spatstat v1.14-3

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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
murchison Murchison gold deposits
lurking Lurking variable plot
clickppp Interactively Add Points
pcf.ppp Pair Correlation Function of Point Pattern
contour.im Contour plot of pixel image
nncorr Nearest-Neighbour Correlation of Marked Point Pattern
is.marked Test Whether Marks Are Present
as.im Convert to Pixel Image
Kcross.inhom Inhomogeneous Cross K Function
angles.psp Orientation Angles of Line Segments
coef.ppm Coefficients of Fitted Point Process Model
owin.object Class owin
MultiStrauss The Multitype Strauss Point Process Model
hist.im Histogram of Pixel Values in an Image
model.images Compute Images of Constructed Covariates
as.mask Pixel Image Approximation of a Window
mincontrast Method of Minimum Contrast
Lest L-function
rMatClust Simulate Matern Cluster Process
Strauss The Strauss Point Process Model
pairdist.psp Pairwise distances between line segments
Gest Nearest Neighbour Distance Function G
letterR Window in Shape of Letter R
BadGey Hybrid Geyer Point Process Model
Gmulti Marked Nearest Neighbour Distance Function
rpoisline Generate Poisson Random Line Process
centroid.owin Centroid of a window
SatPiece Piecewise Constant Saturated Pairwise Interaction Point Process Model
matchingdist Distance for a Point Pattern Matching
setmarks Set or Reset the Marks in a Point Pattern
midpoints.psp Midpoints of Line Segment Pattern
AreaInter The Area Interaction Point Process Model
duplicated.ppp Determine Duplicated Points in a Spatial Point Pattern
Kest K-function
nndist.psp Nearest neighbour distances between line segments
lansing Lansing Woods Point Pattern
delaunay Delaunay Triangulation of Point Pattern
compatible.im Test Whether Two Pixel Images Are Compatible
kaplan.meier Kaplan-Meier Estimator using Histogram Data
is.marked.ppm Test Whether A Point Process Model is Marked
rotate.ppp Rotate a Point Pattern
markstat Summarise Marks in Every Neighbourhood in a Point Pattern
pcf.fv Pair Correlation Function obtained from K Function
compatible.fasp Test Whether Two Function Arrays Are Compatible
Pairwise Generic Pairwise Interaction model
kstest.ppm Kolmogorov-Smirnov Test for Point Process Model
Kcross Multitype K Function (Cross-type)
plot.listof Plot a List of Things
model.matrix.ppm Extract Design Matrix from Point Process Model
Kmeasure Reduced Second Moment Measure
subset.psp Extract Subset of Line Segment Pattern
default.dummy Generate a Default Pattern of Dummy Points
longleaf Longleaf Pines Point Pattern
fitin.ppm Extract the Interaction from a Fitted Point Process Model
erode.owin Erode a Window
ants Harkness-Isham ants' nests data
pairdist.ppp Pairwise distances
fv.object Data Frames of Function Values
concatxy Concatenate x,y Coordinate Vectors
compatible.fv Test Whether Two Function Objects Are Compatible
Ord Generic Ord Interaction model
is.multitype.ppp Test Whether A Point Pattern is Multitype
rescue.rectangle Convert Window Back To Rectangle
bdist.pixels Distance to Boundary of Window
Jest Estimate the J-function
betacells Beta Ganglion Cells in Cat Retina
cut.im Convert Pixel Image from Numeric to Factor
spatstat-deprecated Deprecated spatstat functions
OrdThresh Ord's Interaction model
crossdist.ppp Pairwise distances between two different point patterns
allstats Calculate four standard summary functions of a point pattern.
Jcross Multitype J Function (i-to-j)
plot.ppm plot a Fitted Point Process Model
discretise Safely Convert Point Pattern Window to Binary Mask
crossing.psp Crossing Points of Two Line Segment Patterns
PairPiece The Piecewise Constant Pairwise Interaction Point Process Model
clickpoly Interactively Define a Polygon
Linhom L-function
identify.ppp Identify Points in a Point Pattern
density.psp Kernel Smoothing of Line Segment Pattern
is.im Test Whether An Object Is A Pixel Image
nztrees New Zealand Trees Point Pattern
lengths.psp Lengths of Line Segments
Poisson Poisson Point Process Model
area.owin Area of a Window
Kinhom Inhomogeneous K-function
Ldot Multitype L-function (i-to-any)
eroded.areas Areas of Morphological Erosions
eem Exponential Energy Marks
gridcentres Rectangular grid of points
pairdist Pairwise distances
bramblecanes Hutchings' Bramble Canes data
quad.object Class of Quadrature Schemes
simulate.kppm Simulate a fitted cluster point process model.
