function Objects Are Compatible
demopat Artificial Data Point Pattern
persp.im Perspective Plot of Pixel Image
copper Berman-Huntington points and lines data
pairwise.family Pairwise Interaction Process Family
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
rescale.im Convert Pixel Image to Another Unit of Length
adaptive.density Intensity Estimate of Point Pattern Using Tessellation
distmap.psp Distance Map of Line Segment Pattern
applynbd Apply Function to Every Neighbourhood in a Point Pattern
Kmeasure Reduced Second Moment Measure
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
psp.object Class of Line Segment Patterns
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
density.ppp Kernel Smoothed Intensity of Point Pattern
lengths.psp Lengths of Line Segments
density.psp Kernel Smoothing of Line Segment Pattern
is.multitype.ppp Test Whether A Point Pattern is Multitype
Jest Estimate the J-function
affine Apply Affine Transformation
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
owin.object Class owin
as.im Convert to Pixel Image
Poisson Poisson Point Process Model
Linhom L-function
StraussHard The Strauss / Hard Core Point Process Model
clickpoly Interactively Define a Polygon
cut.im Convert Pixel Image from Numeric to Factor
bei Tropical rain forest trees
Kmulti Marked K-Function
multiplicity.ppp Count Multiplicity of Duplicate Points
anova.ppm ANOVA for Fitted Point Process Models
with.fv Evaluate an Expression in a Function Table
letterR Window in Shape of Letter R
rlabel Random Re-Labelling of Point Pattern
Softcore The Soft Core Point Process Model
nbfires Point Patterns of New Brunswick Forest Fires
allstats Calculate four standard summary functions of a point pattern.
Kest K-function
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
affine.ppp Apply Affine Transformation To Point Pattern
ants Harkness-Isham ants' nests data
print.im Print Brief Details of an Image
blur Apply Gaussian Blur to a Pixel Image
erode.owin Erode a Window
Kest.fft K-function using FFT
distmap.owin Distance Map of Window
as.ppp Convert Data To Class ppp
crossdist Pairwise distances
Geyer Geyer's Saturation Point Process Model
fasp.object Function Arrays for Spatial Patterns
anemones Beadlet Anemones Data
cut.ppp Classify Points in a Point Pattern
gridcentres Rectangular grid of points
Kcross.inhom Inhomogeneous Cross K Function
spatstat-internal Internal spatstat functions
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
as.matrix.im Convert Pixel Image to Matrix
plot.ppp plot a Spatial Point Pattern
bdist.pixels Distance to Boundary of Window
finpines Pine saplings in Finland.
convexhull.xy Convex Hull of Points
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
delaunay Delaunay Triangulation of Point Pattern
discretise Safely Convert Point Pattern Window to Binary Mask
quadscheme Generate a Quadrature Scheme from a Point Pattern
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
is.marked.ppp Test Whether A Point Pattern is Marked
distmap.ppp Distance Map of Point Pattern
ord.family Ord Interaction Process Family
print.ppm Print a Fitted Point Process Model
is.owin Test Whether An Object Is A Window
rescale Convert dataset to another unit of length
hist.im Histogram of Pixel Values in an Image
crossing.psp Crossing Points of Two Line Segment Patterns
corners Corners of a rectangle
reduced.sample Reduced Sample Estimator using Histogram Data
residuals.ppm Residuals for Fitted Point Process Model
plot.fasp Plot a Function Array
concatxy Concatenate x,y Coordinate Vectors
diameter Diameter of a Window
Kdot.inhom Inhomogeneous Multitype K Dot Function
plot.psp plot a Spatial Line Segment Pattern
Lcross Multitype L-function (cross-type)
endpoints.psp Endpoints of Line Segment Pattern
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
model.matrix.ppm Extract Design Matrix from Point Process Model
pcf Pair Correlation Function
quadrats Divide Region into Quadrats