multiplicity.ppp Count Multiplicity of Duplicate Points
LennardJones The Lennard-Jones Potential
Saturated Saturated Pairwise Interaction model
plot.owin Plot a Spatial Window
ewcdf Weighted Empirical Cumulative Distribution Function
nbfires Point Patterns of New Brunswick Forest Fires
distmap Distance Map
endpoints.psp Endpoints of Line Segment Pattern
density.ppp Kernel Smoothed Intensity of Point Pattern
plot.fv Plot Function Valuesn
crossdist Pairwise distances
plot.quad plot a Spatial Quadrature Scheme
subset.splitppp Extract or Replace Sub-Patterns
Lcross Multitype L-function (cross-type)
inside.owin Test Whether Points Are Inside A Window
quad.ppm Extract Quadrature Scheme Used to Fit a Point Process Model
rThomas Simulate Thomas Process
Kdot Multitype K Function (i-to-any)
dummy.ppm Extract Dummy Points Used to Fit a Point Process Model
Jdot Multitype J Function (i-to-any)
by.ppp Apply a Function to a Point Pattern Broken Down by Factor
quadrats Divide Region into Quadrats
copper Berman-Huntington points and lines data
interp.im Interpolate a Pixel Image
profilepl Profile Maximum Pseudolikelihood
rotate.psp Rotate a Line Segment Pattern
residuals.ppm Residuals for Fitted Point Process Model
summary.ppp Summary of a Point Pattern Dataset
summary.im Summarizing a Pixel Image
square Square Window
pcf.fasp Pair Correlation Function obtained from array of K functions
pairdist.default Pairwise distances
plot.plotppm Plot a plotppm Object Created by plot.ppm
gridweights Compute Quadrature Weights Based on Grid Counts
plot.kppm Plot a fitted cluster point process
predict.ppm Prediction from a Fitted Point Process Model
japanesepines Japanese Pines Point Pattern
plot.im Plot a Pixel Image
distmap.owin Distance Map of Window
pcfcross Multitype pair correlation function
as.data.frame.ppp Coerce Point Pattern to a Data Frame
summary.quad Summarizing a Quadrature Scheme
nnwhich Nearest neighbour
rescale.owin Convert Window to Another Unit of Length
pppmatching.object Class of Point Matchings
Kmulti Marked K-Function
as.owin Convert Data To Class owin
hamster Aherne's hamster tumour data
markcorr Mark Correlation Function
spatstat.options Internal Options in Spatstat Package
is.multitype.ppm Test Whether A Point Process Model is Multitype
intersect.owin Intersection or Union of Two Windows
affine Apply Affine Transformation
rcell Simulate Baddeley-Silverman Cell Process
quadratcount Quadrat counting for a point pattern
quadrat.test Chi-Squared Dispersion Test for Spatial Point Pattern Based on Quadrat Counts
rmpoint Generate N Random Multitype Points
quadratresample Resample a Point Pattern by Resampling Quadrats
envelope Simulation envelopes of summary function
levelset Level Set of a Pixel Image
rSSI Simulate Simple Sequential Inhibition
pixelquad Quadrature Scheme Based on Pixel Grid
residualspaper Data and Code From JRSS Discussion Paper on Residuals
dirichlet.weights Compute Quadrature Weights Based on Dirichlet Tessellation
corners Corners of a rectangle
rjitter Random Perturbation of a Point Pattern
rsyst Simulate systematic random point pattern
plot.psp plot a Spatial Line Segment Pattern
summary.ppm Summarizing a Fitted Point Process Model
ppm.object Class of Fitted Point Process Models
bei Tropical rain forest trees
density.splitppp Kernel Smoothed Intensity of Split Point Pattern
pppmatching Create a Point Matching
redwoodfull California Redwoods Point Pattern (Entire Dataset)
raster.x Cartesian Coordinates for a Pixel Raster
is.ppm Test Whether An Object Is A Fitted Point Process Model
runifpoint Generate N Uniform Random Points
ponderosa Ponderosa Pine Tree Point Pattern
predict.kppm Prediction from a Fitted Cluster Point Process Model
psp.object Class of Line Segment Patterns
bounding.box Bounding Box of a Window or Point Pattern
append.psp Combine Two Line Segment Patterns
nearest.raster.point Find Pixel Nearest to a Given Point
diameter Diameter of a Window
MultiStraussHard The Multitype/Hard Core Strauss Point Process Model
spruces Spruces Point Pattern
subset.listof Extract or Replace Subset of a List of Things
reach Interaction Distance of a Point Process
applynbd Apply Function to Every Neighbourhood in a Point Pattern
print.psp Print Brief Details of a Line Segment Pattern Dataset
tess Create a Tessellation
ripras Estimate window from points alone
nncross Nearest Neighbour in Another Point Pattern
alltypes Calculate Summary Statistic for All Types in a Multitype Point Pattern
convexhull.xy Convex Hull of Points
marktable Tabulate Marks in Neighbourhood of Every Point in a Point Pattern
expand.owin Expand Window By Factor
progressreport Print Progress Reports
lgcp.estK Fit a Log-Gaussian Cox Point Process by Minimum Contrast
summary.owin Summary of a Spatial Window
[.tess Extract or Replace Subset of Tessellation
rNeymanScott Simulate Neyman-Scott Process
ord.family Ord Interaction Process Family
demopat Artificial Data Point Pattern
plot.tess Plot a tessellation
as.rectangle Window Frame
shift.im Apply Vector Translation To Pixel Image
kppm Fit cluster point process model
km.rs Kaplan-Meier and Reduced Sample Estimator using Histograms
ppm Fit Point Process Model to Data
rmhmodel.list Define Point Process Model for Metropolis-Hastings Simulation.