default.dummy Generate a Default Pattern of Dummy Points
ganglia Beta Ganglion Cells in Cat Retina, Old Version
rGaussPoisson Simulate Gauss-Poisson Process
print.ppp Print Brief Details of a Point Pattern Dataset
Fest Estimate the empty space function F
pppdist Distance Between Two Point Patterns
pcfcross Multitype pair correlation function
pairsat.family Saturated Pairwise Interaction Point Process Family
rsyst Simulate systematic random point pattern
is.im Test Whether An Object Is A Pixel Image
clickppp Interactively Add Points
Kdot Multitype K Function (i-to-any)
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
crossdist.default Pairwise distances between two different sets of points
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
rNeymanScott Simulate Neyman-Scott Process
levelset Level Set of a Pixel Image
hyperframe Hyper Data Frame
fitin.ppm Extract the Interaction from a Fitted Point Process Model
Gmulti Marked Nearest Neighbour Distance Function
envelope Simulation envelopes of summary function
dirichlet Dirichlet Tessellation of Point Pattern
Jmulti Marked J Function
is.marked Test Whether Marks Are Present
disc Circular Window
identify.ppp Identify Points in a Point Pattern
interp.im Interpolate a Pixel Image
longleaf Longleaf Pines Point Pattern
quadratcount Quadrat counting for a point pattern
markcorr Mark Correlation Function
Ldot Multitype L-function (i-to-any)
midpoints.psp Midpoints of Line Segment Pattern
as.data.frame.ppp Coerce Point Pattern to a Data Frame
quadratresample Resample a Point Pattern by Resampling Quadrats
rshift.ppp Randomly Shift a Point Pattern
DiggleGratton Diggle-Gratton model
nearest.raster.point Find Pixel Nearest to a Given Point
rpoispp Generate Poisson Point Pattern
by.im Apply Function to Image Broken Down by Factor
Lest L-function
Kcross Multitype K Function (Cross-type)
is.subset.owin Determine Whether One Window is Contained In Another
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
angles.psp Orientation Angles of Line Segments
pcf.fv Pair Correlation Function obtained from K Function
nnwhich Nearest neighbour
data.ppm Extract Original Data from a Fitted Point Process Model
lurking Lurking variable plot
bdist.points Distance to Boundary of Window
model.images Compute Images of Constructed Covariates
shift Apply Vector Translation
split.im Divide Image Into Sub-images
eval.fasp Evaluate Expression Involving Function Arrays
cells Biological Cells Point Pattern
summary.psp Summary of a Line Segment Pattern Dataset
runifdisc Generate N Uniform Random Points in a Disc
crossdist.ppp Pairwise distances between two different point patterns
MultiStrauss The Multitype Strauss Point Process Model
ponderosa Ponderosa Pine Tree Point Pattern
logLik.ppm Log Likelihood for Poisson Point Process Model
Pairwise Generic Pairwise Interaction model
dilate.owin Dilate a Window
Ord Generic Ord Interaction model
eval.fv Evaluate Expression Involving Functions
affine.psp Apply Affine Transformation To Line Segment Pattern
rotate Rotate
intersect.owin Intersection or Union of Two Windows
Strauss The Strauss Point Process Model
pppmatching.object Class of Point Matchings
rmpoispp Generate Multitype Poisson Point Pattern
subset.im Extract Subset of Image
subset.psp Extract Subset of Line Segment Pattern
subset.splitppp Extract or Replace Sub-Patterns
rescale.ppp Convert Point Pattern to Another Unit of Length
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
im.object Class of Images
fv.object Data Frames of Function Values
plot.plotppm Plot a plotppm Object Created by plot.ppm
summary.splitppp Summary of a Split Point Pattern
clarkevans Clark and Evans Aggregation Index
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
bramblecanes Hutchings' Bramble Canes data
hamster Aherne's hamster tumour data
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
nndist.psp Nearest neighbour distances between line segments
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