print.quad Print a Quadrature Scheme
rMaternII Simulate Matern Model II
amacrine Hughes' Amacrine Cell Data
reduced.sample Reduced Sample Estimator using Histogram Data
Kest.fft K-function using FFT
trim.rectangle Cut margins from rectangle
hyperframe Hyper Data Frame
rStrauss Perfect Simulation of the Strauss Process
tiles Extract List of Tiles in a Tessellation
shift.owin Apply Vector Translation To Window
anova.ppm ANOVA for Fitted Point Process Models
owin Create a Window
rotate.owin Rotate a Window
Geyer Geyer's Saturation Point Process Model
print.im Print Brief Details of an Image
suffstat Sufficient Statistic of Point Process Model
logLik.ppm Log Likelihood for Poisson Point Process Model
cut.ppp Classify Points in a Point Pattern
with.fv Evaluate an Expression in a Function Table
qqplot.ppm Q-Q Plot of Residuals from Fitted Point Process Model
update.ppm Update a Fitted Point Process Model
plot.fasp Plot a Function Array
rpoispp Generate Poisson Point Pattern
unique.ppp Extract Unique Points from a Spatial Point Pattern
persp.im Perspective Plot of Pixel Image
rotate Rotate
rpoint Generate N Random Points
as.matrix.im Convert Pixel Image to Matrix
distmap.ppp Distance Map of Point Pattern
print.ppp Print Brief Details of a Point Pattern Dataset
harmonic Basis for Harmonic Functions
scanpp Read Point Pattern From Data File
pppdist Distance Between Two Point Patterns
fasp.object Function Arrays for Spatial Patterns
im.object Class of Images
spatstat The Spatstat Package
Iest Estimate the I-function
unitname Name for Unit of Length
unmark Remove Marks from a Marked Point Pattern
inforder.family Infinite Order Interaction Family
rmpoispp Generate Multitype Poisson Point Pattern
disc Circular Window
redwood California Redwoods Point Pattern (Ripley's Subset)
rescale Convert dataset to another unit of length
fitted.ppm Fitted Conditional Intensity for Point Process Model
update.kppm Update a Fitted Cluster Point Process Model
rescale.ppp Convert Point Pattern to Another Unit of Length
subset.fasp Extract Subset of Function Array
anemones Beadlet Anemones Data
rmhmodel.default Build Point Process Model for Metropolis-Hastings Simulation.