is.ppp Test Whether An Object Is A Point Pattern
pixelquad Quadrature Scheme Based on Pixel Grid
plot.im Plot a Pixel Image
area.owin Area of a Window
plot.splitppp Plot a List of Point Patterns
unmark Remove Marks from a Marked Point Pattern
is.multitype.ppm Test Whether A Point Process Model is Multitype
harmonic Basis for Harmonic Functions
Jdot Multitype J Function (i-to-any)
quad.object Class of Quadrature Schemes
is.ppm Test Whether An Object Is A Fitted Point Process Model
as.owin Convert Data To Class owin
progressreport Print Progress Reports
lansing Lansing Woods Point Pattern
BadGey Hybrid Geyer Point Process Model
rshift.psp Randomly Shift a Line Segment Pattern
rotate.ppp Rotate a Point Pattern
bounding.box Bounding Box of a Window or Point Pattern
ppm Fit Point Process Model to Data
distmap Distance Map
ripras Estimate window from points alone
rjitter Random Perturbation of a Point Pattern
inside.owin Test Whether Points Are Inside A Window
gpc2owin Convert Polygonal Region into Different Format
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
spatstat The Spatstat Package
expand.owin Expand Window By Factor
nncross Nearest Neighbour in Another Point Pattern
localK Neighbourhood density function
rSSI Simulate Simple Sequential Inhibition
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
vertices Vertices of a Window
Iest Estimate the I-function
mean.im Mean, Median and Range of Pixel Values in an Image
Jcross Multitype J Function (i-to-j)
LennardJones The Lennard-Jones Potential
nztrees New Zealand Trees Point Pattern
nndist Nearest neighbour distances
rmh.ppm Simulate from a Fitted Point Process Model
append.psp Combine Two Line Segment Patterns
betacells Beta Ganglion Cells in Cat Retina
incircle Find Largest Circle Inside Window
bounding.box.xy Convex Hull of Points
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
as.psp Convert Data To Class psp
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
rmpoint Generate N Random Multitype Points
ppp.object Class of Point Patterns
eroded.areas Areas of Morphological Erosions
print.psp Print Brief Details of a Line Segment Pattern Dataset
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
amacrine Hughes' Amacrine Cell Data
centroid.owin Centroid of a window
rpoint Generate N Random Points
compatible.fasp Test Whether Two Function Arrays Are Compatible
compatible.im Test Whether Two Pixel Images Are Compatible
japanesepines Japanese Pines Point Pattern
contour.im Contour plot of pixel image
rthin Random Thinning
pcf.ppp Pair Correlation Function of Point Pattern
reach Interaction Distance of a Point Process
plot.listof Plot a List of Things
coef.ppm Coefficients of Fitted Point Process Model
rpoisline Generate Poisson Random Line Process
ewcdf Weighted Empirical Cumulative Distribution Function
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
redwood California Redwoods Point Pattern (Ripley's Subset)
shift.psp Apply Vector Translation To Line Segment Pattern
[.tess Extract or Replace Subset of Tessellation
setcov Set Covariance of a Window
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
plot.tess Plot a tessellation
selfcrossing.psp Crossing Points in a Line Segment Pattern
eval.im Evaluate Expression Involving Pixel Images
pairdist Pairwise distances
owin Create a Window
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
print.quad Print a Quadrature Scheme
pairdist.psp Pairwise distances between line segments
superimpose Superimpose Several Point Patterns
plot.owin Plot a Spatial Window
is.multitype Test whether Object is Multitype
rMaternII Simulate Matern Model II
spruces Spruces Point Pattern
rotate.owin Rotate a Window
shift.im Apply Vector Translation To Pixel Image
redwoodfull California Redwoods Point Pattern (Entire Dataset)
profilepl Profile Maximum Pseudolikelihood
[.quad Subset of Quadrature Scheme
setmarks Set or Reset the Marks in a Point Pattern
pppmatching Create a Point Matching
rThomas Simulate Thomas Process