ppp Create a Point Pattern
eval.fv Evaluate Expression Involving Functions
rlabel Random Re-Labelling of Point Pattern
is.ppp Test Whether An Object Is A Point Pattern
ganglia Beta Ganglion Cells in Cat Retina, Old Version
superimpose Superimpose Several Point Patterns
quadscheme Generate a Quadrature Scheme from a Point Pattern
spokes Spokes pattern of dummy points
Kdot.inhom Inhomogeneous Multitype K Dot Function
stieltjes Compute Integral of Function Against Cumulative Distribution
runifdisc Generate N Uniform Random Points in a Disc
as.ppp Convert Data To Class ppp
crossdist.default Pairwise distances between two different sets of points
rshift.psp Randomly Shift a Line Segment Pattern
setcov Set Covariance of a Window
crossdist.psp Pairwise distances between two different line segment patterns
DiggleGratton Diggle-Gratton model
smooth.ppp Spatial smoothing of observations at irregular points
eval.im Evaluate Expression Involving Pixel Images
diagnose.ppm Diagnostic Plots for Fitted Point Process Model
rshift.ppp Randomly Shift a Point Pattern
rmh.ppm Simulate from a Fitted Point Process Model
vcov.ppm Variance-Covariance Matrix for a Fitted Point Process Model
clarkevans Clark and Evans Aggregation Index
Gcross Multitype Nearest Neighbour Distance Function (i-to-j)
[.quad Subset of Quadrature Scheme
subsetget.im Reset Values in Subset of Image
rstrat Simulate Stratified Random Point Pattern
simdat Simulated Point Pattern
is.multitype Test whether Object is Multitype
humberside Humberside Data on Childhood Leukaemia and Lymphoma
blur Apply Gaussian Blur to a Pixel Image
split.ppp Divide Point Pattern into Sub-patterns
areadiff Difference of Disc Areas
affine.psp Apply Affine Transformation To Line Segment Pattern
as.psp Convert Data To Class psp
summary.listof Summary of a List of Things
chorley Chorley-Ribble Cancer Data
is.marked.ppp Test Whether A Point Pattern is Marked
effectfun Compute Fitted Effect of a Spatial Covariate in a Point Process Model
union.quad Union of Data and Dummy Points
dirichlet Dirichlet Tessellation of Point Pattern
urkiola Urkiola Woods Point Pattern
rescale.psp Convert Line Segment Pattern to Another Unit of Length
affine.ppp Apply Affine Transformation To Point Pattern
StraussHard The Strauss / Hard Core Point Process Model
rthin Random Thinning
pairwise.family Pairwise Interaction Process Family
is.owin Test Whether An Object Is A Window
thomas.estK Fit the Thomas Point Process by Minimum Contrast
rmhmodel.ppm Interpret Fitted Model for Metropolis-Hastings Simulation.
Softcore The Soft Core Point Process Model
rshift.splitppp Randomly Shift a List of Point Patterns
ppp.object Class of Point Patterns
rmhstart Determine Initial State for Metropolis-Hastings Simulation.
im Create a Pixel Image Object
rmhcontrol Set Control Parameters for Metropolis-Hastings Algorithm.
shift Apply Vector Translation
selfcrossing.psp Crossing Points in a Line Segment Pattern
dilate.owin Dilate a Window
print.ppm Print a Fitted Point Process Model
subset.ppp Extract or Replace Subset of Point Pattern
eval.fasp Evaluate Expression Involving Function Arrays
distmap.psp Distance Map of Line Segment Pattern
shift.ppp Apply Vector Translation To Point Pattern
subset.fv Extract Subset of Function Values
matclust.estK Fit the Matern Cluster Point Process by Minimum Contrast
plot.hyperframe Plot Entries in a Hyperframe
localK Neighbourhood density function
psp Create a Line Segment Pattern
spatstat-internal Internal spatstat functions
pairsat.family Saturated Pairwise Interaction Point Process Family
summary.psp Summary of a Line Segment Pattern Dataset
finpines Pine saplings in Finland.
vertices Vertices of a Window
subset.im Extract Subset of Image
rmhmodel Define Point Process Model for Metropolis-Hastings Simulation.
Fest Estimate the empty space function F
plot.ppp plot a Spatial Point Pattern
Jmulti Marked J Function
print.owin Print Brief Details of a Spatial Window
solutionset Evaluate Logical Expression Involving Pixel Images and Return Region Where Expression is True
rMaternI Simulate Matern Model I
summary.splitppp Summary of a Split Point Pattern
bounding.box.xy Convex Hull of Points
gpc2owin Convert Polygonal Region into Different Format
Gdot Multitype Nearest Neighbour Distance Function (i-to-any)
rshift Random Shift
affine.owin Apply Affine Transformation To Window
rmh Simulate point patterns using the Metropolis-Hastings algorithm.
quantile.im Sample Quantiles of Pixel Image
plot.splitppp Plot a List of Point Patterns
nndist Nearest neighbour distances
rlinegrid Generate grid of parallel lines with random displacement
mean.im Mean Pixel Value in an Image
swedishpines Swedish Pines Point Pattern
bdist.points Distance to Boundary of Window
shift.psp Apply Vector Translation To Line Segment Pattern
rescale.im Convert Pixel Image to Another Unit of Length
complement.owin Take Complement of a Window
data.ppm Extract Original Data from a Fitted Point Process Model
is.subset.owin Determine Whether One Window is Contained In Another
pcf Pair Correlation Function
cells Biological Cells Point Pattern
eval.hyper Evaluate an Expression in Each Row of a Hyperframe
rGaussPoisson Simulate Gauss-Poisson Process
rmh.default Simulate Point Process Models using the Metropolis-Hastings Algorithm.
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Date 26 September 2008
License GPL (>= 2)
URL http://www.spatstat.org
Packaged Sat Sep 27 03:53:07 2008; adrian

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