fitted.ppm Fitted Conditional Intensity for Point Process Model
inforder.family Infinite Order Interaction Family
rescale.psp Convert Line Segment Pattern to Another Unit of Length
pairdist.default Pairwise distances
pcf.fasp Pair Correlation Function obtained from array of K functions
trim.rectangle Cut margins from rectangle
kaplan.meier Kaplan-Meier Estimator using Histogram Data
rstrat Simulate Stratified Random Point Pattern
rescue.rectangle Convert Window Back To Rectangle
rescale.owin Convert Window to Another Unit of Length
plot.ppm plot a Fitted Point Process Model
runifpoint Generate N Uniform Random Points
mincontrast Method of Minimum Contrast
plot.quad plot a Spatial Quadrature Scheme
eem Exponential Energy Marks
square Square Window
affine.owin Apply Affine Transformation To Window
psp Create a Line Segment Pattern
shift.owin Apply Vector Translation To Window
print.owin Print Brief Details of a Spatial Window
gridweights Compute Quadrature Weights Based on Grid Counts
is.marked.ppm Test Whether A Point Process Model is Marked
spatstat.options Internal Options in Spatstat Package
kppm Fit cluster point process model
update.kppm Update a Fitted Cluster Point Process Model
summary.owin Summary of a Spatial Window
subset.fv Extract Subset of Function Values
im Create a Pixel Image Object
suffstat Sufficient Statistic of Point Process Model
summary.ppm Summarizing a Fitted Point Process Model
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
complement.owin Take Complement of a Window
update.ppm Update a Fitted Point Process Model
unitname Name for Unit of Length
crossdist.psp Pairwise distances between two different line segment patterns
urkiola Urkiola Woods Point Pattern
plot.fv Plot Function Valuesn
split.ppp Divide Point Pattern into Sub-patterns
subset.listof Extract or Replace Subset of a List of Things
spatstat-deprecated Deprecated spatstat functions
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
ppm.object Class of Fitted Point Process Models
rlinegrid Generate grid of parallel lines with random displacement
rMaternI Simulate Matern Model I
summary.listof Summary of a List of Things
subset.fasp Extract Subset of Function Array
shift.ppp Apply Vector Translation To Point Pattern
swedishpines Swedish Pines Point Pattern
rStrauss Perfect Simulation of the Strauss Process
raster.x Cartesian Coordinates for a Pixel Raster
smooth.ppp Spatial smoothing of observations at irregular points
humberside Humberside Data on Childhood Leukaemia and Lymphoma
unique.ppp Extract Unique Points from a Spatial Point Pattern
union.quad Union of Data and Dummy Points
residualspaper Data and Code From JRSS Discussion Paper on Residuals
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
pairdist.ppp Pairwise distances
rotate.psp Rotate a Line Segment Pattern
stieltjes Compute Integral of Function Against Cumulative Distribution
predict.kppm Prediction from a Fitted Cluster Point Process Model
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
plot.hyperframe Plot Entries in a Hyperframe
simulate.kppm Simulate a fitted cluster point process model.
summary.ppp Summary of a Point Pattern Dataset
spokes Spokes pattern of dummy points
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
tess Create a Tessellation
rcell Simulate Baddeley-Silverman Cell Process
rshift Random Shift
scanpp Read Point Pattern From Data File
rshift.splitppp Randomly Shift a List of Point Patterns
simdat Simulated Point Pattern
subset.ppp Extract or Replace Subset of Point Pattern
summary.im Summarizing a Pixel Image
thomas.estK Fit the Thomas Point Process by Minimum Contrast
subsetget.im Reset Values in Subset of Image
tiles Extract List of Tiles in a Tessellation
summary.quad Summarizing a Quadrature Scheme
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Date 16 October 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Fri Oct 17 12:12:15 2008; adrian

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